[nco] 11/32: Imported Upstream version 4.4.5
Bas Couwenberg
sebastic at xs4all.nl
Mon Jan 19 00:00:34 UTC 2015
This is an automated email from the git hooks/post-receive script.
sebastic-guest pushed a commit to branch master
in repository nco.
commit de91bb0be73700065c718ace22486f98297f6a8a
Author: Bas Couwenberg <sebastic at xs4all.nl>
Date: Sun Jan 18 16:39:25 2015 +0100
Imported Upstream version 4.4.5
---
AUTHORS | 70 +-
CITATION | 31 +
COPYRIGHT | 20 +
LICENSE | 16 +
bld/Makefile | 451 +-
bld/nco.spec | 11 +-
bld/nco_dst.pl | 41 +-
bm/NCO_rgr.pm | 571 +-
bm/nco_bm.pl | 4 +-
config.h.in | 5 +-
configure | 60 +-
configure.ac | 40 +-
data/Makefile.am | 16 +-
data/Makefile.in | 11 +-
data/dsm.cdl | 54 +-
data/in.cdl | 32 +-
data/mrd.cdl | 30 +
doc/ANNOUNCE | 209 +-
doc/ChangeLog | 260 +-
doc/LICENSE | 690 +-
doc/MANIFEST | 30 +-
doc/TAG | 2 +-
doc/TODO | 12 +-
doc/VERSION | 2 +-
doc/build_hints.shtml | 313 +
doc/debian.txt | 170 +-
doc/endorsements.txt | 151 +
doc/highlights_old.shtml | 239 +
doc/index.shtml | 1579 +---
doc/milestones_old.shtml | 96 +
doc/nco.dvi | Bin 1305096 -> 1324244 bytes
doc/nco.html | 851 +-
doc/nco.pdf | Bin 1207615 -> 1218074 bytes
doc/nco.ps | 21161 ++++++++++++++++++++++----------------------
doc/nco.texi | 1048 ++-
doc/nco.txt | 4210 ++++-----
doc/nco.xml | 3760 ++++----
doc/nco_news.shtml | 8 +-
doc/problems_old.shtml | 440 +
doc/surfit_2014.txt | 8 +
doc/xmp/cmb_fl_grp.sh | 4 +-
man/ncks.1 | 5 +-
man/ncrcat.1 | 30 +-
po/es/nco.po | 42 +
po/fr/nco.po | 42 +
po/nco.pot | 37 +
src/nco++/Makefile.am | 6 +-
src/nco++/Makefile.in | 6 +-
src/nco++/Makefile.old | 335 +-
src/nco++/fmc_all_cls.cc | 394 +-
src/nco++/fmc_all_cls.hh | 17 +-
src/nco++/fmc_cls.hh | 5 +-
src/nco++/fmc_gsl_cls.cc | 7 +-
src/nco++/fmc_gsl_cls.hh | 5 +-
src/nco++/libnco++.hh | 9 +-
src/nco++/ncap2.cc | 67 +-
src/nco++/ncap2_utl.cc | 7 +-
src/nco++/ncap2_utl.hh | 9 +-
src/nco++/ncoGrammer.g | 9 +-
src/nco++/ncoLexer.cpp | 72 +-
src/nco++/ncoLexer.hpp | 15 +-
src/nco++/ncoParser.cpp | 24 +-
src/nco++/ncoParser.hpp | 15 +-
src/nco++/ncoTree.cpp | 224 +-
src/nco++/ncoTree.hpp | 15 +-
src/nco++/prs_cls.cc | 7 +-
src/nco++/prs_cls.hh | 5 +-
src/nco++/sdo_utl.cc | 9 +-
src/nco++/sdo_utl.hh | 9 +-
src/nco/libnco.h | 7 +-
src/nco/mpncbo.c | 22 +-
src/nco/mpncecat.c | 28 +-
src/nco/mpncflint.c | 19 +-
src/nco/mpncpdq.c | 19 +-
src/nco/mpncra.c | 19 +-
src/nco/mpncwa.c | 20 +-
src/nco/ncap.c | 17 +-
src/nco/ncap.h | 7 +-
src/nco/ncap_utl.c | 7 +-
src/nco/ncap_yacc.y | 10 +-
src/nco/ncatted.c | 58 +-
src/nco/ncbo.c | 58 +-
src/nco/ncecat.c | 63 +-
src/nco/ncflint.c | 65 +-
src/nco/ncks.c | 171 +-
src/nco/nco.h | 39 +-
src/nco/nco_att_utl.c | 7 +-
src/nco/nco_att_utl.h | 7 +-
src/nco/nco_aux.c | 11 +-
src/nco/nco_aux.h | 7 +-
src/nco/nco_bnr.c | 7 +-
src/nco/nco_bnr.h | 7 +-
src/nco/nco_cln_utl.c | 7 +-
src/nco/nco_cln_utl.h | 7 +-
src/nco/nco_cnf_dmn.c | 7 +-
src/nco/nco_cnf_dmn.h | 7 +-
src/nco/nco_cnf_typ.c | 7 +-
src/nco/nco_cnf_typ.h | 7 +-
src/nco/nco_cnk.c | 115 +-
src/nco/nco_cnk.h | 10 +-
src/nco/nco_cnv_arm.c | 7 +-
src/nco/nco_cnv_arm.h | 7 +-
src/nco/nco_cnv_csm.c | 9 +-
src/nco/nco_cnv_csm.h | 7 +-
src/nco/nco_ctl.c | 54 +-
src/nco/nco_ctl.h | 7 +-
src/nco/nco_dbg.c | 7 +-
src/nco/nco_dbg.h | 7 +-
src/nco/nco_dmn_utl.c | 7 +-
src/nco/nco_dmn_utl.h | 7 +-
src/nco/nco_fl_utl.c | 73 +-
src/nco/nco_fl_utl.h | 7 +-
src/nco/nco_grp_trv.c | 9 +-
src/nco/nco_grp_trv.h | 9 +-
src/nco/nco_grp_utl.c | 559 +-
src/nco/nco_grp_utl.h | 21 +-
src/nco/nco_lmt.c | 13 +-
src/nco/nco_lmt.h | 7 +-
src/nco/nco_lst_utl.c | 7 +-
src/nco/nco_lst_utl.h | 7 +-
src/nco/nco_md5.c | 11 +-
src/nco/nco_md5.h | 11 +-
src/nco/nco_mmr.c | 13 +-
src/nco/nco_mmr.h | 7 +-
src/nco/nco_mpi.h | 13 +-
src/nco/nco_msa.c | 50 +-
src/nco/nco_msa.h | 7 +-
src/nco/nco_mss_val.c | 7 +-
src/nco/nco_mss_val.h | 7 +-
src/nco/nco_netcdf.c | 86 +-
src/nco/nco_netcdf.h | 46 +-
src/nco/nco_omp.c | 7 +-
src/nco/nco_omp.h | 7 +-
src/nco/nco_pck.c | 7 +-
src/nco/nco_pck.h | 7 +-
src/nco/nco_prn.c | 19 +-
src/nco/nco_prn.h | 7 +-
src/nco/nco_rec_var.c | 7 +-
src/nco/nco_rec_var.h | 7 +-
src/nco/nco_rth_flt.c | 7 +-
src/nco/nco_rth_flt.h | 7 +-
src/nco/nco_rth_utl.c | 7 +-
src/nco/nco_rth_utl.h | 7 +-
src/nco/nco_scl_utl.c | 7 +-
src/nco/nco_scl_utl.h | 7 +-
src/nco/nco_scm.c | 13 +-
src/nco/nco_scm.h | 7 +-
src/nco/nco_sng_utl.c | 105 +-
src/nco/nco_sng_utl.h | 11 +-
src/nco/nco_srm.c | 7 +-
src/nco/nco_srm.h | 7 +-
src/nco/nco_typ.h | 7 +-
src/nco/nco_var_avg.c | 7 +-
src/nco/nco_var_avg.h | 7 +-
src/nco/nco_var_lst.c | 7 +-
src/nco/nco_var_lst.h | 7 +-
src/nco/nco_var_rth.c | 7 +-
src/nco/nco_var_rth.h | 7 +-
src/nco/nco_var_scv.c | 7 +-
src/nco/nco_var_scv.h | 7 +-
src/nco/nco_var_utl.c | 7 +-
src/nco/nco_var_utl.h | 7 +-
src/nco/ncpdq.c | 98 +-
src/nco/ncra.c | 80 +-
src/nco/ncrename.c | 83 +-
src/nco/ncwa.c | 72 +-
src/nco_c++/Makefile.old | 276 +-
src/nco_c++/libnco_c++.hh | 9 +-
src/nco_c++/nco_att.cc | 9 +-
src/nco_c++/nco_att.hh | 11 +-
src/nco_c++/nco_dmn.cc | 9 +-
src/nco_c++/nco_dmn.hh | 9 +-
src/nco_c++/nco_fl.cc | 9 +-
src/nco_c++/nco_fl.hh | 9 +-
src/nco_c++/nco_hgh.cc | 9 +-
src/nco_c++/nco_hgh.hh | 9 +-
src/nco_c++/nco_utl.cc | 9 +-
src/nco_c++/nco_utl.hh | 9 +-
src/nco_c++/nco_var.cc | 9 +-
src/nco_c++/nco_var.hh | 9 +-
src/nco_c++/tst.cc | 13 +-
181 files changed, 21749 insertions(+), 19393 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index 21122d1..57daadf 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,7 +1,63 @@
-Charlie Zender <surname at uci dot edu>
-CZ holds all copyright on NCO code.
-All other contributors have assigned their copyright to Zender,
-or did not make contributions that are legally significant for
-copyright purposes. These contributors are all listed under
-"Contributors" in the Users Guide documentation (nco.texi) at
-http://nco.sf.net/nco.html#ppl
+The User Guide documentation (nco.texi) contains the most up-to-date list
+of contributors to the NCO project, see http://nco.sf.net/nco.html#ppl
+
+Henry Butowsky
+ Non-linear operations and 'min()', 'max()', 'total()' support in
+ 'ncra' and 'ncwa'. Type conversion for arithmetic. Migration to
+ netCDF3 API. 'ncap2' parser, lexer, GSL-support, and I/O.
+ Multislabbing algorithm. Variable wildcarding. Numerous hacks.
+ 'ncap2' language.
+Rorik Peterson
+ Original autotool build support. Long command-line options.
+ Original UDUnits support. Debianization. Numerous bug-fixes.
+Joe Hamman
+ Python bindings (NCOpy).
+Daniel Wang
+ Script Workflow Analysis for MultiProcessing (SWAMP). RPM support.
+Harry Mangalam
+ Benchmarking. OPeNDAP configuration.
+Pedro Vicente
+ Windows Visual Studio support. netCDF4 groups.
+Russ Rew
+ Advice on NCO structural algorithms
+Brian Mays
+ Original packaging for Debian GNU/Linux, 'nroff' man pages.
+George Shapovalov
+ Packaging for Gentoo GNU/Linux.
+Bill Kocik
+ Memory management.
+Len Makin
+ NEC SX architecture support.
+Jim Edwards
+ AIX architecture support.
+Juliana Rew
+ Compatibility with large PIDs.
+Karen Schuchardt
+ Auxiliary coordinate support.
+Gayathri Venkitachalam
+ MPI implementation.
+Scott Capps
+ Large work-load testing
+Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski
+ Excellent bug reports and feature requests.
+Daniel Baumann, Nick Bower, Luk Claebs, Barry deFreese, Aleksandar Jelenak, Francesco Lovergine, Matej Vela
+ Debian packaging
+Patrice Dumas, Ed Hill, Orion Poplawski
+ RedHat packaging
+George Shapavalov, Patrick Kursawe
+ Gentoo packaging
+Filipe Fernandes
+ OpenSuse packaging
+Takeshi Enomoto, Alexander Hansen
+ Mac OS packaging
+Eric Blake
+ Autoconf/M4 help
+Gavin Burris, Kyle Wilcox
+ RHEL and CentOS build scripts and bug reports.
+Andrea Cimatoribus
+ NCO Spiral Logo
+Martin Otte, Etienne Tourigny
+ Single bug reports and fixes
+Wenshan Wang
+ CMIP5 and MODIS processing documentation.
+ Please let me know if your name was omitted!
diff --git a/CITATION b/CITATION
new file mode 100644
index 0000000..43790e1
--- /dev/null
+++ b/CITATION
@@ -0,0 +1,31 @@
+NCO is three things: a geoscience data analysis toolkit, an
+open-source software project, and an academic enterprise that embodies
+fundamental new (research-level) algorithms for geoscience data
+analysis. Successful academic research depends upon peer-evaluation,
+dissemination, and explicit acknowledgement of prior work and original
+results. The accepted way to convey acknowledgement to NCO for ideas
+or assistance in workflow processing is to cite its peer-reviewed
+description and or its User Guide. We encourage users and data science
+researchers to cite NCO for another reason, too: it helps funding
+agencies track the impact of the work they fund.
+
+The recommended citation for NCO software is
+
+Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience
+Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10),
+1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+
+or
+
+Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.3,
+http://nco.sf.net/nco.pdf.
+
+Use the former when referring to overall design, purpose, and
+optimization of NCO, and use the latter when referring to specific
+features and/or the Users Guide itself.
+
+Additional information on citing NCO is in the User Guide at
+http://nco.sf.net#ctt
+A complete list of NCO publications and presentations is at
+http://nco.sf.net#pub
+This list links to the full papers and seminars themselves.
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 0000000..62b2c39
--- /dev/null
+++ b/COPYRIGHT
@@ -0,0 +1,20 @@
+Charlie Zender wrote most of NCO and holds all NCO copyrights.
+He licenses NCO under the GNU GPL3 (see file COPYING).
+Advance permission must be sought from him for any usage or
+(re-)distribution of NCO code not compliant with the GPL.
+Contact him at <surname at uci dot edu>. His surname is zender.
+
+All other NCO contributors either explicitly assigned their copyrights
+to Zender, or their contributions were not legally significant for
+copyright purposes. These contributors are all listed under
+"Contributors" in the User Guide documentation (nco.texi) at
+http://nco.sf.net/nco.html#ppl
+and in the file AUTHORS
+
+The original author of this software, Charlie Zender, seeks to improve
+it with your suggestions, contributions, bug-reports, and patches.
+Please contact the NCO project at http://nco.sf.net or write to
+Charlie Zender
+Department of Earth System Science
+University of California, Irvine
+Irvine, CA 92697-3100
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..1927ef0
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,16 @@
+All source code created by the NCO project and distributed with NCO is
+re-distributable under the terms of the GNU General Public License
+(GPL) Version 3. The full license text is at
+http://www.gnu.org/copyleft/gpl.html and in the file COPYING.
+Copyright information is in the file COPYRIGHT.
+
+As a special exception to the terms of the GPL, you are permitted
+to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
+libraries and to distribute the resulting executables under the terms
+of the GPL, but in addition obeying the extra stipulations of the
+HDF, netCDF, OPeNDAP, and UDUnits licenses.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+See the GNU General Public License for more details.
diff --git a/bld/Makefile b/bld/Makefile
index 9a73850..28acda2 100644
--- a/bld/Makefile
+++ b/bld/Makefile
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/bld/Makefile,v 1.707 2014/05/29 18:00:25 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/bld/Makefile,v 1.729 2014/08/15 19:13:35 zender Exp $ -*-makefile-*-
# Purpose: GNU Makefile for NCO module nco
# Requires GNU Make---AT&T Make chokes on GNU syntax
@@ -13,14 +13,16 @@
# scp ~/nco/bld/Makefile gplogin2.ps.uci.edu:nco/bld
# Machine build parameters
-# givre.ess.uci.edu : Source: NCO + netCDF, Method: Makefile, Packages: All else
-# roulee.ess.uci.edu : Source: NCO + netCDF, Method: Makefile, Packages: All else
-# neige.ess.uci.edu : Source: NCO , Method: Makefile, Packages: All else
-# dust.ess.uci.edu : Source: - , Method: - , Packages: All
-# glace.ess.uci.edu : Source: NCO , Method: Configure, Packages: All else
-# grele.ess.uci.edu : Source: NCO , Method: Makefile, Packages: All else
-# tephra.ess.uci.edu : Source: NCO , Method: Makefile, Packages: All else
-# yellowstone.ucar.edu: Source: NCO , Method: Makefile, Packages: All else
+# Source Method Packages Compiler
+# givre.ess.uci.edu : NCO + netCDF Makefile All else LLVM
+# roulee.ess.uci.edu : NCO + netCDF Makefile All else GCC
+# neige.ess.uci.edu : NCO Makefile All else GCC
+# dust.ess.uci.edu : - - All
+# glace.ess.uci.edu : NCO Configure All else GCC
+# grele.ess.uci.edu : NCO Makefile All else GCC
+# tephra.ess.uci.edu : NCO Makefile All else
+# yellowstone.ucar.e : NCO Makefile All else Intel
+# rhea.ccs.ornl.gov : NCO Makefile All else
# Usage (testing):
# make tst # Vanilla regression test
@@ -29,9 +31,9 @@
# make MPI_PRC=3 bm # MPI benchmarks
# make THR_NBR=2 tst # OpenMP regression test
# make THR_NBR=2 bm # OpenMP benchmarks
+# make MPI=Y # MPI features (HDF5 and PnetCDF I/O)
# make NETCDF4=Y # netCDF4 features
-# make PNETCDF=Y # pnetCDF features
-# make ZNETCDF=Y # znetCDF features
+# make PNETCDF=Y # PnetCDF features
# Usage (Compilation):
# cd ~/nco/qt;qmake;make;cd - # Qt
@@ -41,7 +43,6 @@
# cd ~/nco/bld;make cln bin_cln;cd - # Clean all dependencies for fresh build
# cd ~/nco/bld;make dir all; cd - # Create target directories then build
# cd ~/nco/bld;make dbg;cd - # Print make diagnostics
-# cd ~/nco/bld;make DAP_OPENDAP=Y;cd - # DAP support via OPeNDAP
# cd ~/nco/bld;make DPKG=Y;cd - # Debian hardening
# cd ~/nco/bld;make GSL=Y;cd - # GSL support
# cd ~/nco/bld;make I18N=Y;cd - # Internationalization
@@ -56,39 +57,38 @@
# cd ~/nco/bld;make sys;cd - # Install in /usr/local (must sudo)
# cd ~/nco/bld;make SZ=Y;cd - # Szip support
# cd ~/nco/bld;make UDUNITS=Y;cd - # UDUnits support
-# cd ~/nco/bld;make UDUNITS2=Y;cd - # UDUnits2 support
# cd ~/nco/bld;make --jobs=4;cd - # Parallel make
# Normal (Linux) developer systems:
-# cd ${HOME}/nco/bld;make cln all ncap2;cd - # New default for most machines
-# cd ${HOME}/nco/bld;make OMP=Y CUDA=Y OPTS=D NETCDF4=Y UDUNITS2=Y allinone;cd - # givre
-# cd ${HOME}/nco/bld;make OMP=Y OPTS=D NETCDF4=Y UDUNITS2=Y allinone;cd - # givre, neige
-# cd ${HOME}/nco/bld;make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS2=Y allinone;cd - # glace, virga
+# cd ~/nco/bld;make cln all ncap2;cd - # New default for most machines
+# cd ~/nco/bld;make OMP=Y CUDA=Y OPTS=D NETCDF4=Y UDUNITS=Y allinone;cd - # givre
+# cd ~/nco/bld;make OMP=Y OPTS=D NETCDF4=Y UDUNITS=Y allinone;cd - # givre, neige
+# cd ~/nco/bld;make OMP=Y OPTS=D NETCDF4=N UDUNITS=Y allinone;cd - # glace, virga
# mpi-selector --set openmpi_gcc-1.3.3 # Then use /sopt/netcdf/netcdf3-gcc-serial serial libraries
# mpi-selector --set mpich_pgi_1.2.7p1 # After compiling
-# cd ${HOME}/nco/bld;ANTLR_ROOT=/sopt/gfortran_g++ CNK=N NETCDF_ROOT=/sopt/gfortran_g++ SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=Y SZ=Y UDUNITS2=N allinone;cd - # greenplanet gcc
-# cd ${HOME}/nco/bld;ANTLR=/home/pvicente/install/antlr-2.7.7/bin/antlr ANTLR_ROOT=/home/pvicente/install/antlr-2.7.7 NETCDF_ROOT=/home/pvicente/install/netcdf-4.3.0 UDUNITS_INC=/home/pvicente/install/udunits-2.1.24/include UDUNITS_LIB=/home/pvicente/install/udunits-2.1.24/lib make OPTS=D allinone;cd - # greenplanet gcc pedro
-# cd ${HOME}/nco/bld;ANTLR=/sopt/ifort_icpc/bin/antlr ANTLR_ROOT=/sopt/ifort_icpc CNK=N SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=Y SZ=Y UDUNITS2=N allinone;cd - # greenplanet intel
-# cd ${HOME}/nco/bld;ANTLR=/sopt/pgf90_pgcc/bin/antlr ANTLR_ROOT=/sopt/pgf90_pgcc CNK=N SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=N SZ=Y UDUNITS2=N allinone;cd - # greenplanet pgi
-# cd ${HOME}/nco/bld;make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS2=Y allinone;cd - # pbs
-# cd ${HOME}/nco/bld;make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS2=Y allinone;cd - # grele
-# cd ${HOME}/nco/bld;make NETCDF4=N all ncap2;cd - # tephra
-# cd ${HOME}/nco/bld;make OMP=Y DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS2=N allinone;cd - # silt, clay
-# cd ${HOME}/nco/bld;NETCDF_INC='/usr/include/netcdf-3' NETCDF_LIB='/usr/lib64' make GSL=N OMP=N DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS=N allinone;cd - # snow
-# cd ${HOME}/nco/bld;make OMP=N DAP_OPENDAP=Y OPTS=D NETCDF4=N UDUNITS2=N USR_TKN='-DNEED_NC_INQ_FORMAT' allinone;cd - # snow w/OPeNDAP
-# cd ${HOME}/nco/bld;make OPTS=D USR_TKN='-DNEED_NC_INQ_FORMAT' allinone;cd -
+# cd ~/nco/bld;ANTLR_ROOT=/sopt/gfortran_g++ CNK=N NETCDF_ROOT=/sopt/gfortran_g++ SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y OPTS=D NETCDF4=Y SZ=Y UDUNITS=N allinone;cd - # greenplanet gcc
+# cd ~/nco/bld;ANTLR=/home/pvicente/install/antlr-2.7.7/bin/antlr ANTLR_ROOT=/home/pvicente/install/antlr-2.7.7 NETCDF_ROOT=/home/pvicente/install/netcdf-4.3.0 UDUNITS_INC=/home/pvicente/install/udunits-2.1.24/include UDUNITS_LIB=/home/pvicente/install/udunits-2.1.24/lib make OPTS=D allinone;cd - # greenplanet gcc pedro
+# cd ~/nco/bld;ANTLR=/sopt/ifort_icpc/bin/antlr ANTLR_ROOT=/sopt/ifort_icpc CNK=N SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y OPTS=D NETCDF4=Y SZ=Y UDUNITS=N allinone;cd - # greenplanet intel
+# cd ~/nco/bld;ANTLR=/sopt/pgf90_pgcc/bin/antlr ANTLR_ROOT=/sopt/pgf90_pgcc CNK=N SZ_LIB=/sopt/lib UDUNITS_INC=/sopt/include UDUNITS_LIB=/sopt/lib make OMP=Y OPTS=D NETCDF4=N SZ=Y UDUNITS=N allinone;cd - # greenplanet pgi
+# cd ~/nco/bld;make OMP=Y OPTS=D NETCDF4=N UDUNITS=Y allinone;cd - # pbs
+# cd ~/nco/bld;make OMP=Y OPTS=D NETCDF4=N UDUNITS=Y allinone;cd - # grele
+# cd ~/nco/bld;make NETCDF4=N all ncap2;cd - # tephra
+# cd ~/nco/bld;make OMP=Y OPTS=D NETCDF4=N UDUNITS=N allinone;cd - # silt, clay
+# cd ~/nco/bld;NETCDF_INC='/usr/include/netcdf-3' NETCDF_LIB='/usr/lib64' make GSL=N OMP=N OPTS=D NETCDF4=N UDUNITS=N allinone;cd - # snow
+# cd ~/nco/bld;make OMP=N OPTS=D NETCDF4=N UDUNITS=N USR_TKN='-DNEED_NC_INQ_FORMAT' allinone;cd - # snow w/OPeNDAP
+# cd ~/nco/bld;make OPTS=D USR_TKN='-DNEED_NC_INQ_FORMAT' allinone;cd -
# 64-bit ABI on UCI MPC:
-# cd ${HOME}/nco/bld;env ANTLR='/software/antlr/bin/antlr' ANTLR_ROOT='/software/antlr' UDUNITS_INC='/software/udunits/include' UDUNITS_LIB='/software/udunits/lib' make --jobs=1 ABI=64 allinone;cd -
+# cd ~/nco/bld;env ANTLR='/software/antlr/bin/antlr' ANTLR_ROOT='/software/antlr' UDUNITS_INC='/software/udunits/include' UDUNITS_LIB='/software/udunits/lib' make --jobs=1 ABI=64 allinone;cd -
# 64-bit ABI on UCI IPCC:
-# cd ${HOME}/nco/bld;env ANTLR='/usr/local/pgi/bin/antlr' ANTLR_ROOT='/usr/local/pgi' make --jobs=1 ABI=64 allinone;cd -
+# cd ~/nco/bld;env ANTLR='/usr/local/pgi/bin/antlr' ANTLR_ROOT='/usr/local/pgi' make --jobs=1 ABI=64 allinone;cd -
# 64-bit ABI netCDF3 on NCAR AIX systems (bluefire):
-# cd ~/nco/bld;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' GSL_INC='/contrib/gsl-1.12/include' GSL_LIB='/contrib/gsl-1.12/lib' NETCDF_LIB='/usr/local/lib64/r4i4' UDUNITS_INC='/contrib/udunits-1.12.9/include' UDUNITS_LIB='/contrib/udunits-1.12.9/lib' make --jobs=1 DAP_OPENDAP=N OPTS=D NETCDF4=N UDUNITS2=N allinone ABI=64;cd -
+# cd ~/nco/bld;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' GSL_INC='/contrib/gsl-1.12/include' GSL_LIB='/contrib/gsl-1.12/lib' NETCDF_LIB='/usr/local/lib64/r4i4' UDUNITS_INC='/contrib/udunits-1.12.9/include' UDUNITS_LIB='/contrib/udunits-1.12.9/lib' make --jobs=1 OPTS=D NETCDF4=N UDUNITS=N allinone ABI=64;cd -
# 64-bit ABI netCDF4 on NCAR AIX systems (bluefire):
# cd ~/nco/bld;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' CURL_LIB='/contrib/curl/7.21.2/lib' GSL_INC='/contrib/gsl-1.12/include' GSL_LIB='/contrib/gsl-1.12/lib' HDF5_ROOT='/contrib/hdf5-1.8.7_seq' LDFLAGS='-lnetcdf -lhdf5_hl -lhdf5 -lz' NETCDF_ROOT='/contrib/netcdf/4.1.3_seq' SZ_LIB='/contrib/szip/lib' UDUNITS_LIB='/contrib/zlib/lib' make --jobs=1 OPTS=D SZ=Y allinone ABI=64;cd -
# 64-bit ABI netCDF4 on NCAR AIX systems (bluefire):
-# cd ~/bin/AIX;/usr/local/bin/tar cvzf ~/nco-4.4.4.aix53.tar.gz nc*;scp ~/nco-4.4.4.aix53.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
+# cd ~/bin/AIX;/usr/local/bin/tar cvzf ~/nco-4.4.5.aix53.tar.gz nc*;scp ~/nco-4.4.5.aix53.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
# netCDF4 on NCAR Linux cluster systems (mirage):
# cd ~/nco/bld;make OPTS=D allinone;cd -
-# netCDF4 on ORNL Linux cluster systems (titan, rhea):
+# netCDF4 on ORNL Linux cluster systems (titan, rhea.ccs.ornl.gov):
# module avail
# . ~/.bashrc
# module add intel netcdf udunits gsl
@@ -102,16 +102,18 @@
# cd ~/nco/bld;make NETCDF_ROOT='/glade/apps/opt/netcdf/4.3.0-rc4/gnu/default' UDUNITS_INC='/glade/apps/opt/udunits/2.1.24/gnu/default/include' UDUNITS_LIB='/glade/apps/opt/udunits/2.1.24/gnu/default/lib' OPTS=D allinone;cd -
# Intel (works as of 20140129):
# module add intel;module add gsl;module add netcdf/4.3.0;
+# https://www2.cisl.ucar.edu/sites/default/files/Yellowstone_Started_Nov30-2.pdf
+# module add pnetcdf/1.4.1
# export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}\:/glade/apps/opt/udunits/2.1.24/intel/12.1.4/lib
# cd ~/nco/bld;make NETCDF_ROOT='/glade/apps/opt/netcdf/4.3.0/intel/default' UDUNITS_INC='/glade/apps/opt/udunits/2.1.24/intel/12.1.4/include' UDUNITS_LIB='/glade/apps/opt/udunits/2.1.24/intel/12.1.4/lib' OPTS=D allinone;cd -
# Cygwin on Windows Vista systems:
-# cd ~/nco/bld;ANTLR='antlr' make --jobs=1 GSL=Y OPTS=D NETCDF4=Y UDUNITS2=Y allinone;cd -
-# cd ~/bin/WIN32;tar cvzf ~/nco-4.4.4.win32.cygwin.tar.gz nc* ; scp ~/nco-4.4.4.win32.cygwin.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
+# cd ~/nco/bld;ANTLR='antlr' make --jobs=1 GSL=Y OPTS=D NETCDF4=Y UDUNITS=Y allinone;cd -
+# cd ~/bin/WIN32;tar cvzf ~/nco-4.4.5.win32.cygwin.tar.gz nc* ; scp ~/nco-4.4.5.win32.cygwin.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
# Data files to dust
# cd ~/nco/data;scp cmip5.nc obs.nc mdl_1.nc mdl_2.nc in_grp*.nc in.nc dust.ess.uci.edu:/var/www/html/nco
# Top-level tokens defining directory structure
-# These tokens may be over-ridden by environment variables or when invoking make, e.g., make DAP_OPENDAP=Y
+# These tokens may be over-ridden by environment variables or when invoking make, e.g., make OMP=Y
MY_BLD_DIR := ../bld
ifndef PVM_ARCH
PVM_ARCH := $(shell ${MY_BLD_DIR}/pvmgetarch)
@@ -140,7 +142,7 @@ NCO_CXX_SRC_DIR := ${MY_SRC_DIR}/../nco_c++
NCOXX_SRC_DIR := ${MY_SRC_DIR}/../nco++
# Primary tokens which determine build options
-# Specify non-default when invoking make, e.g. make DAP_OPENDAP=Y
+# Specify non-default when invoking make, e.g. make OMP=Y
ifndef ${ABI}
# 32- vs. 64-bit ABI: 32=32-bit mode, 64=64-bit mode (default) if available
ABI := 64
@@ -155,12 +157,9 @@ endif # endif CNK
ifndef ${CUDA}
CUDA := N
endif # CUDA
-ifndef DAP_NETCDF
- DAP_NETCDF := Y
-endif # DAP_NETCDF
-ifndef DAP_OPENDAP
- DAP_OPENDAP := N
-endif # DAP_OPENDAP
+ifndef DAP
+ DAP := Y
+endif # DAP
ifndef ${DBG}
# Debugging token N=No (default) Y=Yes
DBG := N
@@ -227,7 +226,7 @@ ifdef LIB_NCAR
else # endelse LIB_NCAR
NETCDF_LIB := ${NETCDF_ROOT}/lib # Directory containing libnetcdf.a
endif # endif LIB_NCAR
-endif
+endif # endif NETCDF_LIB
ifndef ${OMP} # OpenMP
OMP := Y
endif # endif OMP
@@ -256,11 +255,7 @@ ifndef SZ
endif
ifndef UDUNITS
# Use UDUnits functionality
- UDUNITS := N
-endif
-ifndef UDUNITS2
-# Use UDUnits2 functionality
- UDUNITS2 := Y
+ UDUNITS := Y
endif
ifndef UNAMES
UNAMES := $(shell uname -s)
@@ -286,53 +281,6 @@ ifndef YFLAGS # Flags for Bison (Yacc)
YFLAGS := -d --name-prefix=${NCO_YY_PFX}
endif
-# Default NCO build: DAP_NETCDF, DAP_OPENDAP, NETCDF4, PNETCDF, and ZNETCDF clauses may overwrite this
-ifndef LIB_NCAR
- NC_LDFLAGS := -L${NETCDF_LIB}
- NC_LIBS := -lnetcdf
-else
- NC_LDFLAGS := ${LIB_NCAR}
-endif
-
-ifeq (${DAP_NETCDF},Y)
-# Build NCO as DAP-enabled clients with netCDF-provided DAP
-ifndef DAP_NETCDF_ROOT
-# Directory containing libcurl.a
- DAP_NETCDF_ROOT := /usr
-endif # DAP_NETCDF_ROOT
- NC_LDFLAGS := -L${DAP_NETCDF_ROOT}/lib
-# netCDF 4.0.1+:
- NC_LIBS += -lcurl
-endif # end DAP_NETCDF
-
-ifeq (${DAP_OPENDAP},Y)
-# Build NCO as DAP-enabled clients with OPe NDAP
-# fxm: OPeNDAP bloats executables, should automagically enable stripping?
-# http://www.opendap.org/user/guide-html/guide_28.html
-ifndef DAP_OPENDAP_ROOT
-# Directory containing libdap.a, libnc-dap.a
- DAP_OPENDAP_ROOT := /usr/local
-endif # DAP_OPENDAP_ROOT
- NC_LDFLAGS := -L${DAP_OPENDAP_ROOT}/lib
-# NB: nc-dods, dap++ prior to version 3.5.X must be linked twice!
-# Required libraries for
-# DODS 3.3-:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lwww -lz -lrx
-# DODS 3.4.X:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lxml2 -lcurl -lpthread -ldl -lz
-# OPeNDAP 3.5.0-3.5.1:
-# NC_LIBS := -lnc-dap -ldap++ -lxml2 -lcurl
-# OPeNDAP 3.5+:
- NC_LIBS += -lnc-dap -ldap -lxml2 -lcurl
-# In addition, AIX OPeNDAP requires these libraries...
-ifneq (${null},$(findstring AIX,${PVM_ARCH}))
- NC_LIBS += -lcrypto -liconv -lssl -lz
-endif # end AIX
-# Get netCDF from OPeNDAP version
- NETCDF_INC=${DAP_OPENDAP_ROOT}/include/libnc-dap
- NETCDF_LIB=${DAP_OPENDAP_ROOT}/lib
-endif # end DAP_OPENDAP
-
# Internationalize NCO with i18n features
ifeq (${I18N},Y)
MY_SHR_DIR := ${HOME}/share
@@ -357,56 +305,10 @@ else # !MPI_PRC
MPI_PRC_SNG :=
endif # !MPI_PRC
-ifeq (${NETCDF4},Y)
-# Enable netCDF4 functionality
-ifndef HDF5_ROOT
- HDF5_ROOT := ${NETCDF4_ROOT}
-endif
-ifndef HDF5_INC
- HDF5_INC := ${HDF5_ROOT}/include # Directory containing hdf5.h
-endif
-ifndef HDF5_LIB
- HDF5_LIB := ${HDF5_ROOT}/lib # Directory containing libhdf5.a
-endif
-# fxm: Temporary kludge: Machines with MPI_ROOT set are assumed to have parallel filesystems for NCO builds
-ifdef MPI_ROOT
- HDF5_INC += -I${MPI_ROOT}/include # Directory containing mpi.h
- HDF5_LIB += ${MPI_ROOT}/lib64 # Directory containing libmpi.a
-endif # !MPI_ROOT
- NETCDF_INC := ${NETCDF4_ROOT}/include
- NETCDF_LIB := ${NETCDF4_ROOT}/lib
- NC_LDFLAGS := -L${NETCDF_LIB} $(addprefix -L,${HDF5_LIB})
-# NC_LIBS := -lnetcdf -lhdf5_hl -lhdf5 -lz ${NC_LIBS}
- NC_LIBS := $(shell nc-config --libs) ${NC_LIBS}
-ifdef MPI_ROOT
- NC_LIBS += -lmpi
-endif # !MPI_ROOT
-ifdef CURL_LIB
- NC_LDFLAGS += -L${CURL_LIB}
-endif # end
-ifeq (${SZ},Y)
-ifndef SZ_LIB
- SZ_LIB := /usr/lib # Directory containing libsz.a
-endif
- NC_LDFLAGS += -L${SZ_LIB}
- NC_LIBS += -lsz
-endif # !SZ
-ifneq (${HDF5_INC},${NETCDF_INC})
- NETCDF_INC += -I${HDF5_INC}
-endif # end
-endif # endif NETCDF4
-
+# PnetCDF implies MPI
ifeq (${PNETCDF},Y)
-# Enable pnetCDF functionality
- NC_LDFLAGS := -L${NETCDF_LIB}
- NC_LIBS += -lpnetcdf
-endif # endif PNETCDF
-
-ifeq (${ZNETCDF},Y)
-# Enable znetcdf functionality
- NC_LDFLAGS := -L${NETCDF_LIB}
- NC_LIBS += -lznetcdf
-endif # endif ZNETCDF
+ MPI := Y
+endif # !PNETCDF
ifneq (${null},$(findstring LINUX,${PVM_ARCH}))
# Decide among the plethora of Linux compilers
@@ -474,62 +376,45 @@ else
GSL_INC := $(shell gsl-config --cflags)
endif # endif GSL_INC
ifdef GSL_LIB
- GSL_LIB := -L${GSL_LIB}
+ GSL_LIB := -L${GSL_LIB} -lgsl
else
GSL_LIB := $(shell gsl-config --libs)
endif # endif GSL_LIB
- NETCDF_INC += ${GSL_INC}
- NC_LDFLAGS += -L${GSL_LIB}
- NC_LIBS += -lgsl
endif # end if GSL
-ifeq (${UDUNITS2},Y)
- UDUNITS := Y
-endif # end if UDUNITS
ifeq (${UDUNITS},Y)
-# Build UDUnits-enabled NCO
-# Place UDUNITS block after DAP blocks for both to work together
-ifndef UDUNITS_INC
- UDUNITS_INC := /usr/local/include # Directory containing udunits.h
-endif
-ifndef UDUNITS_LIB
- UDUNITS_LIB := /usr/local/lib # Directory containing libudunits.a
-endif
-ifneq (${UDUNITS_INC},${NETCDF_INC})
- NETCDF_INC += -I${UDUNITS_INC}
-endif # end
-ifneq (${UDUNITS_LIB},${NETCDF_LIB})
- NC_LDFLAGS += -L${UDUNITS_LIB}
-endif # end if
-ifeq (${UDUNITS2},Y)
# 20130607: -lexpat needed on .deb systems, not on RPM systems
-UDUNITS_RPM_DRC := /usr/include/udunits2
-ifneq (${UDUNITS_INC},/usr/local/include)
-# UDUNITS_RPM_TST := $(shell ls ${UDUNITS_RPM_DRC}/udunits2.h)
- UDUNITS_RPM_TST := ${UDUNITS_RPM_DRC}/udunits2.h
+ifdef UDUNITS_INC
+ UDUNITS_INC := -I${UDUNITS_INC}
else
- UDUNITS_RPM_TST := /usr/include/udunits2.h
-endif # end if
-ifeq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NETCDF_INC += -I${UDUNITS_RPM_DRC}
+ UDUNITS_INC := -I/usr/include/udunits2
+endif # endif UDUNITS_INC
+ifdef UDUNITS_LIB
+ UDUNITS_LIB := -L${UDUNITS_LIB} -ludunits2
else
- NETCDF_INC += -I${UDUNITS_INC}
-endif # end if
-ifneq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NC_LIBS += -ludunits2 -lexpat
-else # end if UDUNITS2 Fedora
- NC_LIBS += -ludunits2
-endif # end if UDUNITS2 Fedora
-else
- NC_LIBS += -ludunits
-endif # end if UDUNITS2
+ UDUNITS_LIB := -ludunits2
+endif # end if UDUNITS_LIB
endif # end if UDUNITS
-# TMP_* and NCO_* are required to play nicely with DAP flags
-NCO_LDFLAGS := -L${MY_LIB_DIR}
-NCO_LIBS := -lnco
-TMP_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS}
-TMP_LIBS := ${NCO_LIBS} ${NC_LIBS}
+# At this point we change NETCDF_INC from a directory to a flag
+NC_CFLAGS := $(shell ${NETCDF_ROOT}/bin/nc-config --cflags)
+NC_LDFLAGS := $(shell ${NETCDF_ROOT}/bin/nc-config --libs)
+NCO_LDFLAGS := -L${MY_LIB_DIR} -lnco
+
+ifeq (${MPI},Y)
+# Enable MPI functionality
+ NC_CFLAGS := $(shell /usr/local/parallel/bin/nc-config --cflags)
+ NC_LDFLAGS := $(shell /usr/local/parallel/bin/nc-config --libs)
+ MPI_CFLAGS := -I/usr/include/openmpi-x86_64
+ MPI_LDFLAGS := -L/usr/lib64/openmpi/lib -lmpi
+endif # endif MPI
+
+ifdef LIB_NCAR
+ NC_LDFLAGS := ${LIB_NCAR} ${NC_LDFLAGS}
+endif
+
+OTHER_CFLAGS := ${NC_CFLAGS} ${MPI_CFLAGS} ${GSL_INC} ${UDUNITS_INC}
+OTHER_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS} ${MPI_LDFLAGS} ${GSL_LIB} ${UDUNITS_LIB}
# NB: Do NOT add comment lines, e.g., # This is a comma, to character definitions
null :=
@@ -569,9 +454,11 @@ CPP_PTH := $(foreach dir,${MDL_PTH},-I${dir})
MDL_BIN_TRG := ncap ncatted ncbo ncecat ncflint ncks ncpdq ncra ncrename ncwa # NCO binary targets
MDL_BIN_SYM_LNK := ncdiff ncea nces ncrcat # Symbolic links
ifeq (${MPI},Y)
- MDL_MPI_TRG := mpncbo mpncecat mpncflint mpncpdq mpncra mpncwa # MPI binary targets
+# MDL_MPI_TRG := mpncbo mpncecat mpncflint mpncpdq mpncra mpncwa # MPI binary targets
+ MDL_MPI_TRG := # MPI binary targets
MDL_MPI_TRG_SMP := ncbo ncecat ncflint ncpdq ncra ncwa # MPI binary targets
- MDL_MPI_SYM_LNK := mpncdiff mpncea mpnces mpncrcat # MPI Symbolic links
+# MDL_MPI_SYM_LNK := mpncdiff mpncea mpnces mpncrcat # MPI Symbolic links
+ MDL_MPI_SYM_LNK := # MPI Symbolic links
MDL_MPI_STB := ${MDL_MPI_TRG} ${MDL_MPI_SYM_LNK} # All MPI files in MY_BIN_DIR
MDL_MPI_BIN := $(addprefix ${MY_BIN_DIR}/,${MDL_MPI_TRG}) # mpi_cln removes these files
MDL_MPI_OBJ := $(addsuffix .o,$(addprefix ${MY_OBJ_DIR}/,${MDL_MPI_TRG})) # mpi_cln removes these files
@@ -647,8 +534,11 @@ ${MY_INC_DIR}/%.hh : %.hh
cp -f -p $(notdir $@) $@
# Rules for installing i18n files
-%.po : %.cc
- xgettext --default-domain=$* --join-existing $<
+# -k_ : Treat underscore as keyword (so "_" is equivalent to "gettext")
+# --default-domain : Name of program or library
+# --join-existing : Join messages with existing file
+%.po : %.c
+ xgettext --default-domain=$* -k_ --join-existing $<
${MY_ES_DIR}/%.mo : %.po
# Linux version accepts more arguments than Solaris version
# msgfmt --output-file=$@ --statistics $<
@@ -705,12 +595,9 @@ endif # !(AIX || SGI)
ifeq (${CNK},Y)
CPP_TKN_OS += -DHAVE_NEW_CHUNKING_API
endif # !CNK
-ifeq (${DAP_NETCDF},Y)
- CPP_TKN_OS += -DENABLE_DAP -DENABLE_DAP_NETCDF
-endif # !DAP_NETCDF
-ifeq (${DAP_OPENDAP},Y)
- CPP_TKN_OS += -DENABLE_DAP -DENABLE_DAP_OPENDAP
-endif # !DAP_OPENDAP
+ifeq (${DAP},Y)
+ CPP_TKN_OS += -DENABLE_DAP
+endif # !DAP
ifeq (${GSL},Y)
CPP_TKN_OS += -DENABLE_GSL -DHAVE_GSL_H
endif # !GSL
@@ -720,11 +607,15 @@ ifneq (${MPI_FAKE},Y)
endif # MPI_FAKE
endif # !MPI
ifeq (${UDUNITS},Y)
- CPP_TKN_OS += -DENABLE_UDUNITS -DHAVE_UDUNITS_H
-ifeq (${UDUNITS2},Y)
- CPP_TKN_OS += -DHAVE_UDUNITS2_H
-endif # !UDUNITS2
+ CPP_TKN_OS += -DENABLE_UDUNITS -DHAVE_UDUNITS_H -DHAVE_UDUNITS2_H
endif # !UDUNITS
+ifeq (${NETCDF4},Y)
+ CPP_TKN_OS += -DENABLE_NETCDF4 -DHAVE_NETCDF4_H
+endif # endif NETCDF4
+ifeq (${PNETCDF},Y)
+ CPP_TKN_OS += -DENABLE_PNETCDF
+endif # !PNETCDF
+# endif PNETCDF
# Assume strcasecmp() and strdup() routines are present (Comeau, Pathscale are exceptions)
CPP_TKN_OS +=
# fxm: Define HAVE_LIBINTL, HAVE_LOCALE_H, HAVE_GETTEXT, HAVE_OMP_H
@@ -744,11 +635,11 @@ ifneq (${null},$(findstring xl,${CC}))
CPP_TKN_OS += -I/usr/include -I/usr/vacpp/include
endif # xlC compilers
# Add /usr/local/include for libintl.h explicitly until netCDF is moved there
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -DNEED_LOGF
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS} -DNEED_LOGF
LD := ld
# 20020422: -lC links to AIX C++ library which contains float intrinsics cosf()...
# -bh:5 suppresses annoying messages from xlC linker WARNING: Duplicate symbol: ...
-LDFLAGS += -bh:5 ${TMP_LDFLAGS} ${TMP_LIBS} -lm -lC
+LDFLAGS += -bh:5 ${OTHER_LDFLAGS} -lm -lC
LEX := flex
LINT := lint
YACC := bison
@@ -860,13 +751,13 @@ CXX := cxx
CC := cc
CFLAGS := ${OMP_FLG}
CPP := cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
FFLAGS := -r8 -i4 -c ${OMP_FLG} -automatic
FIXEDFLAGS := -extend_source ${OMP_FLG} -automatic
FREEFLAGS := -DHIDE_SHR_MSG -free
LD := ld
-LDFLAGS += ${OMP_FLG} ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OMP_FLG} ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -894,13 +785,13 @@ ifeq (${PVM_ARCH},CRAY)
CXX := CC
CC := cc
CPP := cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
# -F enables macro substitution
# -dp enables DOUBLEPRECISION/double
FFLAGS := -N 132 -F -dp
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -931,10 +822,10 @@ endif
ifeq (${PVM_ARCH},HPPA)
CXX := g++
CC := gcc -std=c99 -pedantic -D_BSD_SOURCE -D_POSIX_SOURCE
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f77
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lnsl -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lnsl -lm
LEX := flex
LINT := lint
YACC := bison
@@ -953,17 +844,20 @@ endif
endif
# endif HPPA
-# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD
-ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSD))
+# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD and MACOSX
+ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSDMACOSX))
CXX := ${LINUX_CXX}
CC := ${LINUX_CC}
CPP := ${CC}
# NB: nameser.h needs -Di386, but gcc sends -Di586 (on pentiums)
CPP_TKN_OS += -Di386
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := ${LINUX_FC}
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
+ifeq (${PVM_ARCH},MACOSX)
+ LDFLAGS += -lresolv
+endif # endif MACOSX
LEX := flex
LINT := lint
YACC := bison
@@ -1022,7 +916,7 @@ ifeq (${GCC_OR_CLANG},Y)
# -fno-common: Prevent global variables from being simultaneously defined in different files
# -g: Put debugging symbols in executable
# -pg: Enable profiling, generate gmon.out output files (also needed by linker)
-# -O4: Turn on optimization so uninitialized variables are flagged. Downside: optimizes-out many symblols useful for debugging
+# -O4: Turn on optimization so uninitialized variables are flagged. Downside: optimizes-out many debugging symbols
# Compilation flags recommended by GSL that I do not like and do not use:
# -ansi: Support only strict ANSI C. Equivalent to -std=c89, conflicts with -std=c99
# --no-alias? -fstrict-aliasing
@@ -1038,8 +932,8 @@ ifneq (clang,$(firstword ${CC}))
# 20140526 clang does not recognize/utilize -fopenmp
OMP_FLG_C := -fopenmp
OMP_FLG_F := -fopenmp
-endif # endif clang
LDFLAGS += -lgomp -lpthread
+endif # endif clang
endif # endif OMP
ifeq (${OPTS},O)
CFLAGS += -O4 -g ${GCC_RCH_ARG}
@@ -1074,7 +968,7 @@ ifeq (${ABI},64)
endif # endif ABI
endif # endif LINUXAMD64
CXXFLAGS := ${CFLAGS}
-endif # endif GNU Compiler Collection
+endif # endif GNU Compiler Collection or LLVM
# Intel (Kai) C Compiler
ifeq (icc,$(firstword ${CC}))
# -fast: enable -xP -O3 -ipo -static
@@ -1274,19 +1168,20 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG_C} ${LDFLAGS}
endif # endif OMP
endif
-# endif LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, FREEBSD
+# endif LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, FREEBSD, MACOSX
-ifeq (${PVM_ARCH},MACOSX)
-CXX := c++
+ifeq (${PVM_ARCH},MACOSXOLD)
+CXX := ${LINUX_CXX}
# NB: -D_POSIX_SOURCE breaks MACOSX build in nco_fl_utl.c, nco_mmr.c
-CC := cc -std=c99 -pedantic -D_BSD_SOURCE
+#CC := cc -std=c99 -pedantic -D_BSD_SOURCE
+CC := ${LINUX_CC} -std=c99 -pedantic -D_BSD_SOURCE
+CPP := ${CC}
# -fno-common: Allows shared libraries to build
CFLAGS := -Wall -Werror=format-security -fno-common
-CPP := ${CC}
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lresolv -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lresolv -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1310,7 +1205,7 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG} ${LDFLAGS}
endif # endif OMP
endif
-# endif MACOSX
+# endif MACOSXOLD
ifeq (${PVM_ARCH},NECSX)
ifeq (${OMP},Y)
@@ -1321,10 +1216,10 @@ CXX := c++
CC := cc
CPP := c++ -E
#CPP := /usr/lib/cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1352,10 +1247,10 @@ ifeq (${PVM_ARCH},RS6K)
CXX := g++
CC := gcc -std=c99 -pedantic -D_BSD_SOURCE -D_POSIX_SOURCE
CPP := /lib/cpp -P
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := xlf
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1389,7 +1284,7 @@ CC := cc -c99
# 20000302: -w suppresses warnings which will swamp linker
#CXX := g++ -w
#CC := gcc -std=c99 -pedantic -D_BSD_SOURCE -D_POSIX_SOURCE
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
ifdef $(MIPSPRO_SGI)
# SGIs like dataproc keep omp.h in special location determined by module MIPSpro
CPPFLAGS := -I$(MIPSPRO_SGI)/usr/include ${CPPFLAGS}
@@ -1415,7 +1310,7 @@ else # ABI=32
endif # endif ABI
endif # endif SGI64, SGIMP64
ifeq (gcc,$(firstword ${CC}))
- LDFLAGS += ${GCC_LDFLAGS_SZ_SPC} ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS += ${GCC_LDFLAGS_SZ_SPC} ${OTHER_LDFLAGS} -lm
CFLAGS := ${GCC_ABI_FLG} -Wall -Werror=format-security
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1433,7 +1328,7 @@ endif
endif
# endif CC=gcc
ifeq (cc,$(firstword ${CC}))
- LDFLAGS += ${SGI_ABI_FLG} ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS += ${SGI_ABI_FLG} ${OTHER_LDFLAGS} -lm
CFLAGS := ${SGI_ABI_FLG}
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1476,12 +1371,12 @@ CPP := cc -E
#CC := gcc -std=c99 -pedantic -D_BSD_SOURCE -D_POSIX_SOURCE
#CFLAGS := -Wall
#CPP := cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90 -DHIDE_SHR_MSG
#FFLAGS := -xs -stackvar -e -Qoption f90comp -r8const
FFLAGS := -xs -stackvar -e
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lsunmath -lresolv -lsocket -lnsl -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lsunmath -lresolv -lsocket -lnsl -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1511,10 +1406,10 @@ CC := gcc -std=c99 -pedantic -D_BSD_SOURCE -D_POSIX_SOURCE
# NB: nameser.h needs -Di386, but gcc sends -Di586 (on pentiums)
#CPP_TKN_OS += -Di386 -DNEED_STRCASECMP -DNEED_STRDUP -I/usr/include
CPP_TKN_OS += -Di386 -DNEED_STRDUP -I/usr/include
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := g77
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1531,20 +1426,6 @@ ${MY_OBJ_DIR}/%.o : %.f
endif
# endif WIN32
-# Link to OPeNDAP libraries first, see OPeNDAP User's Guide
-# Currently this is invoked by using 'make DAP_OPENDAP=Y'
-ifeq (${DAP_OPENDAP},Y)
-# OPeNDAP >= 3.7.0 defines NC_64BIT_OFFSET correctly
-# CPPFLAGS += -DNC_64BIT_OFFSET=0
-ifneq (${CC},g++)
-ifeq (${null},$(findstring xl,${CC}))
-# g++ automatically links to -lstdc++, other compilers may need help
- LDFLAGS := ${LDFLAGS} -lstdc++
-endif # !xl*
-endif # !g++
-endif # !DAP_OPENDAP
-# endif DAP_OPENDAP
-
# Resolve nvcc CUDA run-time library functions
ifeq (${CUDA},Y)
CUDA_FLG_C :=
@@ -1555,27 +1436,12 @@ endif # endif CUDA
# Internationalize NCO with i18n features
ifeq (${I18N},Y)
CPPFLAGS += -DI18N
-ifneq (${null},$(findstring SGI,${PVM_ARCH}))
+ifneq (${null},$(findstring MACOSX,${PVM_ARCH}))
LDFLAGS += -lintl
endif
endif
# endif I18N
-ifeq (${NETCDF4},Y)
- CPPFLAGS += -DENABLE_NETCDF4 -DHAVE_NETCDF4_H
-endif
-# endif NETCDF4
-
-ifeq (${PNETCDF},Y)
- CPPFLAGS += -DENABLE_PNETCDF
-endif
-# endif PNETCDF
-
-ifeq (${ZNETCDF},Y)
- CPPFLAGS += -DENABLE_ZNETCDF
-endif
-# endif ZNETCDF
-
# Default to MPICC, MPICXX to CC, CXX and cross your fingers
MPICC := ${CC}
MPICXX := ${CXX}
@@ -1661,7 +1527,7 @@ allinone: all nco_c++ nco++
nco_c++:
-cd ../src/nco_c++; ${MAKE} -f Makefile.old DBG=${DBG} NETCDF4=${NETCDF4} OMP=${OMP} OPTS=${OPTS} SZ=${SZ} lib dat all
nco++:
- -cd ../src/nco++; ${MAKE} -f Makefile.old CNK=${CNK} DAP_NETCDF=${DAP_NETCDF} DAP_OPENDAP=${DAP_OPENDAP} DBG=${DBG} GSL=${GSL} NETCDF4=${NETCDF4} OMP=${OMP} OPTS=${OPTS} SZ=${SZ} UDUNITS2=${UDUNITS2} lib all
+ -cd ../src/nco++; ${MAKE} -f Makefile.old CNK=${CNK} DAP=${DAP} DBG=${DBG} GSL=${GSL} MPI=${MPI} NETCDF4=${NETCDF4} OMP=${OMP} OPTS=${OPTS} PNETCDF=${PNETCDF} SZ=${SZ} UDUNITS=${UDUNITS} lib all
# Targets in bin
mpi: mpi_nco
mpinco: mpi_nco
@@ -1779,7 +1645,7 @@ libnco_c++_tst: ${MY_BLD_DIR}/libnco_c++_tst
${MY_BLD_DIR}/libnco_c++_tst: ${MY_BLD_DIR}/libnco_c++_tst.o lib
${CXX} -o $@${BNR_SFX} $< ${LDFLAGS}
chmod 755 $@${BNR_SFX}
-rpm: ${MY_BLD_DIR}/nco.spec # Building rpm requires root priveleges, e.g., sudo make NCO_VRS=4.4.4 rpm
+rpm: ${MY_BLD_DIR}/nco.spec # Building rpm requires root priveleges, e.g., sudo make NCO_VRS=4.4.5 rpm
# Building NCO RPM requires following packages
# rpm -q bison flex netcdf-devel libtool automake autoconf udunits udunits-devel curl-devel libxml2 libxml2-devel librx-devel
# sudo yum install bison flex netcdf-devel libtool automake autoconf udunits udunits-devel curl-devel libxml2 libxml2-devel librx-devel
@@ -1834,7 +1700,7 @@ ${MY_DAT_DIR}/buggy.nc: ${MY_DAT_DIR}/buggy.cdl
dap: data
-cd ~/nco/data; scp in.nc in.cdl dust.ess.uci.edu:/var/www/html/dodsdata; scp in.nc in.cdl esmf.ess.uci.edu:/var/www/html/dodsdata; scp in.nc in.cdl esmf.ess.uci.edu:/data/dodsdata
data: dat
-dat: ${MY_DAT_DIR}/cmip5.nc ${MY_DAT_DIR}/obs.nc ${MY_DAT_DIR}/dsm.nc ${MY_DAT_DIR}/hdn.nc ${MY_DAT_DIR}/hdf.hdf ${MY_DAT_DIR}/mdl_1.nc ${MY_DAT_DIR}/mdl_2.nc ${MY_DAT_DIR}/mdl_3.nc ${MY_DAT_DIR}/in.nc ${MY_DAT_DIR}/in_grp.nc ${MY_DAT_DIR}/in_4.nc ${MY_DAT_DIR}/in_grp_1.nc ${MY_DAT_DIR}/in_grp_2.nc ${MY_DAT_DIR}/in_grp_3.nc ${MY_DAT_DIR}/in_grp_4.nc ${MY_DAT_DIR}/in_grp_5.nc ${MY_DAT_DIR}/in_grp_6.nc ${MY_DAT_DIR}/in_grp_7.nc ${MY_DAT_DIR}/in_rec_zero.nc
+dat: ${MY_DAT_DIR}/cmip5.nc ${MY_DAT_DIR}/obs.nc ${MY_DAT_DIR}/dsm.nc ${MY_DAT_DIR}/hdn.nc ${MY_DAT_DIR}/hdf.hdf ${MY_DAT_DIR}/mdl_1.nc ${MY_DAT_DIR}/mdl_2.nc ${MY_DAT_DIR}/mdl_3.nc ${MY_DAT_DIR}/mrd.nc ${MY_DAT_DIR}/in.nc ${MY_DAT_DIR}/in_grp.nc ${MY_DAT_DIR}/in_4.nc ${MY_DAT_DIR}/in_grp_1.nc ${MY_DAT_DIR}/in_grp_2.nc ${MY_DAT_DIR}/in_grp_3.nc ${MY_DAT_DIR}/in_grp_4.nc ${MY_DAT_DIR}/in_grp_5.nc ${MY_DAT_DIR}/in_grp_6.nc ${MY_DAT_DIR}/in_grp_7.nc ${MY_DAT_DIR}/in_rec_zero.nc
-for fl in ${MDL_DAT_STB}; do cd ${MY_DAT_DIR}; ln -s -f in.nc $$fl; done
${MY_DAT_DIR}/in.nc: ${MY_DAT_DIR}/in.cdl
ncgen -b -o $@ $<
@@ -1866,6 +1732,8 @@ ${MY_DAT_DIR}/cmip5.nc: ${MY_DAT_DIR}/cmip5.cdl
-ncgen -k netCDF-4 -b -o $@ $<
${MY_DAT_DIR}/hdn.nc: ${MY_DAT_DIR}/hdn.cdl
-ncgen -k netCDF-4 -b -o $@ $<
+${MY_DAT_DIR}/mrd.nc: ${MY_DAT_DIR}/mrd.cdl
+ -ncgen -k netCDF-4 -b -o $@ $<
${MY_DAT_DIR}/dsm.nc: ${MY_DAT_DIR}/dsm.cdl
-ncgen -k netCDF-4 -b -o $@ $<
${MY_DAT_DIR}/obs.nc: ${MY_DAT_DIR}/obs.cdl
@@ -2034,16 +1902,16 @@ dbg:
@printf "CURL_LIB = ${CURL_LIB}\n"
@printf "CXX = ${CXX}\n"
@printf "CXXFLAGS = ${CXXFLAGS}\n"
- @printf "DAP_NETCDF = ${DAP_NETCDF}\n"
- @printf "DAP_NETCDF_ROOT = ${DAP_NETCDF_ROOT}\n"
- @printf "DAP_OPENDAP = ${DAP_OPENDAP}\n"
- @printf "DAP_OPENDAP_ROOT = ${DAP_OPENDAP_ROOT}\n"
+ @printf "DAP = ${DAP}\n"
+ @printf "DAP_ROOT = ${DAP_ROOT}\n"
@printf "DBG = ${DBG}\n"
@printf "FC = ${FC}\n"
@printf "FFLAGS = ${FFLAGS}\n"
@printf "FL_FMT = ${FL_FMT}\n"
@printf "GCC_RCH_ARG = ${GCC_RCH_ARG}\n"
- @printf "GSL = $(GSL)\n"
+ @printf "GSL = ${GSL}\n"
+ @printf "GSL_INC = ${GSL_INC}\n"
+ @printf "GSL_LIB = ${GSL_LIB}\n"
@printf "HDF5_ROOT = ${HDF5_ROOT}\n"
@printf "HDF5_INC = ${HDF5_INC}\n"
@printf "HDF5_LIB = ${HDF5_LIB}\n"
@@ -2057,8 +1925,8 @@ dbg:
@printf "LEX = ${LEX}\n"
@printf "LFLAGS = ${LFLAGS}\n"
@printf "LIB_NCAR = ${LIB_NCAR}\n"
- @printf "LINUX_CC = $(LINUX_CC)\n"
- @printf "LINUX_CXX = $(LINUX_CXX)\n"
+ @printf "LINUX_CC = ${LINUX_CC}\n"
+ @printf "LINUX_CXX = ${LINUX_CXX}\n"
@printf "MDL_BIN_TRG = ${MDL_BIN_TRG}\n"
@printf "MDL_DPN = ${MDL_DPN}\n"
@printf "MDL_MAN = ${MDL_MAN}\n"
@@ -2067,6 +1935,7 @@ dbg:
@printf "MDL_PTH = ${MDL_PTH}\n"
@printf "MDL_RPM_NST_NM = ${MDL_RPM_NST_NM}\n"
@printf "MDL_SRC = ${MDL_SRC}\n"
+ @printf "MPI = ${MPI}\n"
@printf "MPICC = ${MPICC}\n"
@printf "MPICH_CC = ${MPICH_CC}\n"
@printf "MPICH_CXX = ${MPICH_CXX}\n"
@@ -2084,40 +1953,38 @@ dbg:
@printf "MY_LIB_DIR = ${MY_LIB_DIR}\n"
@printf "MY_MAN_DIR = ${MY_MAN_DIR}\n"
@printf "MY_OBJ_DIR = ${MY_OBJ_DIR}\n"
- @printf "NCO_LDFLAGS = $(NCO_LDFLAGS)\n"
- @printf "NCO_LIBS = $(NCO_LIBS)\n"
+ @printf "NCO_LDFLAGS = ${NCO_LDFLAGS}\n"
@printf "NCO_VRS = ${NCO_VRS}\n"
- @printf "NC_LDFLAGS = $(NC_LDFLAGS)\n"
- @printf "NC_LIBS = $(NC_LIBS)\n"
+ @printf "NC_CFLAGS = ${NC_CFLAGS}\n"
+ @printf "NC_LDFLAGS = ${NC_LDFLAGS}\n"
@printf "NETCDF4 = ${NETCDF4}\n"
@printf "NETCDF4_ROOT = ${NETCDF4_ROOT}\n"
@printf "NETCDF_INC = ${NETCDF_INC}\n"
@printf "NETCDF_LIB = ${NETCDF_LIB}\n"
@printf "NETCDF_ROOT = ${NETCDF_ROOT}\n"
@printf "OMP = ${OMP}\n"
+ @printf "OPTS = ${OPTS}\n"
+ @printf "OTHER_CFLAGS = ${OTHER_CFLAGS}\n"
+ @printf "OTHER_LDFLAGS = ${OTHER_LDFLAGS}\n"
@printf "PGI_RCH_ARG = ${PGI_RCH_ARG}\n"
- @printf "PSC_RCH_ARG = ${PSC_RCH_ARG}\n"
@printf "PNETCDF = ${PNETCDF}\n"
+ @printf "PSC_RCH_ARG = ${PSC_RCH_ARG}\n"
@printf "PVM_ARCH = ${PVM_ARCH}\n"
@printf "RPM = ${RPM}\n"
- @printf "SRC_LST = $(SRC_LST)\n"
+ @printf "SRC_LST = ${SRC_LST}\n"
@printf "STC = ${STC}\n"
@printf "SZ = ${SZ}\n"
@printf "TAGS_FILES = ${TAGS_FILES}\n"
@printf "TAGS_FILTER_FILES = ${TAGS_FILTER_FILES}\n"
@printf "THR_NBR = ${THR_NBR}\n"
@printf "THR_NBR_SNG = ${THR_NBR_SNG}\n"
- @printf "TMP_LDFLAGS = ${TMP_LDFLAGS}\n"
- @printf "TMP_LIBS = ${TMP_LIBS}\n"
- @printf "UDUNITS = $(UDUNITS)\n"
- @printf "UDUNITS2 = $(UDUNITS2)\n"
- @printf "UDUNITS_INC = $(UDUNITS_INC)\n"
- @printf "UDUNITS_LIB = $(UDUNITS_LIB)\n"
+ @printf "UDUNITS = ${UDUNITS}\n"
+ @printf "UDUNITS_INC = ${UDUNITS_INC}\n"
+ @printf "UDUNITS_LIB = ${UDUNITS_LIB}\n"
@printf "VPATH = ${VPATH}\n"
@printf "VRS_SNG = ${VRS_SNG}\n"
@printf "YACC = ${YACC}\n"
@printf "YFLAGS = ${YFLAGS}\n"
- @printf "ZNETCDF = ${ZNETCDF}\n"
distclean: dst_cln
dst_cln: cln bin_cln dat_cln doc_cln root_cln
cd ${MY_BLD_DIR}; rm -f *~
@@ -2180,7 +2047,7 @@ else
endif
chmod 755 ${MY_BIN_DIR}/$@${BNR_SFX}
ncap2 :
- -cd ../src/nco++; ${MAKE} -f Makefile.old DAP_NETCDF=${DAP_NETCDF} DAP_OPENDAP=${DAP_OPENDAP} DBG=${DBG} GSL=${GSL} NETCDF4=${NETCDF4} OMP=${OMP} OPTS=${OPTS} SZ=${SZ} UDUNITS2=${UDUNITS2} all
+ -cd ../src/nco++; ${MAKE} -f Makefile.old DAP=${DAP} DBG=${DBG} GSL=${GSL} MPI=${MPI} NETCDF4=${NETCDF4} OMP=${OMP} OPTS=${OPTS} PNETCDF=${PNETCDF} SZ=${SZ} UDUNITS=${UDUNITS} all
# /bin/rm -f ${MDL_NCAP} ${MY_OBJ_DIR}/$@_lex.o ${MY_OBJ_DIR}/ncap_yacc.h ${MY_OBJ_DIR}/ncap_yacc.c
diff --git a/bld/nco.spec b/bld/nco.spec
index da00fd6..25046dd 100644
--- a/bld/nco.spec
+++ b/bld/nco.spec
@@ -2,17 +2,17 @@
# http://cvs.fedoraproject.org/viewvc/devel/nco/nco.spec?view=co
Name: nco
-Version: 4.4.4
+Version: 4.4.5
Release: 1%{?dist}
Summary: Programs that manipulate netCDF files
Group: Applications/Engineering
License: GPL3
URL: http://nco.sf.net/
-# Obtain NCO version 4.4.4-1 tar.gz from Sourceforge using CVS:
+# Obtain NCO version 4.4.5-1 tar.gz from Sourceforge using CVS:
# cvs -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco login
-# cvs -z3 -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco co -r nco-4.4.4-1 -d nco-%{version} nco
-# tar czf nco-%{version}.tar.gz --exclude='nco-4.4.4/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
+# cvs -z3 -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco co -r nco-4.4.5-1 -d nco-%{version} nco
+# tar czf nco-%{version}.tar.gz --exclude='nco-4.4.5/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude='ncap_yacc.[ch]' ./nco-%{version}
Source0: nco-%{version}.tar.gz
#Patch0: nco_install_C_headers.patch
#Patch1: nco_find_udunits-dat.patch
@@ -108,6 +108,9 @@ fi
# %{_libdir}/libnco++.so
%changelog
+* Tue Aug 26 2014 Charlie Zender <zender at uci.edu> - 4.4.5-1
+- new upstream 4.4.5
+
* Thu May 29 2014 Charlie Zender <zender at uci.edu> - 4.4.4-1
- new upstream 4.4.4
diff --git a/bld/nco_dst.pl b/bld/nco_dst.pl
index 1e1077f..b367a84 100755
--- a/bld/nco_dst.pl
+++ b/bld/nco_dst.pl
@@ -5,19 +5,20 @@
# Usage:
# Export tagged, public versions
-
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4_4_4 # Build, do not release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4_4_4 # Build, release on SF
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4_4_4 # Install, do not build
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4_4_4 # Build and install
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4_4_4
-# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4_4_4
+# /usr/bin/scp ${DATA}/nco-4.4.4.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
+
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4_4_5 # Build, do not release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --sf nco-4_4_5 # Build, release on SF
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --nst_all nco-4_4_5 # Install, do not build
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln --nst_all nco-4_4_5 # Build and install
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_cnt nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --acd_prs nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cgd_cnt nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --cray_prs nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --bbl_cnt nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --blk_cnt nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --dat_cnt nco-4_4_5
+# ${HOME}/nco/bld/nco_dst.pl --dbg=2 --cln --ute_prs nco-4_4_5
# Export daily snapshot
# ${HOME}/nco/bld/nco_dst.pl --dbg=2
@@ -31,7 +32,7 @@ BEGIN{
unshift @INC,$ENV{'HOME'}.'/perl'; # Location of csz.pl and DBG.pm HaS98 p. 170
} # end BEGIN
-my $CVS_Header='$Header: /cvsroot/nco/nco/bld/nco_dst.pl,v 1.214 2014/05/01 19:05:38 zender Exp $';
+my $CVS_Header='$Header: /cvsroot/nco/nco/bld/nco_dst.pl,v 1.216 2014/05/30 04:23:44 zender Exp $';
# Specify modules
use strict; # Protect all namespaces
@@ -68,9 +69,9 @@ my ($rsh_cmd,$rcp_cmd,$cp_cmd,$rm_cmd,$mkdir_cmd,$cvs_cmd);
my $False=0;
my $True=1;
-my $CVS_Date='$Date: 2014/05/01 19:05:38 $';
-my $CVS_Id='$Id: nco_dst.pl,v 1.214 2014/05/01 19:05:38 zender Exp $';
-my $CVS_Revision='$Revision: 1.214 $';
+my $CVS_Date='$Date: 2014/05/30 04:23:44 $';
+my $CVS_Id='$Id: nco_dst.pl,v 1.216 2014/05/30 04:23:44 zender Exp $';
+my $CVS_Revision='$Revision: 1.216 $';
my $CVSROOT='zender at nco.cvs.sf.net:/cvsroot/nco'; # CVS repository
my $DATA=$ENV{'DATA'};
my $HOME=$ENV{'HOME'};
@@ -255,7 +256,7 @@ if($bld){
# Set up FTP server
chdir $dst_pth_pfx or die "$prg_nm: ERROR unable to chdir to $dst_pth_pfx: $!\n"; # $! is system error string
cmd_prc("$cp_cmd $doc_fl ./$dst_vrs/doc"); # Copy derived documentation to source directory
- cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.4.4/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
+ cmd_prc("$tar_cmd cvzf $dst_fl --exclude='nco-4.4.5/debian*' --exclude='.cvsignore' --exclude=ncap_lex.c --exclude=ncap_yacc.[ch] ./$dst_vrs"); # Create gzipped tarfile
cmd_prc("$rsh_cmd $www_mch $rm_cmd $www_drc/src/$dst_fl"); # Remove any distribution with same name
if($dly_snp){cmd_prc("$rsh_cmd $www_mch $rm_cmd -r $www_drc/src/nco-????????.tar.gz");} # Remove previous daily snapshots from WWW server
cmd_prc("$rcp_cmd $dst_fl $www_mch:$www_drc/src"); # Copy local tarfile to WWW server
@@ -282,7 +283,9 @@ if($bld){
if($sf){
cmd_prc("$rcp_cmd_no_prs_prm $dst_pth_bld/doc/index.shtml $dst_pth_bld/doc/nco.png $dst_pth_bld/doc/nco_news.shtml $dst_pth_bld/doc/README $dst_pth_bld/doc/TODO $dst_pth_bld/doc/VERSION $dst_pth_bld/doc/ChangeLog $usr_nm,nco\@$www_mch_mrr:$www_drc_mrr");
cmd_prc("$rcp_cmd_no_prs_prm $dst_pth_bld/doc/nco.html $dst_pth_bld/doc/nco.info* $dst_pth_bld/doc/nco.dvi $dst_pth_bld/doc/nco.pdf $dst_pth_bld/doc/nco.ps $dst_pth_bld/doc/nco.ps $dst_pth_bld/doc/nco.texi $usr_nm,nco\@$www_mch_mrr:$www_drc_mrr");
- cmd_prc("$rcp_cmd_no_prs_prm $dst_pth_pfx/$dst_fl $DATA/$dst_fl_chg $DATA/$dst_fl_deb $DATA/$dst_fl_dsc $DATA/$dst_fl_tgz $usr_nm,nco\@$www_mch_mrr:$www_drc_mrr/src"); # Copy Debian files to WWW server
+ cmd_prc("$rcp_cmd_no_prs_prm $dst_pth_pfx/$dst_fl $usr_nm,nco\@$www_mch_mrr:$www_drc_mrr/src"); # Copy tarball to WWW server
+# 20140529: Disable Debian copying until .debs built again
+# cmd_prc("$rcp_cmd_no_prs_prm $dst_pth_pfx/$dst_fl $DATA/$dst_fl_chg $DATA/$dst_fl_deb $DATA/$dst_fl_dsc $DATA/$dst_fl_tgz $usr_nm,nco\@$www_mch_mrr:$www_drc_mrr/src"); # Copy Debian files to WWW server
# Shell commands on SourceForge disabled 20081018
# cmd_prc("$rsh_cmd $www_mch_mrr \"cd $www_drc_mrr; ln -s -f ./src/$dst_fl nco.tar.gz\"");
} # endif SourceForge
diff --git a/bm/NCO_rgr.pm b/bm/NCO_rgr.pm
index a6528b7..90f2086 100644
--- a/bm/NCO_rgr.pm
+++ b/bm/NCO_rgr.pm
@@ -1,6 +1,6 @@
package NCO_rgr;
-# $Header: /cvsroot/nco/nco/bm/NCO_rgr.pm,v 1.496 2014/05/27 16:51:56 zender Exp $
+# $Header: /cvsroot/nco/nco/bm/NCO_rgr.pm,v 1.506 2014/08/25 22:36:00 zender Exp $
# Purpose: All REGRESSION tests for NCO operators
# BENCHMARKS are coded in "NCO_benchmarks.pm"
@@ -85,36 +85,30 @@ sub tst_rgr {
print "\n";
-
my $RUN_NETCDF4_TESTS=0;
-my $RUN_NETCDF4_TESTS_VERSION_43=0;
+my $RUN_NETCDF4_TESTS_VERSION_GE_431=0;
system("ncks --get_prg_info");
# system() runs a command and returns exit status information as a 16 bit value:
# Low 7 bits are signal process died from, if any, and high 8 bits are actual exit value
if($? == -1){
- print "failed to execute: ncks --get_prg_info: $!\n";
+ print "failed to execute: ncks --get_prg_info: $!\n";
}else{
- my $exit_value=$? >> 8;
+# my $exit_value=$? >> 8;
+ my $exit_value=$?;
# nco_get_prg_info() returns codes
# 3 (for library 3.x)
- # 41 (for library 4.1.x)
- # 43 (for library 4.3.1.x)
-
- if ($exit_value==40) {$RUN_NETCDF4_TESTS=1;}
- if ($exit_value==41) {$RUN_NETCDF4_TESTS=1;}
- if ($exit_value==43) {$RUN_NETCDF4_TESTS=1;}
- if ($exit_value==43) {$RUN_NETCDF4_TESTS_VERSION_43=1;}
-
- if ($exit_value==41)
- {
- print "netCDF version 4.1.x detected\n";
- }
- if ($exit_value==43)
- {
- print "netCDF version 4.3.1.x detected\n";
- }
+ # 410 (for library 4.1.x)
+ # 430 (for library 4.3.0)
+
+ if($exit_value >= 400){$RUN_NETCDF4_TESTS=1;}
+ if($exit_value >= 431){$RUN_NETCDF4_TESTS_VERSION_GE_431=1;}
+
+ if($exit_value == 410){print "netCDF version 4.1.x detected\n";}
+ if($exit_value == 431){print "netCDF version 4.3.1 detected\n";}
+ if($exit_value == 432){print "netCDF version 4.3.2 detected\n";}
+ if($exit_value == 433){print "netCDF version 4.3.3 detected\n";}
}
print "\n";
@@ -261,7 +255,6 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncatted #3
-
$tst_cmd[0]="ncatted -h -O $nco_D_flg -a _FillValue,wgt_one,c,f,200.0 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -s '%g' -d lat,1 -v wgt_one %tmp_fl_00%";
$dsc_sng="Create new _FillValue attribute ";
@@ -271,8 +264,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncatted #4
-
-# Fragile: This test fails when length of command changes
+# Fragile: Test fails when command length changes, e.g., on MACOSX
$tst_cmd[0]="ncatted -O --hdr_pad=1000 $nco_D_flg -a missing_value,val_one_mss,m,f,0.0 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -M %tmp_fl_00% | grep hdr_pad | wc > %tmp_fl_01%";
$tst_cmd[2]="cut -c 14-15 %tmp_fl_01%"; ## Daniel:fxm cut/ncks, but how to do grep and wc???
@@ -286,7 +278,7 @@ print "\n";
$tst_cmd[0]="ncatted -O $nco_D_flg -a nw1,'^three*',c,i,999 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncap2 -v -C -O -s 'n2=three_dmn_var_int\@nw1;' %tmp_fl_00% %tmp_fl_01%";
- $tst_cmd[2]="ncks -O -C -H -s '%i' -v n2 %tmp_fl_01%";
+ $tst_cmd[2]="ncks -O -C -H -s '%i' -v n2 %tmp_fl_01%";
$dsc_sng="Variable wildcarding (requires regex)";
$tst_cmd[3]="999";
$tst_cmd[4]="SS_OK";
@@ -295,7 +287,7 @@ print "\n";
#4.3.8
#ncatted #6
-#ncatted -O -a purpose,rlev,m,c,new_value in_grp_3.nc out.nc
+#ncatted -O -a purpose,rlev,m,c,new_value in_grp_3.nc ~/foo.nc
#######################################
#### Group tests (requires netCDF4) ###
@@ -396,7 +388,7 @@ print "\n";
$#tst_cmd=0; # Reset array - ok
# ncbo #3
-# ncbo -h -O --op_typ='-' -v mss_val_scl in.nc in.nc out.nc
+# ncbo -h -O --op_typ='-' -v mss_val_scl -p ~/nco/data in.nc in.nc ~/foo.nc
$tst_cmd[0]="ncbo $omp_flg -h -O $fl_fmt $nco_D_flg --op_typ='-' -v mss_val_scl $in_pth_arg in.nc in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H --no_blank -s '%g' -v mss_val_scl %tmp_fl_00%";
@@ -558,8 +550,8 @@ print "\n";
# NCO 4.3.0: added support for groups; ncbo -g
#
#ncbo #16
-# ncbo -O -y add -g g4 -v one_dmn_rec_var in_grp.nc in_grp.nc out.nc
-# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var out.nc
+# ncbo -O -y add -g g4 -v one_dmn_rec_var in_grp.nc in_grp.nc ~/foo.nc
+# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var ~/foo.nc
# /g4/one_dmn_rec_var
# time[0]=1 one_dmn_rec_var[0]=2
@@ -572,8 +564,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncbo #17
-# ncbo -O -y add -g g4 -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc out.nc
-# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var out.nc
+# ncbo -O -y add -g g4 -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc ~/foo.nc
+# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var ~/foo.nc
# /g4/one_dmn_rec_var
$dsc_sng="(Groups) Addition with limits -d time,1,1,1 -y add -g g4 -v one_dmn_rec_var";
@@ -585,8 +577,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncbo #18
-# ncbo -O -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc out.nc
-# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var out.nc
+# ncbo -O -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc ~/foo.nc
+# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var ~/foo.nc
# /g4/one_dmn_rec_var
$dsc_sng="(Groups) Subtraction -v one_dmn_rec_var";
@@ -598,8 +590,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncbo #19
-# ncbo -O -y mlt -g g4 -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc out.nc
-# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var out.nc
+# ncbo -O -y mlt -g g4 -v one_dmn_rec_var ~/nco/data/in_grp.nc ~/nco/data/in_grp.nc ~/foo.nc
+# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var ~/foo.nc
# /g4/one_dmn_rec_var
$dsc_sng="(Groups) Multiplication with limits -d time,2,2,1 -y add -g g4 -v one_dmn_rec_var";
@@ -611,8 +603,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncbo #20
-# ncbo -O -y mlt -g g4 -v one_dmn_rec_var in_grp.nc in_grp.nc out.nc
-# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var out.nc
+# ncbo -O -y mlt -g g4 -v one_dmn_rec_var in_grp.nc in_grp.nc ~/foo.nc
+# ncks -C -H -s '%d' -d time,0,0,1 -g g4 -v one_dmn_rec_var ~/foo.nc
# /g4/one_dmn_rec_var
@@ -630,7 +622,7 @@ print "\n";
# Absolute match test
# ncbo #21
-# ncbo -O in_grp_1.nc in_grp_2.nc out.nc
+# ncbo -O in_grp_1.nc in_grp_2.nc ~/foo.nc
$dsc_sng="(Groups) Process absolute match variables -v var1 in_grp_1.nc in_grp_2.nc";
$tst_cmd[0]="ncbo -O $fl_fmt $nco_D_flg $in_pth_arg in_grp_1.nc in_grp_2.nc %tmp_fl_00%";
@@ -642,7 +634,7 @@ print "\n";
# ncbo #22
-# ncbo -O -v var1 in_grp_1.nc in_grp_2.nc out.nc
+# ncbo -O -v var1 in_grp_1.nc in_grp_2.nc ~/foo.nc
$dsc_sng="(Groups) Process absolute match variables -v var1 in_grp_1.nc in_grp_2.nc";
$tst_cmd[0]="ncbo -O $fl_fmt $nco_D_flg -v var1 $in_pth_arg in_grp_1.nc in_grp_2.nc %tmp_fl_00%";
@@ -654,8 +646,8 @@ print "\n";
# ncbo #23
-#ncbo -O --op_typ=add mdl_1.nc mdl_2.nc out.nc
-#ncks -C -g cesm_01 -v tas1 out.nc
+#ncbo -O --op_typ=add mdl_1.nc mdl_2.nc ~/foo.nc
+#ncks -C -g cesm_01 -v tas1 ~/foo.nc
# 544.4 = (file 1 tas1) 272.1 + (file 2 tas1) 272.3
$dsc_sng="(Groups) Process ensembles in both files mdl_1.nc mdl_2.nc";
@@ -667,8 +659,8 @@ print "\n";
$#tst_cmd=0; # Reset array
# ncbo #24
-#ncbo -O mdl_1.nc mdl_2.nc out.nc
-#ncks -g cesm_01 -v time out.nc
+#ncbo -O mdl_1.nc mdl_2.nc ~/foo.nc
+#ncks -g cesm_01 -v time ~/foo.nc
$dsc_sng="(Groups) Process ensembles in both files mdl_1.nc mdl_2.nc (check fixed variables)";
$tst_cmd[0]="ncbo -O $fl_fmt $nco_D_flg $in_pth_arg mdl_1.nc mdl_2.nc %tmp_fl_00%";
@@ -679,8 +671,8 @@ print "\n";
$#tst_cmd=0; # Reset array
# ncbo #25
-#ncbo -O --op_typ=add mdl_1.nc obs.nc out.nc
-#ncks -C -g cesm_01 -v tas1 out.nc
+#ncbo -O --op_typ=add mdl_1.nc obs.nc ~/foo.nc
+#ncks -C -g cesm_01 -v tas1 ~/foo.nc
# 544.1 = (file 1 tas1) 272.1 + (file 2 tas1) 273.0
$dsc_sng="(Groups) Process ensembles in file 1 with common variable at root in file 2";
@@ -692,7 +684,7 @@ print "\n";
$#tst_cmd=0; # Reset array
# ncbo #26
-#ncbo -O mdl_1.nc obs.nc out.nc
+#ncbo -O mdl_1.nc obs.nc ~/foo.nc
#ncks -g ecmwf_01 -v time
$dsc_sng="(Groups) Process ensembles in file 1 with common variable at root in file 2 (check fixed variables)";
@@ -705,8 +697,8 @@ print "\n";
# ncbo
-#ncbo -O --op_typ=add obs.nc mdl_1.nc out.nc
-#ncks -C -g cesm_01 -v tas1 out.nc
+#ncbo -O --op_typ=add obs.nc mdl_1.nc ~/foo.nc
+#ncks -C -g cesm_01 -v tas1 ~/foo.nc
# 544.1 = (file 1 tas1) 273.0 + (file 2 tas1) 272.1
#FXM ncbo group broadcasting, "time" dimension is created at root because conflicting logic in nco_prc_cmn() uses
@@ -724,8 +716,8 @@ print "\n";
}
# ncbo #27
-#ncbo -O cmip5.nc obs.nc out.nc
-#ncks -C -g ecmwf -v tas1 out.nc
+#ncbo -O cmip5.nc obs.nc ~/foo.nc
+#ncks -C -g ecmwf -v tas1 ~/foo.nc
# obs.nc tas1=273, cmip5.nc giss tas1=274
$dsc_sng="(Groups) Process relative matches, first file greater (cmip5.nc obs.nc)";
@@ -737,8 +729,8 @@ print "\n";
$#tst_cmd=0; # Reset array
# ncbo #28
-#ncbo -O obs.nc cmip5.nc out.nc
-#ncks -C -g ecmwf -v tas1 out.nc
+#ncbo -O obs.nc cmip5.nc ~/foo.nc
+#ncks -C -g ecmwf -v tas1 ~/foo.nc
# obs.nc tas1=273, cmip5.nc giss tas1=274
$dsc_sng="(Groups) Process relative matches, second file greater (obs.nc cmip5.nc)";
@@ -752,8 +744,8 @@ print "\n";
# ncbo #29
#ncbo ensemble with 1 member
#ncra -Y ncge -O mdl_3.nc ncge_out.nc
-#ncbo -O --op_typ=add ncge_out.nc mdl_3.nc out.nc
-#ncks -H -C -g cesm_01 -v tas1 out.nc
+#ncbo -O --op_typ=add ncge_out.nc mdl_3.nc ~/foo.nc
+#ncks -H -C -g cesm_01 -v tas1 ~/foo.nc
#ncge_out.nc =
#/cesm/tas1
#time[0]=1 tas1[0]=272.15
@@ -912,9 +904,9 @@ print "\n";
#nces #12
# 2 groups, each one with a record (part 1)
-# ncra -Y nces -h -O -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 in_grp_3.nc in_grp_3.nc out.nc
+# ncra -Y nces -h -O -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 in_grp_3.nc in_grp_3.nc ~/foo.nc
- $tst_cmd[0]="ncra -Y ncfe $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
+ $tst_cmd[0]="ncra -Y ncfe $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -s '%d' -g g25g1 -v one_dmn_rec_var %tmp_fl_00%";
$dsc_sng="(Groups) 2 groups ensemble mean of int across two files (part 1)";
$tst_cmd[2]="5";
@@ -924,9 +916,9 @@ print "\n";
#nces #13
# 2 groups, each one with a record (part 2)
-# ncra -Y nces -h -O -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 in_grp_3.nc in_grp_3.nc out.nc
+# ncra -Y nces -h -O -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 in_grp_3.nc in_grp_3.nc ~/foo.nc
- $tst_cmd[0]="ncra -Y ncfe $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
+ $tst_cmd[0]="ncra -Y ncfe $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var -d time,4 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -s '%d' -g g25g2 -v one_dmn_rec_var %tmp_fl_00%";
$dsc_sng="(Groups) 2 groups ensemble mean of int across two files (part 2)";
$tst_cmd[2]="5";
@@ -955,8 +947,8 @@ print "\n";
if($RUN_NETCDF4_TESTS == 1){
#nces #15
-# ncra -Y ncge -h -O mdl_1.nc out.nc
-# ncks -g cesm -v tas1 out.nc
+# ncra -Y ncge -h -O mdl_1.nc ~/foo.nc
+# ncks -g cesm -v tas1 ~/foo.nc
$tst_cmd[0]="ncra -Y ncge $omp_flg -h -O $fl_fmt $nco_D_flg $in_pth_arg mdl_1.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g cesm -v tas1 %tmp_fl_00%";
@@ -977,7 +969,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#nces #17
-# ncra -Y ncge -h -O -G /gpe_grp mdl_1.nc out.nc
+# ncra -Y ncge -h -O -G /gpe_grp mdl_1.nc ~/foo.nc
$tst_cmd[0]="ncra -Y ncge $omp_flg -h -O -G /gpe_grp $fl_fmt $nco_D_flg $in_pth_arg mdl_1.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g /gpe_grp/ecmwf -v tas1 %tmp_fl_00%";
@@ -988,7 +980,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#nces #18
-#ncra -Y ncge -O mdl_1.nc mdl_2.nc out.nc
+#ncra -Y ncge -O mdl_1.nc mdl_2.nc ~/foo.nc
$dsc_sng="(Groups) Two-file ensembles";
$tst_cmd[0]="ncra -Y ncge $omp_flg -h -O $fl_fmt $nco_D_flg $in_pth_arg mdl_1.nc mdl_2.nc %tmp_fl_00%";
@@ -1000,8 +992,8 @@ print "\n";
# NEW NCO 4.4.2
#nces #19 (check coordinate variables)
-# ncra -Y ncge -h -O mdl_1.nc out.nc
-# ncks -g cesm -v time out.nc
+# ncra -Y ncge -h -O mdl_1.nc ~/foo.nc
+# ncks -g cesm -v time ~/foo.nc
# NB: This test succeeds when it fails, i.e., the NCO command fails as it should because the input files do not conform
$dsc_sng="(Groups) Ensemble record coordinate variables";
@@ -1014,7 +1006,7 @@ print "\n";
# NEW NCO 4.4.3
#nces #20 (error checking of ensemble variable dimensions)
-# ncra -Y ncge -O in_grp_4.nc in_grp_5.nc out.nc
+# ncra -Y ncge -O in_grp_4.nc in_grp_5.nc ~/foo.nc
$dsc_sng="(Groups) Invalid input, expect ERROR because dimensions do not conform between ensemble variables";
$tst_cmd[0]="ncra -Y ncge $omp_flg -h -O $fl_fmt $nco_D_flg $in_pth_arg in_grp_4.nc in_grp_5.nc %tmp_fl_00%";
@@ -1025,7 +1017,7 @@ print "\n";
# NEW NCO 4.4.3
#nces #21
-# ncra -Y ncge -h -O mdl_1.nc out.nc
+# ncra -Y ncge -h -O mdl_1.nc ~/foo.nc
$dsc_sng="(Groups) Test CCM/CAM/CCSM special fixed variables";
$tst_cmd[0]="ncra -Y ncge $omp_flg -h -O $fl_fmt $nco_D_flg $in_pth_arg mdl_1.nc %tmp_fl_00%";
@@ -1077,8 +1069,8 @@ print "\n";
if($RUN_NETCDF4_TESTS == 1){
+# Fragile, depends on cut, expect failure on MACOSX
#ncecat #3
-
$tst_cmd[0]="ncks -C -h -O $fl_fmt $nco_D_flg -v area $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncecat -C -h -O $omp_flg $fl_fmt $nco_D_flg -G ensemble -d lat,1,1 -v area %tmp_fl_00% %tmp_fl_00% %tmp_fl_01%";
$tst_cmd[2]="ncks -C -O -h -m -v area %tmp_fl_01% | grep \"ensemble../area\" | wc | cut -c 7";
@@ -1093,8 +1085,8 @@ print "\n";
# NCO 4.3.1 - ncecat for groups
#
#ncecat #4 part1
-#ncecat -h -O -g g1g1 -v v1 in_grp.nc in_grp.nc out.nc
-#ncks -d record,1,1,1 out.nc
+#ncecat -h -O -g g1g1 -v v1 in_grp.nc in_grp.nc ~/foo.nc
+#ncks -d record,1,1,1 ~/foo.nc
$dsc_sng="(Groups) Concatenate variables/groups 1: scalars -g g1g1 -v v1";
$tst_cmd[0]="ncecat $nco_D_flg -h -O -g g1g1 -v v1 $in_pth_arg in_grp.nc in_grp.nc %tmp_fl_00%";
@@ -1105,8 +1097,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncecat #5 same as #4 but look metadata
-#ncecat -h -O -g g1g1 -v v1 in_grp.nc in_grp.nc out.nc
-#ncks -d record,1,1,1 out.nc
+#ncecat -h -O -g g1g1 -v v1 in_grp.nc in_grp.nc ~/foo.nc
+#ncks -d record,1,1,1 ~/foo.nc
$dsc_sng="(Groups) Concatenate variables/groups 2: scalars -g g1g1 -v v1";
$tst_cmd[0]="ncecat $nco_D_flg -h -O -g g1g1 -v v1 $in_pth_arg in_grp.nc in_grp.nc %tmp_fl_00%";
@@ -1117,8 +1109,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncecat #6 part1
-#ncecat -h -O -g g6g1 -v area in_grp.nc in_grp.nc out.nc
-#ncks -H -C -d record,1,1,1 -d lat,1,1,1 -g g6g1 -v area out.nc
+#ncecat -h -O -g g6g1 -v area in_grp.nc in_grp.nc ~/foo.nc
+#ncks -H -C -d record,1,1,1 -d lat,1,1,1 -g g6g1 -v area ~/foo.nc
$dsc_sng="(Groups) Concatenate variables/groups 1: 1D -g g6g1 -v area";
$tst_cmd[0]="ncecat $nco_D_flg -h -O -g g6g1 -v area $in_pth_arg in_grp.nc in_grp.nc %tmp_fl_00%";
@@ -1129,8 +1121,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncecat #7 same as #6 but look metadata
-#ncecat -h -O -g g6g1 -v area in_grp.nc in_grp.nc out.nc
-#ncks -C -g g6g1 -v area out.nc
+#ncecat -h -O -g g6g1 -v area in_grp.nc in_grp.nc ~/foo.nc
+#ncks -C -g g6g1 -v area ~/foo.nc
#area dimension 0: record, size = 2 (Record non-coordinate dimension)
$dsc_sng="(Groups) Concatenate variables/groups 2: 1D -g g6g1 -v area";
@@ -1142,8 +1134,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncecat #8 part1
-#ncecat -h -O -v two_dmn_rec_var in_grp.nc in_grp.nc out.nc
-#ncks -C -d record,1,1,1 -d time,9,9,1 -d lev,2,2,1 -v two_dmn_rec_var out.nc
+#ncecat -h -O -v two_dmn_rec_var in_grp.nc in_grp.nc ~/foo.nc
+#ncks -C -d record,1,1,1 -d time,9,9,1 -d lev,2,2,1 -v two_dmn_rec_var ~/foo.nc
$dsc_sng="(Groups) Concatenate variables/groups 1: 2D -v two_dmn_rec_var";
$tst_cmd[0]="ncecat $nco_D_flg -h -O -v two_dmn_rec_var $in_pth_arg in_grp.nc in_grp.nc %tmp_fl_00%";
@@ -1156,23 +1148,23 @@ print "\n";
#ncecat #9
#Check that "time" is eliminated as record
-#ncecat -O in_grp_3.nc in_grp_3.nc out.nc
-#ncks -m -C -g g25g1 -v one_dmn_rec_var out.nc
+#ncecat -O in_grp_3.nc in_grp_3.nc ~/foo.nc
+#ncks -m -C -g g25g1 -v one_dmn_rec_var ~/foo.nc
$dsc_sng="(Groups) Concatenate variables/groups";
$tst_cmd[0]="ncecat $nco_D_flg -h -O $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
- $tst_cmd[1]="ncks -m -C -g g25g1 -v one_dmn_rec_var %tmp_fl_00%";
+ $tst_cmd[1]="ncks -m -C -g g25g1 -v one_dmn_rec_var %tmp_fl_00%";
$tst_cmd[2]="one_dmn_rec_var dimension 1: time, size = 10 NC_DOUBLE, chunksize = 10 (Coordinate is time)";
$tst_cmd[3]="SS_OK";
NCO_bm::tst_run(\@tst_cmd);
$#tst_cmd=0; # Reset array
#ncecat #10
-#Chunking
-# ncecat -O -4 -D 5 -C --cnk_plc=all -v date_int in.nc in.nc out.nc
+#Chunking
+# ncecat -O -4 -D 5 -C --cnk_plc=all --cnk_map=rd1 -v date_int -p ~/nco/data in.nc in.nc ~/foo.nc
- $dsc_sng="Chunking --cnk_plc=all -v date_int";
- $tst_cmd[0]="ncecat -O -4 $nco_D_flg --cnk_plc=all -v date_int $in_pth_arg in.nc in.nc %tmp_fl_00%";
+ $dsc_sng="Chunking --cnk_plc=all --cnk_map=rd1 -v date_int";
+ $tst_cmd[0]="ncecat -O -C -4 $nco_D_flg --cnk_plc=all --cnk_map=rd1 -v date_int $in_pth_arg in.nc in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks %tmp_fl_00% | grep 'date_int dimension 0'";
$tst_cmd[2]="date_int dimension 0: record, size = 2, chunksize = 1 (Record non-coordinate dimension)";
$tst_cmd[3]="SS_OK";
@@ -1181,10 +1173,10 @@ print "\n";
#ncecat #11
#Chunking
-#ncecat -O -C -4 -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 in.nc in.nc out.nc
+#ncecat -O -C -4 -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 -p ~/nco/data in.nc in.nc ~/foo.nc
$dsc_sng="Chunking -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4";
- $tst_cmd[0]="ncecat -O -C -4 $nco_D_flg -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 $in_pth_arg in.nc in.nc %tmp_fl_00%";
+ $tst_cmd[0]="ncecat -O -C -4 $nco_D_flg -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 $in_pth_arg in.nc in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks %tmp_fl_00% | grep 'four_dmn_rec_var dimension 2'";
$tst_cmd[2]="four_dmn_rec_var dimension 2: lat, size = 2, chunksize = 2 (Non-coordinate dimension)";
$tst_cmd[3]="SS_OK";
@@ -1302,8 +1294,8 @@ print "\n";
#ncflint #6
-# ncflint -4 -O -w 0.8,0.0 in.nc in.nc out.nc
-# ncks -H -C -v time -d time,9,9,1 out.nc
+# ncflint -4 -O -w 0.8,0.0 -p ~/nco/data in.nc in.nc ~/foo.nc
+# ncks -H -C -v time -d time,9,9,1 ~/foo.nc
$dsc_sng="-w 0.8,0.0 in.nc in.nc";
$tst_cmd[0]="ncflint $nco_D_flg -4 -O -w 0.8,0.0 $in_pth_arg in.nc in.nc %tmp_fl_00%";
@@ -1314,8 +1306,8 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncflint #7
-# ncflint -4 -O -w 0.8,0.0 in.nc in.nc out.nc
-# ncks -H -C -v time -d time,9,9,1 out.nc
+# ncflint -4 -O -w 0.8,0.0 -p ~/nco/data in.nc in.nc ~/foo.nc
+# ncks -H -C -v time -d time,9,9,1 ~/foo.nc
# --fix_rec_crd prevents ncflint from multiplying or interpolating any coordinate variables, including record coordinate variables
$dsc_sng="--fix_rec_crd -w 0.8,0.0 in.nc in.nc";
@@ -1329,8 +1321,8 @@ print "\n";
# NCO 4.3.2 ncflint -- groups
#ncflint #8
-# ncflint -h -O -g g4 -v one_dmn_rec_var -w 1,1 in_grp.nc in_grp.nc out.nc
-# ncks -H -C -O -g g4 -d time,9 -v one_dmn_rec_var out.nc
+# ncflint -h -O -g g4 -v one_dmn_rec_var -w 1,1 in_grp.nc in_grp.nc ~/foo.nc
+# ncks -H -C -O -g g4 -d time,9 -v one_dmn_rec_var ~/foo.nc
$dsc_sng="(Groups) Weight 1D -g g4 -v one_dmn_rec_var -w 1,1 in_grp.nc in_grp.nc";
$tst_cmd[0]="ncflint $nco_D_flg -h -O -v one_dmn_rec_var -w 1,1 $in_pth_arg in_grp.nc in_grp.nc %tmp_fl_00%";
@@ -2037,7 +2029,7 @@ print "\n";
# The test greps chunksize = 2 for lat
# Policy: Chunk All Variables [default]
# Map:Chunksize Equals Dimension Size [default]
-#ncks -O -4 -v lat_lon --cnk_plc=all in_grp.nc out.nc"
+#ncks -O -4 -v lat_lon --cnk_plc=all in_grp.nc ~/foo.nc"
$dsc_sng="(Groups) Chunking --cnk_plc=all --v lat_lon";
$tst_cmd[0]="ncks $nco_D_flg -O -4 -v lat_lon --cnk_plc=all $in_pth_arg in_grp.nc %tmp_fl_00%";
@@ -2070,7 +2062,7 @@ print "\n";
#
#ncks #56:
-# ncks -H -C --dmn time,1,3,2 --dmn lev,1,1,1 -v two_dmn_rec_var ~/nco/data/in_grp.nc
+# ncks -H -C --dmn time,1,3,2 --dmn lev,1,1,1 -v two_dmn_rec_var ~/nco/data/in_grp.nc
# /g10/two_dmn_rec_var
# time[1]=2 lev[1]=500 two_dmn_rec_var[4]=2.1
# time[3]=4 lev[1]=500 two_dmn_rec_var[10]=2.3
@@ -2085,7 +2077,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #57:
-# ncks -H -C --dmn time,1,1,1 --dmn time,3,3,1 --dmn lev,0,0,1 --dmn lev,2,2,1 -v two_dmn_rec_var ~/nco/data/in_grp.nc
+# ncks -H -C --dmn time,1,1,1 --dmn time,3,3,1 --dmn lev,0,0,1 --dmn lev,2,2,1 -v two_dmn_rec_var ~/nco/data/in_grp.nc
#/g10/two_dmn_rec_var
#time[1]=2 lev[0]=100 two_dmn_rec_var[3]=1
#time[1]=2 lev[2]=1000 two_dmn_rec_var[5]=3
@@ -2102,7 +2094,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #58 This test uses limits to print a dimension "lon2(4)" that does NOT have a coordinate variable
-# ncks -H -d lon2,1,3,2 -v lon2_var in_grp.nc
+# ncks -H -d lon2,1,3,2 -v lon2_var in_grp.nc
#/g16/lon2_var
#lon2[1] lon2_var[1]=1
#lon2[3] lon2_var[3]=3
@@ -2117,7 +2109,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #59 same as #58 but with 2 limits with the same result
-# ncks -H -d lon2,1,1,1 -d lon2,3,3,1 -v lon2_var in_grp.nc
+# ncks -H -d lon2,1,1,1 -d lon2,3,3,1 -v lon2_var in_grp.nc
#/g16/lon2_var
#lon2[1] lon2_var[1]=1
#lon2[3] lon2_var[3]=3
@@ -2154,7 +2146,7 @@ print "\n";
#ncks #61
# This test tests both limits printing of coordinates that are in ancestor groups
-# ncks -H -v gds_var -d gds_crd,1,1,1 in_grp.nc
+# ncks -H -v gds_var -d gds_crd,1,1,1 in_grp.nc
# ncks -H -C -g g7g1 -v gds_var -d gds_crd,1,1,1 -d gds_crd,3,3,1 in_grp.nc
#/g7/g7g1/gds_var
# gds_crd[1]=1 gds_var[1]=273.2
@@ -2172,7 +2164,7 @@ print "\n";
#ncks #62
# Test "parallel" scope
#ncks: INFO nco_bld_var_dmn() reports variable </g16/g16g1/lon1> with dimension coordinate [0]/g16/g16g1/lon1
-# ncks -H -g g16g1 -v lon1 -d lon1,3,3,1 in_grp.nc
+# ncks -H -g g16g1 -v lon1 -d lon1,3,3,1 in_grp.nc
#/g16/g16g1/lon1
#lon1[3]=3
@@ -2213,7 +2205,7 @@ print "\n";
#ncks #65
# Test creation of variables with ancestor group dimensions
-#ncks -O -g g6g1 -v area in_grp.nc out.nc
+#ncks -O -g g6g1 -v area in_grp.nc ~/foo.nc
#/g6/g6g1/area
#lat[1]=90 area[1]=50
@@ -2229,7 +2221,7 @@ print "\n";
#ncks #66
# Test creation of variables with ancestor group dimensions, with GPE
-#ncks -O -G o1 -g g6g1 -v area in_grp.nc out.nc
+#ncks -O -G o1 -g g6g1 -v area in_grp.nc ~/foo.nc
#/o1/g6/g6g1/area
#lat[0]=-90 area[0]=40
#lat[1]=90 area[1]=50
@@ -2246,7 +2238,7 @@ print "\n";
#ncks #67
# Test "out of scope" coordinate
-# ncks -H -v lon3_var in_grp.nc
+# ncks -H -v lon3_var in_grp.nc
$dsc_sng="(Groups) Out of scope coordinate -v lon3_var";
$tst_cmd[0]="ncks $nco_D_flg -H -v lon3_var $in_pth_arg in_grp_3.nc";
@@ -2259,7 +2251,7 @@ print "\n";
#ncks #68
# Test 2 "intermediate scope " coordinates
-# ncks -H -v lon4_var in_grp.nc
+# ncks -H -v lon4_var in_grp.nc
$dsc_sng="(Groups) Order coordinates by group depth -v lon4_var";
$tst_cmd[0]="ncks $nco_D_flg -C -H -v lon4_var $in_pth_arg in_grp_3.nc";
@@ -2309,7 +2301,7 @@ print "\n";
#ncks #72
#same as #70, with group
-# ncks -h -O -v three_dmn_var_dbl -d time,,2 -d lat,0,0 -d lon,0,0 -d lon,3,3 in_grp_3.nc
+# ncks -h -O -v three_dmn_var_dbl -d time,,2 -d lat,0,0 -d lon,0,0 -d lon,3,3 in_grp_3.nc
$dsc_sng="(Groups) Limits -C -v three_dmn_var_dbl -d time,,2 -d lat,0,0 -d lon,0,0 -d lon,3,3 in.nc";
$tst_cmd[0]="ncks $nco_D_flg -C -g g19g3 -v three_dmn_var_dbl -d time,,2 -d lat,0,0 -d lon,0,0 -d lon,3,3 $in_pth_arg in_grp_3.nc";
@@ -2347,9 +2339,9 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #75
-# ncks -O -c in_grp.nc out.nc
+# ncks -O -c in_grp.nc ~/foo.nc
- if($RUN_NETCDF4_TESTS_VERSION_43 == 1){
+ if($RUN_NETCDF4_TESTS_VERSION_GE_431 == 1){
$dsc_sng="(Groups) -c Extract all coordinate variables";
$tst_cmd[0]="ncks -O $nco_D_flg $in_pth_arg -c in_grp.nc %tmp_fl_00%";
@@ -2359,10 +2351,10 @@ print "\n";
NCO_bm::tst_run(\@tst_cmd);
$#tst_cmd=0; # Reset array
- } #RUN_NETCDF4_TESTS_VERSION_43
+ } #RUN_NETCDF4_TESTS_VERSION_GE_431
#ncks #76
-# ncks -O in_grp.nc out.nc
+# ncks -O in_grp.nc ~/foo.nc
$dsc_sng="(Groups) Default input dataset";
$tst_cmd[0]="ncks -O $nco_D_flg $in_pth_arg in_grp.nc %tmp_fl_00%";
@@ -2373,7 +2365,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #77
-# ncks -O in.nc out.nc
+# ncks -O in.nc ~/foo.nc
$dsc_sng="Default input dataset";
$tst_cmd[0]="ncks -O $nco_D_flg $in_pth_arg in.nc %tmp_fl_00%";
@@ -2384,7 +2376,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #78
-#ncks -O -3 -G : -g /g27g1/ in_grp_3.nc out.nc
+#ncks -O -3 -G : -g /g27g1/ in_grp_3.nc ~/foo.nc
$dsc_sng="(Groups) Test flatenning with parallel variables (-3 -G : -g)";
$tst_cmd[0]="ncks -O -3 -G : -g /g27g1/ $nco_D_flg $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -2395,7 +2387,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #79
-#ncks -O -3 -G : -g g28 -v delta_time_stop in_grp_3.nc out.nc
+#ncks -O -3 -G : -g g28 -v delta_time_stop in_grp_3.nc ~/foo.nc
# simpler case of ncks -O -D 2 -3 -G : -g /altimetry/${DATA}/hdf/mabel_l2_20130927t201800_008_1.h5 ~/foo_mabel.nc
$dsc_sng="(Groups) Test CF extraction with flattening (-3 -G : -g)";
@@ -2406,11 +2398,11 @@ print "\n";
NCO_bm::tst_run(\@tst_cmd);
$#tst_cmd=0; # Reset array
- if($RUN_NETCDF4_TESTS_VERSION_43 == 1){
+ if($RUN_NETCDF4_TESTS_VERSION_GE_431 == 1){
#ncks #80
-#ncks -O -4 -L 0 --cnk_dmn lev,1 -v two_dmn_var in_grp_7.nc out.nc
-#ncks -C -g g19g1g1 --hdn --cdl out.nc | grep _DeflateLevel
+#ncks -O -4 -L 0 --cnk_dmn lev,1 -v two_dmn_var in_grp_7.nc ~/foo.nc
+#ncks -C -g g19g1g1 --hdn --cdl ~/foo.nc | grep _DeflateLevel
$dsc_sng="(Groups) Chunking and uncompression -L 0 --cnk_dmn lev,1 -v two_dmn_var";
$tst_cmd[0]="ncks -O -L 0 -4 --cnk_dmn lev,1 -v two_dmn_var $nco_D_flg $in_pth_arg in_grp_7.nc %tmp_fl_00%";
@@ -2422,8 +2414,8 @@ print "\n";
#ncks #81
# there are 2 'two_dmn_var' beneath /g19/g19g1, chunking only 1
-#ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var in_grp_7.nc out.nc
-#ncks -m -C -v /g19/g19g1/two_dmn_var --hdn out.nc
+#ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var in_grp_7.nc ~/foo.nc
+#ncks -m -C -v /g19/g19g1/two_dmn_var --hdn ~/foo.nc
$dsc_sng="(Groups) Chunking and full dimension names --cnk_dmn /g19/g19g1/g19g1g1/lev,1";
$tst_cmd[0]="ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var $nco_D_flg $in_pth_arg in_grp_7.nc %tmp_fl_00%";
@@ -2435,8 +2427,8 @@ print "\n";
#ncks #82
# there are 2 'two_dmn_var' beneath /g19/g19g1, chunking only 1
-#ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var in_grp_7.nc out.nc
-#ncks -m -C -v /g19/g19g1/g19g1g1/two_dmn_var --hdn out.nc
+#ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var in_grp_7.nc ~/foo.nc
+#ncks -m -C -v /g19/g19g1/g19g1g1/two_dmn_var --hdn ~/foo.nc
$dsc_sng="(Groups) Chunking and full dimension names --cnk_dmn /g19/g19g1/g19g1g1/lev,1";
$tst_cmd[0]="ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var $nco_D_flg $in_pth_arg in_grp_7.nc %tmp_fl_00%";
@@ -2448,8 +2440,8 @@ print "\n";
#ncks #83 (part 1)
# there are 2 'two_dmn_var' beneath /g19/g19g1, chunking both, one with absolute other with relative
-# ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 --cnk_dmn lev,3 -v two_dmn_var in_grp_7.nc out.nc
-# ncks -m -C -v /g19/g19g1/g19g1g1/two_dmn_var --hdn out.nc | grep _ChunkSizes
+# ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 --cnk_dmn lev,3 -v two_dmn_var in_grp_7.nc ~/foo.nc
+# ncks -m -C -v /g19/g19g1/g19g1g1/two_dmn_var --hdn ~/foo.nc | grep _ChunkSizes
$dsc_sng="(Groups) Chunking and full dimension names --cnk_dmn /g19/g19g1/g19g1g1/lev,1";
$tst_cmd[0]="ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 -v two_dmn_var $nco_D_flg $in_pth_arg in_grp_7.nc %tmp_fl_00%";
@@ -2461,8 +2453,8 @@ print "\n";
#ncks #84 (part 2)
# there are 2 'two_dmn_var' beneath /g19/g19g1, chunking the 2 , one with absolute other with relative
-# ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 --cnk_dmn lev,3 -v two_dmn_var in_grp_7.nc out.nc
-# ncks -m -C -v /g19/g19g1/two_dmn_var --hdn out.nc | grep _ChunkSizes
+# ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 --cnk_dmn lev,3 -v two_dmn_var in_grp_7.nc ~/foo.nc
+# ncks -m -C -v /g19/g19g1/two_dmn_var --hdn ~/foo.nc | grep _ChunkSizes
$dsc_sng="(Groups) Chunking and full dimension names --cnk_dmn /g19/g19g1/g19g1g1/lev,1";
$tst_cmd[0]="ncks -O -4 --cnk_dmn /g19/g19g1/g19g1g1/lev,1 --cnk_dmn lev,3 -v two_dmn_var $nco_D_flg $in_pth_arg in_grp_7.nc %tmp_fl_00%";
@@ -2473,10 +2465,10 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #85
-#ncks -O -L 0 --cnk_dmn lat,2 -v one in_grp.nc out.nc
-#ncks -C -m --hdn -v one -g g13 out.nc | grep _Storage
+#ncks -O -L 0 --cnk_dmn lat,2 -v one in_grp.nc ~/foo.nc
+#ncks -C -m --hdn -v one -g g13 ~/foo.nc | grep _Storage
- $dsc_sng="(Groups) Chunking and shuffle filter -L 0 --cnk_dmn lat,2 -v one (expect failuse with netCDF 4.1.1-)";
+ $dsc_sng="(Groups) Chunking and shuffle filter -L 0 --cnk_dmn lat,2 -v one (expect failure with netCDF 4.1.1-)";
$tst_cmd[0]="ncks -O -4 -L 0 --cnk_dmn lat,2 -v one $nco_D_flg $in_pth_arg hdn.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -m --hdn -v one -g g13 %tmp_fl_00% | grep _Storage";
$tst_cmd[2]="one attribute 1: _Storage, size = 10 NC_CHAR, value = contiguous";
@@ -2484,11 +2476,11 @@ print "\n";
NCO_bm::tst_run(\@tst_cmd);
$#tst_cmd=0; # Reset array
- } # RUN_NETCDF4_TESTS_VERSION_43
+ } # RUN_NETCDF4_TESTS_VERSION_GE_431
#ncks #86
-#ncks -h -O --fix_rec_dmn time52 -v one_dmn_rec_var in_grp.nc out.nc
-#ncks -v time52 -m out.nc
+#ncks -h -O --fix_rec_dmn time52 -v one_dmn_rec_var in_grp.nc ~/foo.nc
+#ncks -v time52 -m ~/foo.nc
$dsc_sng="(Groups) Change record dimension to fixed dimension --fix_rec_dmn time52 -v one_dmn_rec_var";
$tst_cmd[0]="ncks -h -O --fix_rec_dmn time52 -v one_dmn_rec_var $nco_D_flg $in_pth_arg in_grp.nc %tmp_fl_00%";
@@ -2499,7 +2491,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#ncks #87
-#ncks -O -v lat29 in_grp_3.nc out.nc
+#ncks -O -v lat29 in_grp_3.nc ~/foo.nc
$dsc_sng="(Groups) Test ";
$tst_cmd[0]="ncks -O -v lat29 $nco_D_flg $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -2511,11 +2503,11 @@ print "\n";
#ncks #88
# Test -X writing (apply limits to all standard 'lat' 'lon')
-# ncks -O -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar in_grp_3.nc out.nc
+# ncks -O -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar in_grp_3.nc ~/foo.nc
- $dsc_sng="(Groups) Auxiliary coordinates writing -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar";
- $tst_cmd[0]="ncks $nco_D_flg -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar $in_pth_arg in_grp_3.nc %tmp_fl_00%";
- $tst_cmd[1]="ncks $nco_D_flg -v lon_gds_1 %tmp_fl_00%";
+ $dsc_sng="(Groups) Auxiliary coordinates writing -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar";
+ $tst_cmd[0]="ncks $nco_D_flg -X 0.,1.,-30.,-29. -g g18g1 -v gds_3dvar $in_pth_arg in_grp_3.nc %tmp_fl_00%";
+ $tst_cmd[1]="ncks $nco_D_flg -v lon_gds_1 %tmp_fl_00%";
$tst_cmd[2]="gds_crd[0]=1 lon_gds_1[0]=0 degree";
$tst_cmd[3]="SS_OK";
NCO_bm::tst_run(\@tst_cmd);
@@ -2523,12 +2515,12 @@ print "\n";
#ncks #89
# Test -X (writing associated coordinates)
-# ncks -O -X 0.,1.,-30.,-29. -g g18 -v gds_3dvar in_grp_3.nc out.nc
-# ncks -g g18g2 -v lat_gds_2 out.nc
+# ncks -O -X 0.,1.,-30.,-29. -g g18 -v gds_3dvar in_grp_3.nc ~/foo.nc
+# ncks -g g18g2 -v lat_gds_2 ~/foo.nc
$dsc_sng="(Groups) Auxiliary coordinates (writing associated coordinates) -X 0.,1.,-30.,-29. -g g18 -v gds_3dvar in_grp_3.nc";
$tst_cmd[0]="ncks $nco_D_flg -X 0.,1.,-30.,-29. -g g18 -v gds_3dvar $in_pth_arg in_grp_3.nc %tmp_fl_00%";
- $tst_cmd[1]="ncks $nco_D_flg -g g18g2 -C -v lat_gds_2 %tmp_fl_00%";
+ $tst_cmd[1]="ncks $nco_D_flg -g g18g2 -C -v lat_gds_2 %tmp_fl_00%";
$tst_cmd[2]="gds_crd[0]=1 lat_gds_2[0]=-30 degree";
$tst_cmd[3]="SS_OK";
NCO_bm::tst_run(\@tst_cmd);
@@ -2536,19 +2528,44 @@ print "\n";
} #### Group tests
-
#ncks #90
# Test -X writing
-# ncks -O -X 0.,1.,-30.,-29. -v gds_3dvar in.nc out.nc
+# ncks -O -X 0.,1.,-30.,-29. -v gds_3dvar in.nc ~/foo.nc
$dsc_sng="Auxiliary coordinates writing -X 0.,1.,-30.,-29. -v gds_3dvar";
$tst_cmd[0]="ncks $nco_D_flg -X 0.,1.,-30.,-29. -v gds_3dvar $in_pth_arg in.nc %tmp_fl_00%";
- $tst_cmd[1]="ncks $nco_D_flg -v gds_crd %tmp_fl_00%";
+ $tst_cmd[1]="ncks $nco_D_flg -v gds_crd %tmp_fl_00%";
$tst_cmd[2]="gds_crd[0]=1 lon_gds[0]=0 degree";
$tst_cmd[3]="SS_OK";
NCO_bm::tst_run(\@tst_cmd);
$#tst_cmd=0; # Reset array
+#ncks #91 Extract CF 'ancillary_variables' variables (netCDF3 file)
+#ncks -O -d time,5 -v cnv_CF_ncl ~/nco/data/in.nc ~/foo.nc
+#ncks -C -H -v cnv_CF_ncl_var_2 ~/foo.nc
+ $dsc_sng="Extract CF 'ancillary_variables' variables (netCDF3 file)";
+ $tst_cmd[0]="ncks -O $nco_D_flg -d time,5 -v cnv_CF_ncl $in_pth_arg in.nc %tmp_fl_00%";
+ $tst_cmd[1]="ncks -C -H $nco_D_flg -v cnv_CF_ncl_var_2 %tmp_fl_00%";
+ $tst_cmd[2]="time[0]=6 cnv_CF_ncl_var_2[0]=36";
+ $tst_cmd[3]="SS_OK";
+ NCO_bm::tst_run(\@tst_cmd);
+ $#tst_cmd=0; # Reset array
+
+#ncks #92
+#ncks -O -D 5 -C -d lat,0 -v one,four --cnk_plc=xst --cnk_map=xst ~/nco/data/hdn.nc ~/foo.nc
+
+ if($RUN_NETCDF4_TESTS_VERSION_GE_431 == 1){
+
+ $dsc_sng="Chunking multiple variables while hyperslabbing";
+ $tst_cmd[0]="ncks -O $nco_D_flg -C -d lat,0 -v one,four --cnk_plc=xst --cnk_map=xst $in_pth_arg hdn.nc %tmp_fl_00%";
+ $tst_cmd[1]="ncks -v one %tmp_fl_00% | grep 'chunksize'";
+ $tst_cmd[2]="one dimension 0: /lat, size = 1, chunksize = 1 (Non-coordinate dimension)";
+ $tst_cmd[3]="SS_OK";
+ NCO_bm::tst_run(\@tst_cmd);
+ $#tst_cmd=0; # Reset array
+
+ } # RUN_NETCDF4_TESTS_VERSION_GE_431
+
#####################
#### ncpdq tests #### -OK !
#####################
@@ -2626,8 +2643,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #7 MSA stride
-#ncpdq -h -O -a lat,lon,time -d time,1,3,2 -d lat,1,1,1 -d lon,1,3,2 -v three_dmn_var_dbl in.nc out.nc
-#ncks -C -H -v three_dmn_var_dbl -d lat,0,0 -d lon,1,1 -d time,0 out.nc
+#ncpdq -h -O -a lat,lon,time -d time,1,3,2 -d lat,1,1,1 -d lon,1,3,2 -v three_dmn_var_dbl in.nc ~/foo.nc
+#ncks -C -H -v three_dmn_var_dbl -d lat,0,0 -d lon,1,1 -d time,0 ~/foo.nc
#lat[0]=90 lon[1]=270 time[0]=2 three_dmn_var_dbl[2]=16
$tst_cmd[0]="ncpdq $omp_flg -h -O $fl_fmt $nco_D_flg -a lat,lon,time -d time,1,3,2 -d lat,1,1,1 -d lon,1,3,2 -v three_dmn_var_dbl $in_pth_arg in.nc %tmp_fl_00%";
@@ -2661,8 +2678,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #10
# two_dmn_var (lat,lev) no change
-# ncpdq -O -C -a lat,lev -v two_dmn_var in.nc out.nc
-# ncks -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -a lat,lev -v two_dmn_var in.nc ~/foo.nc
+# ncks -d lat,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O -C $fl_fmt $nco_D_flg -a lat,lev -v two_dmn_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -2675,8 +2692,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #11
# two_dmn_var (lat,lev) -C, no MSA (no associated coordinates)
-# ncpdq -O -C -a lev,lat -v two_dmn_var in.nc out.nc
-# ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -a lev,lat -v two_dmn_var in.nc ~/foo.nc
+# ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -C -a lev,lat -v two_dmn_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -2689,8 +2706,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #12
# two_dmn_var (lat,lev) no MSA (associated coordinates)
-# ncpdq -O -a lev,lat -v two_dmn_var in.nc out.nc
-# ncks -C -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -a lev,lat -v two_dmn_var in.nc ~/foo.nc
+# ncks -C -d lat,1,1 -d lev,1,1 ~/foo.nc
#$tst_cmd[2]="lev[1]=500 lat[1]=90 two_dmn_var[3]=17.5 fraction";
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -a lev,lat -v two_dmn_var $in_pth_arg in.nc %tmp_fl_00%";
@@ -2705,8 +2722,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #13
# two_dmn_var (lat,lev) -C, MSA (no associated coordinates)
-# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc ~/foo.nc
+# ncks ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O -C $fl_fmt $nco_D_flg -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_var %tmp_fl_00%";
@@ -2719,8 +2736,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #14
# two_dmn_var (lat,lev) MSA (associated coordinates)
-# ncpdq -O -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc ~/foo.nc
+# ncks ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_var %tmp_fl_00%";
@@ -2733,8 +2750,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #15
# two_dmn_rec_var(time,lev) 2D variable with record (-C , no MSA)
-# ncpdq -O -C -a lev,time -v two_dmn_rec_var in.nc out.nc
-# ncks -d time,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -a lev,time -v two_dmn_rec_var in.nc ~/foo.nc
+# ncks -d time,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -C -a lev,time -v two_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_rec_var -d time,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -2748,8 +2765,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #16
# two_dmn_rec_var(time,lev) 2D variable with record (no MSA)
-# ncpdq -O -a lev,time -v two_dmn_rec_var in.nc out.nc
-# ncks -d time,1,1 -d lev,1,1 out.nc
+# ncpdq -O -a lev,time -v two_dmn_rec_var in.nc ~/foo.nc
+# ncks -d time,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -a lev,time -v two_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_rec_var -d time,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -2762,8 +2779,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #17
# two_dmn_rec_var(time,lev) 2D variable with record (MSA)
-# ncpdq -O -C -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -C -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in.nc ~/foo.nc
+# ncks ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -C -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_rec_var %tmp_fl_00%";
@@ -2776,8 +2793,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #18
# two_dmn_rec_var(time,lev) 2D variable with record (MSA)
-# ncpdq -O -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in.nc ~/foo.nc
+# ncks ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -O $fl_fmt $nco_D_flg -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v two_dmn_rec_var %tmp_fl_00%";
@@ -2790,7 +2807,7 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #19
#three_dmn_var_dbl(time,lat,lon);
-#ncpdq -h -O -a lat,time -v three_dmn_var -d time,1,1 -d lat,1,1 -d lon,1,1 in.nc out.nc
+#ncpdq -h -O -a lat,time -v three_dmn_var -d time,1,1 -d lat,1,1 -d lon,1,1 in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg -h -O $fl_fmt $nco_D_flg -a -lat,-time -v three_dmn_var_dbl -d time,1,6,2 -d lat,0,1 -d lon,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -H -C -v three_dmn_var_dbl -d lat,1,1 -d time,2,2 %tmp_fl_00%";
@@ -2804,7 +2821,7 @@ print "\n";
#ncpdq #20
#three_dmn_rec_var(time,lat,lon);
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v ty -d time,1,1 -d lat,1,1 %tmp_fl_00%";
@@ -2818,7 +2835,7 @@ print "\n";
#ncpdq #21 (same run as #20)
#three_dmn_rec_var(time,lat,lon);
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v three_dmn_rec_var -d time,1,1 -d lat,1,1 -d lon,1,1 %tmp_fl_00%";
@@ -2832,7 +2849,7 @@ print "\n";
#ncpdq #22
#three_dmn_rec_var(time,lat,lon); MSA
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v ty -d time,2,2 %tmp_fl_00%";
@@ -2846,7 +2863,7 @@ print "\n";
#ncpdq #23 (same run as #22)
#three_dmn_rec_var(time,lat,lon); MSA
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var -d time,1,6,2 -d lat,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v three_dmn_rec_var -d lat,0,0 -d time,1,1 -d lon,1,1 %tmp_fl_00%";
@@ -2860,7 +2877,7 @@ print "\n";
#ncpdq #24 (same run as #22) check if output is the right record
#three_dmn_rec_var(time,lat,lon);
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -m -C -v three_dmn_rec_var %tmp_fl_00% | grep 'three_dmn_rec_var dimension 0: lat, size = 2 NC_FLOAT (Record coordinate is lat)'";
@@ -2874,7 +2891,7 @@ print "\n";
#ncpdq #25 (same run as #22) check if output is the right record
#three_dmn_rec_var(time,lat,lon);
#ty(time,lat);
-#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc out.nc
+#ncpdq -h -O -a lat,time -v ty,three_dmn_rec_var in.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v ty,three_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -m -C -v three_dmn_rec_var %tmp_fl_00% | grep 'three_dmn_rec_var dimension 1: time, size = 10 NC_DOUBLE (Coordinate is time)'";
@@ -2887,8 +2904,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #26
#four_dmn_rec_var(time,lat,lev,lon); MSA
-#ncpdq -h -O -a lev,time,-lon,-lat -v four_dmn_rec_var -d time,1,6,2 -d lat,1,1 -d lon,1,1 -d lev,1,1 in.nc out.nc
-#ncks -C -H -v four_dmn_rec_var -d time,2,2 out.nc
+#ncpdq -h -O -a lev,time,-lon,-lat -v four_dmn_rec_var -d time,1,6,2 -d lat,1,1 -d lon,1,1 -d lev,1,1 in.nc ~/foo.nc
+#ncks -C -H -v four_dmn_rec_var -d time,2,2 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lev,time,-lon,-lat -v four_dmn_rec_var -d time,1,6,2 -d lat,1,1 -d lon,1,1 -d lev,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v four_dmn_rec_var -d time,2,2 %tmp_fl_00%";
@@ -2902,8 +2919,8 @@ print "\n";
#ncpdq #27 : reorder 2 variables with -a lat,time and check a variable that only has 1 (lat)
#PS(time,lat,lon)
#three_dmn_var_crd(lev,lat,lon);
-#ncpdq -h -O -a lat,time -v PS,three_dmn_var_crd -d lev,1,1 -d lat,1,1 -d lon,1,1 -d lev,1,1 in.nc out.nc
-#ncks -C -H -v three_dmn_var_crd out.nc
+#ncpdq -h -O -a lat,time -v PS,three_dmn_var_crd -d lev,1,1 -d lat,1,1 -d lon,1,1 -d lev,1,1 in.nc ~/foo.nc
+#ncks -C -H -v three_dmn_var_crd ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -v PS,three_dmn_var_crd -d lev,1,1 -d lat,1,1 -d lon,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -H -C -v three_dmn_var_crd %tmp_fl_00%";
@@ -2915,8 +2932,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #28
-#ncpdq -h -O -a lat,time -d time,1,6,2 -d lat,1,1 in.nc out.nc
-#ncks -C -H -v -d time,2,2 four_dmn_rec_var out.nc
+#ncpdq -h -O -a lat,time -d time,1,6,2 -d lat,1,1 in.nc ~/foo.nc
+#ncks -C -H -v -d time,2,2 four_dmn_rec_var ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -h -O -a lat,time -d time,1,1 -d lat,1,1 $in_pth_arg in.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -H -v four_dmn_rec_var -d lon,2,2 -d lev,2,2 %tmp_fl_00%";
@@ -2976,8 +2993,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #11
# two_dmn_var (lat,lev) -C, no MSA (no associated coordinates)
-# ncpdq -O -C -a lev,lat -v two_dmn_var in.nc out.nc
-# ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -a lev,lat -v two_dmn_var in.nc ~/foo.nc
+# ncks -v two_dmn_var -d lat,1,1 -d lev,1,1 ~/foo.nc
# same as previous but with group
@@ -2988,8 +3005,8 @@ print "\n";
# dimensions:lat=2;lev=3;lon=4;time=unlimited;
#ncpdq #11
# two_dmn_var (lat,lev) -C, no MSA (no associated coordinates)
-# ncpdq -O -C -g g19g1 -a lev,lat -v two_dmn_var in_grp_3.nc out.nc
-# ncks -g g19g1 -v two_dmn_var -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -g g19g1 -a lev,lat -v two_dmn_var in_grp_3.nc ~/foo.nc
+# ncks -g g19g1 -v two_dmn_var -d lat,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -C -g g19g1 -a lev,lat -v two_dmn_var $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -3004,8 +3021,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #12
# two_dmn_var (lat,lev) no -C, no MSA
-# ncpdq -O -a lev,lat -v two_dmn_var in.nc out.nc
-# ncks -C -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -a lev,lat -v two_dmn_var in.nc ~/foo.nc
+# ncks -C -d lat,1,1 -d lev,1,1 ~/foo.nc
# same as previous but with group
@@ -3016,8 +3033,8 @@ print "\n";
# dimensions:lat=2;lev=3;lon=4;time=unlimited;
#ncpdq #12
# two_dmn_var (lat,lev) no -C, no MSA
-# ncpdq -O -g g19g1 -a lev,lat -v two_dmn_var in_grp_3.nc out.nc
-# ncks -C -g g19g1 -v two_dmn_var -d lat,1,1 -d lev,1,1 out.nc
+# ncpdq -O -g g19g1 -a lev,lat -v two_dmn_var in_grp_3.nc ~/foo.nc
+# ncks -C -g g19g1 -v two_dmn_var -d lat,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -g g19g1 -a lev,lat -v two_dmn_var $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g g19g1 -v two_dmn_var -d lat,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -3030,8 +3047,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #13
# two_dmn_var (lat,lev) -C, MSA (no associated coordinates)
-# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc ~/foo.nc
+# ncks ~/foo.nc
# same as previous but with group
@@ -3042,8 +3059,8 @@ print "\n";
# dimensions:lat=2;lev=3;lon=4;time=unlimited;
#ncpdq #13
# two_dmn_var (lat,lev) -C, MSA (no associated coordinates)
-# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in_grp_3.nc out.nc
-# ncks out.nc
+# ncpdq -O -C -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in_grp_3.nc ~/foo.nc
+# ncks ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -g g19g1 -C -a lev,lat -v two_dmn_var -d lat,1,1 -d lev,1,1 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -3057,8 +3074,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #14
# two_dmn_var (lat,lev) MSA (associated coordinates)
-# ncpdq -O -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc out.nc
-# ncks out.nc
+# ncpdq -O -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in.nc ~/foo.nc
+# ncks ~/foo.nc
#$tst_cmd[2]="lev[0]=500 lat[0]=90 two_dmn_var[0]=17.5 fraction";
# same as previous but with group
@@ -3068,8 +3085,8 @@ print "\n";
# group: g19 {
# dimensions:lat=2;lev=3;lon=4;time=unlimited;
# two_dmn_var (lat,lev) MSA (associated coordinates)
-# ncpdq -O -g g19g1 -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in_grp_3.nc out.nc
-# ncks -C -g g19g1 -v two_dmn_var out.nc
+# ncpdq -O -g g19g1 -a lev,lat -d lat,1,1 -d lev,1,1 -v two_dmn_var in_grp_3.nc ~/foo.nc
+# ncks -C -g g19g1 -v two_dmn_var ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -g g19g1 -a lev,lat -v two_dmn_var -d lat,1,1 -d lev,1,1 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g g19g1 -v two_dmn_var %tmp_fl_00%";
@@ -3082,8 +3099,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #15
# two_dmn_rec_var(time,lev) 2D variable with record (-C , no MSA)
-# ncpdq -O -C -a lev,time -v two_dmn_rec_var in.nc out.nc
-# ncks -d time,1,1 -d lev,1,1 out.nc
+# ncpdq -O -C -a lev,time -v two_dmn_rec_var in.nc ~/foo.nc
+# ncks -d time,1,1 -d lev,1,1 ~/foo.nc
# same as previous but with group
@@ -3091,8 +3108,8 @@ print "\n";
#ncpdq #36
# group: g19 {
# dimensions:lat=2;lev=3;lon=4;time=unlimited;
-# ncpdq -O -g g19g2 -C -a lev,time -v two_dmn_rec_var in_grp_3.nc out.nc
-# ncks -d time,1,1 -d lev,1,1 out.nc
+# ncpdq -O -g g19g2 -C -a lev,time -v two_dmn_rec_var in_grp_3.nc ~/foo.nc
+# ncks -d time,1,1 -d lev,1,1 ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -g g19g2 -C -a lev,time -v two_dmn_rec_var $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -g g19g2 -v two_dmn_rec_var -d time,1,1 -d lev,1,1 %tmp_fl_00%";
@@ -3105,8 +3122,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #37
# two_dmn_rec_var(time,lev) 2D variable with record (no -C, no MSA)
-# ncpdq -O -g g19g2 -a lev,time -v two_dmn_rec_var in_grp_3.nc out.nc
-# ncks -C -g g19g2 -d time,1,1 -d lev,1,1 out.nc
+# ncpdq -O -g g19g2 -a lev,time -v two_dmn_rec_var in_grp_3.nc ~/foo.nc
+# ncks -C -g g19g2 -d time,1,1 -d lev,1,1 ~/foo.nc
# same #16 as previous but with group
@@ -3121,8 +3138,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #38
# two_dmn_rec_var(time,lev) 2D variable with record (MSA)
-# ncpdq -O -C -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in_grp_3.nc out.nc
-# ncks -g g19g2 -v two_dmn_rec_var out.nc
+# ncpdq -O -C -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in_grp_3.nc ~/foo.nc
+# ncks -g g19g2 -v two_dmn_rec_var ~/foo.nc
# same as #17 but with group
@@ -3137,8 +3154,8 @@ print "\n";
#NEW NCO 4.3.2
#ncpdq #39
# two_dmn_rec_var(time,lev) 2D variable with record (MSA)
-# ncpdq -O -g g19g2 -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in_grp_3.nc out.nc
-# ncks -C -g g19g2 -v two_dmn_rec_var out.nc
+# ncpdq -O -g g19g2 -a lev,time -d time,1,1 -d lev,1,1 -v two_dmn_rec_var in_grp_3.nc ~/foo.nc
+# ncks -C -g g19g2 -v two_dmn_rec_var ~/foo.nc
# $tst_cmd[2]="lev[0]=500 time[0]=2 two_dmn_rec_var[0]=2.1 watt meter-2";
# same as #18 but with group
@@ -3152,7 +3169,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#NEW NCO 4.3.5
-#ncpdq -O -a -lat -g g23,g24 ~/nco/data/in_grp_3.nc out.nc
+#ncpdq -O -a -lat -g g23,g24 ~/nco/data/in_grp_3.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -a -lat -g g23,g24 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v lat -g g23 %tmp_fl_00%";
@@ -3163,7 +3180,7 @@ print "\n";
$#tst_cmd=0; # Reset array
#NEW NCO 4.3.5
-#ncpdq -O -a -lat -g g23,g24 ~/nco/data/in_grp_3.nc out.nc
+#ncpdq -O -a -lat -g g23,g24 ~/nco/data/in_grp_3.nc ~/foo.nc
$tst_cmd[0]="ncpdq $omp_flg $fl_fmt $nco_D_flg -O -a -lat -g g23,g24 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v lat -g g24 %tmp_fl_00%";
@@ -3179,9 +3196,9 @@ print "\n";
#NEW NCO 4.3.2patch
#ncpdq #40
-#ncpdq -h -O -P all_new -v upk in.nc out.nc
-#ncpdq -h -O -P upk -v upk out.nc out.nc
-#ncks -C -H -s '%g' -v upk out.nc
+#ncpdq -h -O -P all_new -v upk in.nc ~/foo.nc
+#ncpdq -h -O -P upk -v upk ~/foo.nc ~/foo.nc
+#ncks -C -H -s '%g' -v upk ~/foo.nc
# same as #29 but with group
@@ -3197,8 +3214,8 @@ print "\n";
#NEW NCO 4.3.2patch
#ncpdq #41
# same as ncpdq #30
-#ncpdq -g g19g4 -h -O -C -P upk -v rec_var_dbl_mss_val_dbl_pck -d time,0,4 -d time,6 in_grp_3.nc out.nc
-#ncks -g g19g4 -C -H -s '%f' -v rec_var_dbl_mss_val_dbl_pck -d time,5 out.nc
+#ncpdq -g g19g4 -h -O -C -P upk -v rec_var_dbl_mss_val_dbl_pck -d time,0,4 -d time,6 in_grp_3.nc ~/foo.nc
+#ncks -g g19g4 -C -H -s '%f' -v rec_var_dbl_mss_val_dbl_pck -d time,5 ~/foo.nc
#$tst_cmd[2]="7";
# same as #30 but with group
@@ -3214,7 +3231,7 @@ print "\n";
#NEW NCO 4.4.0
#ncpdq #46
-# ncpdq -O -4 -a lon,lat --cnk_dmn lat,1 --cnk_dmn lon,2 -v lat_2D_rct in.nc out.nc
+# ncpdq -O -4 -a lon,lat --cnk_dmn lat,1 --cnk_dmn lon,2 -v lat_2D_rct in.nc ~/foo.nc
$dsc_sng="Chunking -a lon,lat --cnk_dmn lat,1 --cnk_dmn lon,2 -v lat_2D_rct";
$tst_cmd[0]="ncpdq $omp_flg -4 $nco_D_flg -a lon,lat --cnk_dmn lat,1 --cnk_dmn lon,2 -v lat_2D_rct $in_pth_arg in.nc %tmp_fl_00%";
@@ -3322,7 +3339,7 @@ print "\n";
#ncrcat #05
- $tst_cmd[0]="ncra -Y ncrcat $omp_flg -h -O $fl_fmt $nco_D_flg -v four_dmn_rec_var $in_pth_arg -d time,0,,4 -d lat,0,0 -d lon,0,1 -d lon,3,3 in.nc in.nc %tmp_fl_00% 2> %tmp_fl_02%";
+ $tst_cmd[0]="ncra -Y ncrcat $omp_flg -h -O $fl_fmt $nco_D_flg -v four_dmn_rec_var $in_pth_arg -d time,0,,4 -d lat,0,0 -d lon,0,1 -d lon,3,3 in.nc in.nc %tmp_fl_00% 2> %tmp_fl_02%";
$tst_cmd[1]="ncwa $omp_flg -h -y max -O $fl_fmt $nco_D_flg %tmp_fl_00% %tmp_fl_01%";
$tst_cmd[2]="ncks -C -H -s '%f' -v four_dmn_rec_var %tmp_fl_01%";
$dsc_sng="Concatenate float 4D variable with multislabs across two files";
@@ -3564,7 +3581,7 @@ print "\n";
#ncrcat #23
# 2 groups each one with a record (part 1)
-# ncra -Y ncrcat -h -O -g g25g1,g25g2 -v one_dmn_rec_var in_grp_3.nc in_grp_3.nc -d time,2.,3. out.nc
+# ncra -Y ncrcat -h -O -g g25g1,g25g2 -v one_dmn_rec_var in_grp_3.nc in_grp_3.nc -d time,2.,3. ~/foo.nc
$tst_cmd[0]="ncra -Y ncrcat $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var $in_pth_arg in_grp_3.nc in_grp_3.nc -d time,2.,3. %tmp_fl_00% 2> %tmp_fl_02%";
$tst_cmd[1]="ncks -C -H -s '%d ' -g g25g1 -v one_dmn_rec_var %tmp_fl_00%";
@@ -3576,7 +3593,7 @@ print "\n";
#ncrcat #24
# 2 groups each one with a record (part 2)
-# ncra -Y ncrcat -h -O -g g25g1,g25g2 -v one_dmn_rec_var in_grp_3.nc in_grp_3.nc -d time,2.,3. out.nc
+# ncra -Y ncrcat -h -O -g g25g1,g25g2 -v one_dmn_rec_var in_grp_3.nc in_grp_3.nc -d time,2.,3. ~/foo.nc
$tst_cmd[0]="ncra -Y ncrcat $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 -v one_dmn_rec_var $in_pth_arg in_grp_3.nc in_grp_3.nc -d time,2.,3. %tmp_fl_00% 2> %tmp_fl_02%";
$tst_cmd[1]="ncks -C -H -s '%d ' -g g25g2 -v one_dmn_rec_var %tmp_fl_00%";
@@ -3663,8 +3680,8 @@ print "\n";
#ncrcat #30
#ncks -h -O -g g5 -v one_dmn_rec_var,time51,time52 in_grp.nc in_grp1.nc
#ncks -h -O -g g5 -v one_dmn_rec_var,time51,time52 in_grp.nc in_grp2.nc
-#ncrcat -O -h -g g5 -v one_dmn_rec_var in_grp1.nc in_grp2.nc out.nc
-#ncks -C -g g5 -v one_dmn_rec_var out.nc
+#ncrcat -O -h -g g5 -v one_dmn_rec_var in_grp1.nc in_grp2.nc ~/foo.nc
+#ncks -C -g g5 -v one_dmn_rec_var ~/foo.nc
$tst_cmd[0]="ncks $omp_flg -h -O $fl_fmt $nco_D_flg -g g5 -v one_dmn_rec_var,time51,time52 $in_pth_arg in_grp.nc %tmp_fl_00%";
$tst_cmd[1]="ncks $omp_flg -h -O $fl_fmt $nco_D_flg -v one_dmn_rec_var,time51,time52 $in_pth_arg in_grp.nc %tmp_fl_01%";
@@ -3971,7 +3988,7 @@ print "\n";
# ncra #27
# (Groups) 1D var 2 records to process in 2 groups (part 1)
-# ncra -h -O -g g25g1,g25g2 in_grp_3.nc in_grp_3.nc out.nc
+# ncra -h -O -g g25g1,g25g2 in_grp_3.nc in_grp_3.nc ~/foo.nc
$tst_cmd[0]="ncra $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g g25g1 -v one_dmn_rec_var %tmp_fl_00%";
@@ -3983,7 +4000,7 @@ print "\n";
# ncra #28 same as #27
# (Groups) 1D var 2 records to process in 2 groups (part 2)
-# ncra -h -O -g g25g1,g25g2 in_grp_3.nc in_grp_3.nc out.nc
+# ncra -h -O -g g25g1,g25g2 in_grp_3.nc in_grp_3.nc ~/foo.nc
$tst_cmd[0]="ncra $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1,g25g2 $in_pth_arg in_grp_3.nc in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -C -g g25g2 -v one_dmn_rec_var %tmp_fl_00%";
@@ -3995,8 +4012,8 @@ print "\n";
# ncra #29 Generate a file with 2 records
# ncecat -O -g g25g1 in_grp_3.nc in1.nc -> generate "record"
-# ncpdq -O -a time,record in1.nc in2.nc -> switch "record" and "time"
-# ncra -O in2.nc out.nc
+# ncpdq -O -a time,record in1.nc in2.nc -> switch "record" and "time"
+# ncra -O in2.nc ~/foo.nc
$tst_cmd[0]="ncecat $omp_flg -h -O $fl_fmt $nco_D_flg -g g25g1 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncpdq $omp_flg -h -O $fl_fmt $nco_D_flg -a time,record %tmp_fl_00% %tmp_fl_01%";
@@ -4047,7 +4064,7 @@ print "\n";
#NEW 4.4.2
#ncra #32
-#ncra -O -v time301 -C in_grp_3.nc out.nc
+#ncra -O -v time301 -C in_grp_3.nc ~/foo.nc
if (0){
$dsc_sng="(Groups) Cell methods (Create) -v time301";
$tst_cmd[0]="ncra $omp_flg $nco_D_flg -O -v time301 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -4368,7 +4385,7 @@ if (0){
@tst_cmd=(); # Reset array
#ncwa #28
-# ncwa -h -O -y max -v three_dmn_var_dbl -a lat,lon in.nc out.nc
+# ncwa -h -O -y max -v three_dmn_var_dbl -a lat,lon in.nc ~/foo.nc
# will fail SS - ncks not the last cmd
push(@tst_cmd, "ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y max -v three_dmn_var_dbl -a lat,lon $in_pth_arg in.nc %tmp_fl_00%");
@@ -4558,8 +4575,8 @@ if (0){
#ncwa #44
#NEW NCO 4.3.3
#same as #ncwa #25
-#ncwa -h -O -y min -g g10 -v three_dmn_rec_var in_grp.nc out.nc
-#ncks -C -H -s '%f' -g g10 -v three_dmn_rec_var out.nc
+#ncwa -h -O -y min -g g10 -v three_dmn_rec_var in_grp.nc ~/foo.nc
+#ncks -C -H -s '%f' -g g10 -v three_dmn_rec_var ~/foo.nc
#$tst_cmd[0]="ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y min -v three_dmn_rec_var $in_pth_arg in.nc %tmp_fl_00% 2> %tmp_fl_02%";
#$tst_cmd[1]="ncks -C -H -s '%f' -v three_dmn_rec_var %tmp_fl_00%";
#$dsc_sng="Dimension reduction with min flag on type float variable";
@@ -4576,8 +4593,8 @@ if (0){
#ncwa #45
#NEW NCO 4.3.3
#same as #ncwa #27
-# ncwa -h -O -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon in_grp_3.nc out.nc
-# ncks -C -H --no_blank -s '%f' -g g19g3 -v three_dmn_var_dbl -d time,3 out.nc
+# ncwa -h -O -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon in_grp_3.nc ~/foo.nc
+# ncks -C -H --no_blank -s '%f' -g g19g3 -v three_dmn_var_dbl -d time,3 ~/foo.nc
# will fail SS - ncks not the last cmd
push(@tst_cmd, "ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon $in_pth_arg in_grp_3.nc %tmp_fl_00%");
@@ -4592,8 +4609,8 @@ if (0){
#ncwa #46
#NEW NCO 4.3.3
#same as #ncwa #28
-# ncwa -h -O -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon in_grp_3.nc out.nc
-# ncks -C -H -s '%f' -g g19g3 -v three_dmn_var_dbl -d time,4 out.nc
+# ncwa -h -O -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon in_grp_3.nc ~/foo.nc
+# ncks -C -H -s '%f' -g g19g3 -v three_dmn_var_dbl -d time,4 ~/foo.nc
# will fail SS - ncks not the last cmd
push(@tst_cmd, "ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y max -g g19g3 -v three_dmn_var_dbl -a lat,lon $in_pth_arg in_grp_3.nc %tmp_fl_00%");
@@ -4609,11 +4626,11 @@ if (0){
#ncwa #47
#NEW NCO 4.3.3
#same as #ncwa #33
-# ncwa -h -O -y rms -w lat_wgt -g g20g1 -v lat_cpy in_grp_3.nc out.nc
-# ncks -C -H -s '%f' -g g20g1 -v lat_cpy out.nc
+# ncwa -h -O -y rms -w lat_wgt -g g20g1 -v lat_cpy in_grp_3.nc ~/foo.nc
+# ncks -C -H -s '%f' -g g20g1 -v lat_cpy ~/foo.nc
$tst_cmd[0]="ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -y rms -w lat_wgt -g g20g1 -v lat_cpy $in_pth_arg in_grp_3.nc %tmp_fl_00% 2> %tmp_fl_02%";
- $tst_cmd[1]="ncks -C -H -s '%f' -g g20g1 -v lat_cpy %tmp_fl_00%";;
+ $tst_cmd[1]="ncks -C -H -s '%f' -g g20g1 -v lat_cpy %tmp_fl_00%";;
$dsc_sng="(Groups) rms with weights";
$tst_cmd[2]="90";
$tst_cmd[3]="SS_OK";
@@ -4622,7 +4639,7 @@ if (0){
#ncwa #48
#NEW NCO 4.3.6
-#ncwa -O -w gw_lat -d lat,1,2 -d lon,0,1 -a lat,lon -g g26 in_grp_3.nc out.nc
+#ncwa -O -w gw_lat -d lat,1,2 -d lon,0,1 -a lat,lon -g g26 in_grp_3.nc ~/foo.nc
$tst_cmd[0]="ncwa $omp_flg -O $fl_fmt $nco_D_flg -w gw_lat -d lat,1,2 -d lon,0,1 -a lat,lon -g g26 $in_pth_arg in_grp_3.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -v a %tmp_fl_00%";;
@@ -4633,7 +4650,7 @@ if (0){
$#tst_cmd=0; # Reset array
#ncwa #49
-# ncwa -h -O -v lev -a lev -w lev_wgt in_grp_3.nc out.nc
+# ncwa -h -O -v lev -a lev -w lev_wgt in_grp_3.nc ~/foo.nc
# lev = 230.769 lev_wgt=10,2,1; /g19/lev
# lev = 241.667 lev_wgt=9,2,1; /g8/lev
@@ -4646,7 +4663,7 @@ if (0){
$#tst_cmd=0; # Reset array
#ncwa #50
-# ncwa -h -O -v lev -a lev -w lev_wgt in_grp_3.nc out.nc
+# ncwa -h -O -v lev -a lev -w lev_wgt in_grp_3.nc ~/foo.nc
# lev = 230.769 lev_wgt=10,2,1; /g19/lev
# lev = 241.667 lev_wgt=9,2,1; /g8/lev
@@ -4660,8 +4677,8 @@ if (0){
#NEW 4.3.7
#ncwa #51
-# ncwa -h -O -a time -b -v time in_grp.nc out.nc
-# ncks out.nc | grep 'time dimension 0'
+# ncwa -h -O -a time -b -v time in_grp.nc ~/foo.nc
+# ncks ~/foo.nc | grep 'time dimension 0'
$tst_cmd[0]="ncwa $omp_flg -h -O $fl_fmt $nco_D_flg -a time -b -v time $in_pth_arg in_grp.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -H -v /g2/time %tmp_fl_00% | grep '=5.5'";
@@ -4673,7 +4690,7 @@ if (0){
#NEW 4.4.0
#ncwa #52 Use -w /g8/lev_wgt
-# ncwa -h -O -v lev -a lev -w /g8/lev_wgt in_grp_3.nc out.nc
+# ncwa -h -O -v lev -a lev -w /g8/lev_wgt in_grp_3.nc ~/foo.nc
# lev = 230.769 lev_wgt=10,2,1; /g19/lev
# lev = 241.667 lev_wgt=9,2,1; /g8/lev
@@ -4687,7 +4704,7 @@ if (0){
#NEW 4.4.0
#ncwa #53 Use -w /g8/lev_wgt
-# ncwa -h -O -v lev -a lev -w /g19/lev_wgt in_grp_3.nc out.nc
+# ncwa -h -O -v lev -a lev -w /g19/lev_wgt in_grp_3.nc ~/foo.nc
# lev = 230.769 lev_wgt=10,2,1; /g19/lev
# lev = 241.667 lev_wgt=9,2,1; /g8/lev
@@ -4702,7 +4719,7 @@ if (0){
#NEW 4.4.0
#ncwa #54
#Use -a /g8/lev, -w /g8/lev_wgt
-# ncwa -h -O -v lev -a /g8/lev -w /g8/lev_wgt in_grp_3.nc out.nc
+# ncwa -h -O -v lev -a /g8/lev -w /g8/lev_wgt in_grp_3.nc ~/foo.nc
# lev = 230.769 lev_wgt=10,2,1; /g19/lev
# lev = 241.667 lev_wgt=9,2,1; /g8/lev
@@ -4716,7 +4733,7 @@ if (0){
#NEW 4.4.0
#ncwa #55
-#ncwa -O -4 -a time --cnk_dmn lon,4 -v byt_3D_rec in.nc out.nc
+#ncwa -O -4 -a time --cnk_dmn lon,4 -v byt_3D_rec ~/nco/data/in.nc ~/foo.nc
$dsc_sng="Chunking -a time --cnk_dmn lon,4 -v byt_3D_rec";
$tst_cmd[0]="ncwa $omp_flg -O -4 $nco_D_flg -a time --cnk_dmn lon,4 -v byt_3D_rec $in_pth_arg in.nc %tmp_fl_00%";
@@ -4728,7 +4745,7 @@ if (0){
#NEW 4.4.0
#ncwa #56
-#ncwa -O -4 -a /time --cnk_dmn /time,1 -v time in.nc out.nc
+#ncwa -O -4 -a /time --cnk_dmn /time,1 -v time in.nc ~/foo.nc
$dsc_sng="Chunking -a /time --cnk_dmn /time,1 -v time";
$tst_cmd[0]="ncwa $omp_flg -O -4 $nco_D_flg -a /time --cnk_dmn /time,1 -v time $in_pth_arg in.nc %tmp_fl_00%";
@@ -4740,8 +4757,8 @@ if (0){
#NEW 4.4.0
#ncwa #57
-#ncwa -O -C -4 -D 12 --rdd -a lon,lat -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 in.nc out.nc
-#ncks --hdn --cdl -v four_dmn_rec_var out.nc
+#ncwa -O -C -4 -D 12 --rdd -a lon,lat -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 ~/nco/data/in.nc ~/foo.nc
+#ncks --hdn --cdl -v four_dmn_rec_var ~/foo.nc
$dsc_sng="Chunking with --rdd -a lon,lat -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 ";
$tst_cmd[0]="ncwa $omp_flg -O -C -4 $nco_D_flg --rdd -a lon,lat -v four_dmn_rec_var --cnk_dmn lat,2 --cnk_dmn lon,4 $in_pth_arg in.nc %tmp_fl_00%";
@@ -4753,8 +4770,8 @@ if (0){
#NEW 4.4.2
#ncwa #58
-#ncwa -O -y avg -a time301 -v time301 -C in_grp_3.nc out.nc
-#ncks -m out.nc
+#ncwa -O -y avg -a time301 -v time301 -C in_grp_3.nc ~/foo.nc
+#ncks -m ~/foo.nc
$dsc_sng="Groups (Cell methods) (Create, average) -y avg -a time -v time";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg -O -y avg -a time301 -v time301 -C $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -4766,8 +4783,8 @@ if (0){
#NEW 4.4.2
#ncwa #59
-#ncwa -O -y max -a time301 -v time301 -C in_grp_3.nc out.nc
-#ncks -m out.nc
+#ncwa -O -y max -a time301 -v time301 -C in_grp_3.nc ~/foo.nc
+#ncks -m ~/foo.nc
$dsc_sng="Groups (Cell methods) (Create, maximum) -y max -a time -v time";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg -O -y max -a time301 -v time301 -C $in_pth_arg in_grp_3.nc %tmp_fl_00%";
@@ -4781,8 +4798,8 @@ if (0){
#NEW 4.4.2
#ncwa #60 (part 1)
-#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc out.nc
-#ncks -m -C -v three_dmn_rec_var out.nc
+#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc ~/foo.nc
+#ncks -m -C -v three_dmn_rec_var ~/foo.nc
$dsc_sng="Cell methods (Create, average) -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon $in_pth_arg in.nc %tmp_fl_00%";
@@ -4794,8 +4811,8 @@ if (0){
#NEW 4.4.2
#ncwa #61 (part 2)
-#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc out.nc
-#ncks -m -C -v one_dmn_rec_var out.nc
+#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc ~/foo.nc
+#ncks -m -C -v one_dmn_rec_var ~/foo.nc
$dsc_sng="Cell methods (Create, average) -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon $in_pth_arg in.nc %tmp_fl_00%";
@@ -4807,8 +4824,8 @@ if (0){
#NEW 4.4.2
#ncwa #62 max
-#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc out.nc
-#ncks -m -C -v one_dmn_rec_var out.nc
+#ncwa --op_typ=avg -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon in.nc ~/foo.nc
+#ncks -m -C -v one_dmn_rec_var ~/foo.nc
$dsc_sng="Cell methods (Create, maximum) -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg --op_typ=max -O -v one,one_dmn_rec_var,three_dmn_rec_var -a time,lon $in_pth_arg in.nc %tmp_fl_00%";
@@ -4823,8 +4840,8 @@ if (0){
#NEW 4.4.3
#ncwa #63
-#ncwa -g cesm,ecmwf -v time -a time -O cmip5.nc out.nc
-#ncks -m out.nc
+#ncwa -g cesm,ecmwf -v time -a time -O cmip5.nc ~/foo.nc
+#ncks -m ~/foo.nc
$dsc_sng="Groups (Cell methods, repeated dimension names) -g cesm,ecmwf -v time -a time";
$tst_cmd[0]="ncwa $omp_flg $nco_D_flg -O -g cesm,ecmwf -v time -a time $in_pth_arg cmip5.nc %tmp_fl_00%";
$tst_cmd[1]="ncks -m -g ecmwf -v time %tmp_fl_00%";
@@ -4861,7 +4878,7 @@ if (0){
#################### Attributes
#ncrename #1
-#ncrename -O -a .nothing,new_nothing in_grp.nc out.nc
+#ncrename -O -a .nothing,new_nothing in_grp.nc ~/foo.nc
#optional relative rename nothing to new_nothing (print warning)
$dsc_sng="Attributes: Optional relative rename '.nothing' to 'new_nothing'";
@@ -4872,7 +4889,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #2
-#ncrename -O -a history,new_history in_grp.nc out.nc
+#ncrename -O -a history,new_history in_grp.nc ~/foo.nc
#relative rename history to new_history
$dsc_sng="Attributes: Relative rename 'history' to 'new_history'";
@@ -4884,8 +4901,8 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #3
-#ncrename -D 1 -O -a /g1 at history,new_history in_grp.nc out.nc
-#ncks -g g1 out.nc | grep 'History group attribute'
+#ncrename -D 1 -O -a /g1 at history,new_history in_grp.nc ~/foo.nc
+#ncks -g g1 ~/foo.nc | grep 'History group attribute'
# absolute rename /g1/history group/global att to /g1/new_history
# NB: use escape in '/g1\@history,new_history'
@@ -4899,7 +4916,7 @@ if (0){
#ncrename #4
-#ncrename -O -a global at history,new_history in_grp.nc out.nc
+#ncrename -O -a global at history,new_history in_grp.nc ~/foo.nc
# relative rename history group/global att to new_history
$dsc_sng="Attributes: Relative rename 'global\@history' to 'new_history'";
@@ -4911,7 +4928,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #5
-#ncrename -O -a /g1/lon at units,new_units in_grp.nc out.nc
+#ncrename -O -a /g1/lon at units,new_units in_grp.nc ~/foo.nc
# absolute rename /g1/lon at units att to /g1/lon at new_units
$dsc_sng="Attributes: Absolute rename '/g1/lon\@units' to 'new_units'";
@@ -4923,7 +4940,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #6
-#ncrename -D 1 -O -a /g1/lon at units,/g1/lon at new_units in_grp.nc out.nc
+#ncrename -D 1 -O -a /g1/lon at units,/g1/lon at new_units in_grp.nc ~/foo.nc
#absolute rename /g1/lon at units att to /g1/lon at new_units
$dsc_sng="Attributes: Absolute rename '/g1/lon\@units' to '/g1/lon\@new_units'";
@@ -4935,7 +4952,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #7
-#ncrename -O -a /g1/lon at .units,new_units in_grp.nc out.nc
+#ncrename -O -a /g1/lon at .units,new_units in_grp.nc ~/foo.nc
# optional absolute rename /g1/lon at .units att to new_units
$dsc_sng="Attributes: Optional absolute rename '/g1/lon\@.units' to '/g1/lon\@new_units'";
@@ -4948,10 +4965,10 @@ if (0){
#################### Dimensions
- if($RUN_NETCDF4_TESTS_VERSION_43 == 1){
+ if($RUN_NETCDF4_TESTS_VERSION_GE_431 == 1){
#ncrename #8
-#ncrename -O -d lat,new_lat in_grp.nc out.nc
+#ncrename -O -d lat,new_lat in_grp.nc ~/foo.nc
# relative rename lat to new_lat
$dsc_sng="Dimensions: Relative rename 'lat' to 'new_lat' (expect failure with netCDF < 4.3.1)";
@@ -4963,7 +4980,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #9
-#ncrename -O -d /lat,new_lat in_grp.nc out.nc
+#ncrename -O -d /lat,new_lat in_grp.nc ~/foo.nc
# Absolute rename /lat to new_lat
$dsc_sng="Dimensions: Absolute rename '/lat' to 'new_lat' (expect failure with netCDF < 4.3.1)";
@@ -4975,7 +4992,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #10
-#ncrename -O -d .lat,new_lat in_grp.nc out.nc
+#ncrename -O -d .lat,new_lat in_grp.nc ~/foo.nc
# optional relative rename lat to new_lat
$dsc_sng="Dimensions: Optional existing relative rename '.lat' to 'new_lat' (expect failure with netCDF < 4.3.1)";
@@ -4987,7 +5004,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #11
-#ncrename -O -d /lat,new_lat in_grp.nc out.nc
+#ncrename -O -d /lat,new_lat in_grp.nc ~/foo.nc
# Absolute rename /lat to new_lat
$dsc_sng="Dimensions: Optional existing absolute rename './lat' to 'new_lat' (expect failure with netCDF < 4.3.1)";
@@ -4998,10 +5015,10 @@ if (0){
NCO_bm::tst_run(\@tst_cmd);
@tst_cmd=(); # really reset array.
- } # RUN_NETCDF4_TESTS_VERSION_43
+ } # RUN_NETCDF4_TESTS_VERSION_GE_431
#ncrename #12
-#ncrename -O -d ./lat_non_existing,new_lat in_grp.nc out.nc
+#ncrename -O -d ./lat_non_existing,new_lat in_grp.nc ~/foo.nc
# Absolute non existing absolute rename
$dsc_sng="Dimensions: Optional non-existing absolute rename './lat_non_existing,new_lat' to 'new_lat'";
@@ -5014,7 +5031,7 @@ if (0){
#################### Variables
#ncrename #13
-#ncrename -D 1 -O -v /g1/v1,new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v /g1/v1,new_v1 in_grp.nc ~/foo.nc
#Absolute rename /g1/v1 to /g1/new_v1
$dsc_sng="Variables: Absolute rename '/g1/v1' to '/g1/new_v1'";
@@ -5027,7 +5044,7 @@ if (0){
#ncrename #14
-#ncrename -D 1 -O -v v1,new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v v1,new_v1 in_grp.nc ~/foo.nc
#Relative rename v1 to new_v1
$dsc_sng="Variables: Relative rename 'v1' to 'new_v1'";
@@ -5039,7 +5056,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #15
-#ncrename -D 1 -O -v ./g1/v1,new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v ./g1/v1,new_v1 in_grp.nc ~/foo.nc
#Absolute rename /g1/v1 to /g1/new_v1
$dsc_sng="Variables: Optional absolute rename '/g1/v1' to '/g1/new_v1'";
@@ -5051,7 +5068,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #16
-#ncrename -D 1 -O -v .v1,new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v .v1,new_v1 in_grp.nc ~/foo.nc
#Optional Relative rename v1 to new_v1
$dsc_sng="Variables: Optional relative rename 'v1' to 'new_v1'";
@@ -5063,7 +5080,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #17
-#ncrename -D 1 -O -v ./g1/v1_not,new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v ./g1/v1_not,new_v1 in_grp.nc ~/foo.nc
#Optional non-existing absolute rename '/g1/v1_not'
$dsc_sng="Variables: Optional non-existing absolute rename './g1/v1_not' to '/g1/new_v1'";
@@ -5076,10 +5093,10 @@ if (0){
#################### Groups
#ncrename #18
-#ncrename -O -g g1,new_g1 in_grp.nc out.nc
+#ncrename -O -g g1,new_g1 in_grp.nc ~/foo.nc
# relative rename g1 to new_g1
- if($RUN_NETCDF4_TESTS_VERSION_43 == 1){
+ if($RUN_NETCDF4_TESTS_VERSION_GE_431 == 1){
$dsc_sng="Groups: Relative rename 'g1' to 'new_g1' (expect failure with netCDF < 4.3.1)";
$tst_cmd[0]="ncrename -O $fl_fmt $nco_D_flg -g g1,new_g1 $in_pth_arg in_grp.nc %tmp_fl_00%";
@@ -5090,7 +5107,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #19
-#ncrename -O -g g1g1,new_g1g1 in_grp.nc out.nc
+#ncrename -O -g g1g1,new_g1g1 in_grp.nc ~/foo.nc
#relative rename g1g1 to new_g1g1
$dsc_sng="Groups: Relative rename 'g1g1' to 'new_g1g1' (expect failure with netCDF < 4.3.1)";
@@ -5102,7 +5119,7 @@ if (0){
@tst_cmd=(); # really reset array.
#ncrename #20
-#ncrename -D 1 -O -g /g1/g1g1,new_g1g1 in_grp.nc out.nc
+#ncrename -D 1 -O -g /g1/g1g1,new_g1g1 in_grp.nc ~/foo.nc
#Absolute rename -g /g1/g1g1,new_g1g1
$dsc_sng="Groups: Absolute rename '/g1/g1g1' to '/g1/new_g1g1' (expect failure with netCDF < 4.3.1)";
@@ -5113,10 +5130,10 @@ if (0){
NCO_bm::tst_run(\@tst_cmd);
@tst_cmd=(); # really reset array.
- } # RUN_NETCDF4_TESTS_VERSION_43
+ } # RUN_NETCDF4_TESTS_VERSION_GE_431
#ncrename #21
-#ncrename -O -g .gfoo,new_g1 in_grp.nc out.nc
+#ncrename -O -g .gfoo,new_g1 in_grp.nc ~/foo.nc
# optional relative rename gfoo to new_g1 (print warning)
$dsc_sng="Groups: Optional relative rename '.gfoo' to 'new_g1'";
@@ -5129,7 +5146,7 @@ if (0){
#################### Variables
#ncrename #22 (same as #13)
-#ncrename -D 1 -O -v /g1/v1,/g1/new_v1 in_grp.nc out.nc
+#ncrename -D 1 -O -v /g1/v1,/g1/new_v1 in_grp.nc ~/foo.nc
#Absolute rename /g1/v1 to /g1/new_v1
$dsc_sng="Variables: Absolute rename '/g1/v1' to '/g1/new_v1' (input absolute name)";
diff --git a/bm/nco_bm.pl b/bm/nco_bm.pl
index c3bf62a..7b85794 100755
--- a/bm/nco_bm.pl
+++ b/bm/nco_bm.pl
@@ -2,7 +2,7 @@
# Shebang line above may have to be set explicitly to /usr/local/bin/perl
# on ESMF when running in queue. Otherwise it may pick up older perl
-# $Header: /cvsroot/nco/nco/bm/nco_bm.pl,v 1.154 2013/10/22 03:12:10 zender Exp $
+# $Header: /cvsroot/nco/nco/bm/nco_bm.pl,v 1.155 2014/07/07 06:04:22 zender Exp $
# Usage: bm_usg(), below, has more information
# ~/nco/bm/nco_bm.pl # Tests all operators
@@ -41,7 +41,7 @@ use vars qw(
$foo1_fl $foo2_fl $foo_avg_fl $foo_fl $foo_T42_fl $foo_tst $foo_x_fl
$foo_xy_fl $foo_xymyx_fl $foo_y_fl $foo_yx_fl $gnu_cut $hiresfound
@ifls $itmp $localhostname $md5 $md5found %MD5_tbl $mpi_fk $mpi_prc
- $mpi_upx
+ $mpi_upx
$pfx_mpi $MY_BIN_DIR $nco_D_flg %NCO_RC $nco_vrs_sng $ncwa_scl_tst $notbodi
$nsr_xpc $fl_nbr $nvr_my_bin_dir $omp_flg $opr_fmt $opr_lng_max
@opr_lst @opr_lst_all @opr_lst_mpi $opr_nm $opr_rgr_mpi $opr_sng_mpi
diff --git a/config.h.in b/config.h.in
index f196657..3e069af 100644
--- a/config.h.in
+++ b/config.h.in
@@ -6,12 +6,9 @@
/* Compatibility pvmgetarch token for UNICOS on DEC Alpha */
#undef CRAY
-/* Compile operators with DAP support */
+/* Compile operators with DAP support from libnetcdf */
#undef ENABLE_DAP
-/* DAP support is from libnetcdf */
-#undef ENABLE_DAP_NETCDF
-
/* Custom debugging: Pedantic, bounds checking (slowest execution) */
#undef ENABLE_DEBUG_CUSTOM
diff --git a/configure b/configure
index 0b2fcee..98b9598 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.4.4.
+# Generated by GNU Autoconf 2.69 for NCO netCDF Operators 4.4.5.
#
# Report bugs to <nco-bugs at lists.sourceforge.net>.
#
@@ -592,8 +592,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='NCO netCDF Operators'
PACKAGE_TARNAME='nco'
-PACKAGE_VERSION='4.4.4'
-PACKAGE_STRING='NCO netCDF Operators 4.4.4'
+PACKAGE_VERSION='4.4.5'
+PACKAGE_STRING='NCO netCDF Operators 4.4.5'
PACKAGE_BUGREPORT='nco-bugs at lists.sourceforge.net'
PACKAGE_URL=''
@@ -1385,7 +1385,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
-\`configure' configures NCO netCDF Operators 4.4.4 to adapt to many kinds of systems.
+\`configure' configures NCO netCDF Operators 4.4.5 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
@@ -1456,7 +1456,7 @@ fi
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of NCO netCDF Operators 4.4.4:";;
+ short | recursive ) echo "Configuration of NCO netCDF Operators 4.4.5:";;
esac
cat <<\_ACEOF
@@ -1485,7 +1485,7 @@ Optional Features:
enable-netcdf4) [[default=yes]]
--disable-openmp do not use OpenMP
--enable-openmp Build NCO with OpenMP [[default=yes]]
- --enable-dap-netcdf Build DAP-enabled NCO with netCDF-provided DAP
+ --enable-dap Build DAP-enabled NCO with netCDF-provided DAP
[[default=yes]]
--enable-ncoxx Build libnco++ and ncap2 (same as enable-ncap2)
[[default=yes]]
@@ -1617,7 +1617,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-NCO netCDF Operators configure 4.4.4
+NCO netCDF Operators configure 4.4.5
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2483,7 +2483,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
-It was created by NCO netCDF Operators $as_me 4.4.4, which was
+It was created by NCO netCDF Operators $as_me 4.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
@@ -3732,7 +3732,7 @@ fi
# Define the identity of the package.
PACKAGE='nco'
- VERSION='4.4.4'
+ VERSION='4.4.5'
cat >>confdefs.h <<_ACEOF
@@ -17738,7 +17738,7 @@ fi
fi
-# OpenMP
+# Begin OpenMP
OPENMP_CFLAGS=
# Check whether --enable-openmp was given.
@@ -17813,7 +17813,6 @@ else
enable_openmp=yes
fi
-
# Enable OpenMP unless told not to
if ((test "${enable_openmp}" != 'no') && (test "${enable_netcdf4}" = 'xyes')); then
CFLAGS="${CFLAGS} ${OPENMP_CFLAGS}"
@@ -17826,15 +17825,13 @@ echo "Beginning generic tests for DAP support"
nco_LIBS_no_DAP="${LIBS}"
# Check whether --enable-dap-netcdf was given.
if test "${enable_dap_netcdf+set}" = set; then :
- enableval=$enable_dap_netcdf; enable_dap_netcdf=${enableval}
+ enableval=$enable_dap_netcdf; enable_dap=${enableval}
else
- enable_dap_netcdf=yes
+ enable_dap=yes
fi
-
-# Begin DAP-netCDF
-# Check for DAP-netCDF libraries unless told not to
-if test "${enable_dap_netcdf}" != 'no'; then
+# Check for DAP in netCDF library unless told not to
+if test "${enable_dap}" != 'no'; then
echo "Testing for DAP-netCDF support (is DAP in libnetcdf.a?)..."
{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for nc__opendap in -lnetcdf" >&5
$as_echo_n "checking for nc__opendap in -lnetcdf... " >&6; }
@@ -17880,33 +17877,25 @@ _ACEOF
LIBS="-lnetcdf $LIBS"
else
- enable_dap_netcdf=no
+ enable_dap=no
fi
- if test "${enable_dap_netcdf}" = 'no'; then
+ if test "${enable_dap}" = 'no'; then
{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: DAP-netCDF support through libnetcdf.a disabled (missing DAP functions)" >&5
$as_echo "$as_me: WARNING: DAP-netCDF support through libnetcdf.a disabled (missing DAP functions)" >&2;}
fi
-fi
-# End DAP-netCDF
-
-# Begin DAP (all flavors)
-enable_dap='no'
-if (test "x${enable_dap_netcdf}" = 'xyes'); then
-
-$as_echo "#define ENABLE_DAP_NETCDF 1" >>confdefs.h
-
- enable_dap='yes'
+ if (test "x${enable_dap}" = 'xyes'); then
$as_echo "#define ENABLE_DAP 1" >>confdefs.h
- { $as_echo "$as_me:${as_lineno-$LINENO}: DAP support enabled" >&5
+ { $as_echo "$as_me:${as_lineno-$LINENO}: DAP support enabled" >&5
$as_echo "$as_me: DAP support enabled" >&6;}
- LIBS="${LIBS} -lcurl"
-# This would activate conditional GSL tests, if there were any
+ LIBS="${LIBS} -lcurl"
+# This would activate conditional DAP tests, if there were any
# AM_CONDITIONAL(TEST_DAP,[test "${enable_dap}" = 'yes'])
+ fi
fi
-# End DAP (all flavors)
+# End DAP
##################################################
# Check libraries, add to link path if found
@@ -20986,7 +20975,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
-This file was extended by NCO netCDF Operators $as_me 4.4.4, which was
+This file was extended by NCO netCDF Operators $as_me 4.4.5, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
@@ -21052,7 +21041,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
-NCO netCDF Operators config.status 4.4.4
+NCO netCDF Operators config.status 4.4.5
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
@@ -23102,7 +23091,6 @@ echo "CPPFLAGS............. ${CPPFLAGS}"
echo "CXX.................. ${CXX}"
echo "CXXFLAGS............. ${CXXFLAGS}"
echo "OPENMP_CFLAGS........ ${OPENMP_CFLAGS}"
-echo "ENABLE_DAP_NETCDF.... ${enable_dap_netcdf}"
echo "ENABLE_DAP........... ${enable_dap}"
echo "ENABLE_GSL........... ${enable_gsl}"
echo "HAVE_NETCDF4_H....... ${header_defines_nc_chunked}"
diff --git a/configure.ac b/configure.ac
index 6c215f2..a099749 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/configure.ac,v 1.45 2014/05/01 19:05:38 zender Exp $ -*-Shell-script-*-
+# $Header: /cvsroot/nco/nco/configure.ac,v 1.47 2014/07/07 06:04:22 zender Exp $ -*-Shell-script-*-
# Purpose: Template autoconf uses to generate NCO configure script
# Newer convention names this file configure.ac, rather than configure.in
@@ -51,7 +51,7 @@
# Process configure input with autoconf to produce configure script
# (package name,version,bug-report-address,tarball name)
-AC_INIT([NCO netCDF Operators],[4.4.4],[nco-bugs at lists.sourceforge.net],[nco])
+AC_INIT([NCO netCDF Operators],[4.4.5],[nco-bugs at lists.sourceforge.net],[nco])
# Print GNU copyright in configure script
AC_COPYRIGHT
@@ -306,11 +306,10 @@ if (test "x${enable_netcdf4}" = 'xyes' && test "x${header_defines_nc_chunked}" =
])
fi
-# OpenMP
+# Begin OpenMP
AC_OPENMP
AC_SUBST(OPENMP_CFLAGS)
AC_ARG_ENABLE(openmp,AS_HELP_STRING([--enable-openmp],[Build NCO with OpenMP [[default=yes]]]),enable_openmp=${enableval},enable_openmp=yes)
-
# Enable OpenMP unless told not to
if ((test "${enable_openmp}" != 'no') && (test "${enable_netcdf4}" = 'xyes')); then
CFLAGS="${CFLAGS} ${OPENMP_CFLAGS}"
@@ -321,31 +320,23 @@ fi
echo "Beginning generic tests for DAP support"
# Store pre-DAP LIBS value to restore from later
nco_LIBS_no_DAP="${LIBS}"
-AC_ARG_ENABLE(dap-netcdf,AS_HELP_STRING([--enable-dap-netcdf],[Build DAP-enabled NCO with netCDF-provided DAP [[default=yes]]]),enable_dap_netcdf=${enableval},enable_dap_netcdf=yes)
-
-# Begin DAP-netCDF
-# Check for DAP-netCDF libraries unless told not to
-if test "${enable_dap_netcdf}" != 'no'; then
+AC_ARG_ENABLE(dap-netcdf,AS_HELP_STRING([--enable-dap],[Build DAP-enabled NCO with netCDF-provided DAP [[default=yes]]]),enable_dap=${enableval},enable_dap=yes)
+# Check for DAP in netCDF library unless told not to
+if test "${enable_dap}" != 'no'; then
echo "Testing for DAP-netCDF support (is DAP in libnetcdf.a?)..."
- AC_CHECK_LIB([netcdf],[nc__opendap],,enable_dap_netcdf=no,[-lcurl])
- if test "${enable_dap_netcdf}" = 'no'; then
+ AC_CHECK_LIB([netcdf],[nc__opendap],,enable_dap=no,[-lcurl])
+ if test "${enable_dap}" = 'no'; then
AC_MSG_WARN([DAP-netCDF support through libnetcdf.a disabled (missing DAP functions)])
fi
-fi
-# End DAP-netCDF
-
-# Begin DAP (all flavors)
-enable_dap='no'
-if (test "x${enable_dap_netcdf}" = 'xyes'); then
- AC_DEFINE([ENABLE_DAP_NETCDF],[1],[DAP support is from libnetcdf])
- enable_dap='yes'
- AC_DEFINE([ENABLE_DAP],[1],[Compile operators with DAP support])
- AC_MSG_NOTICE([DAP support enabled])
- LIBS="${LIBS} -lcurl"
-# This would activate conditional GSL tests, if there were any
+ if (test "x${enable_dap}" = 'xyes'); then
+ AC_DEFINE([ENABLE_DAP],[1],[Compile operators with DAP support from libnetcdf])
+ AC_MSG_NOTICE([DAP support enabled])
+ LIBS="${LIBS} -lcurl"
+# This would activate conditional DAP tests, if there were any
# AM_CONDITIONAL(TEST_DAP,[test "${enable_dap}" = 'yes'])
+ fi
fi
-# End DAP (all flavors)
+# End DAP
##################################################
# Check libraries, add to link path if found
@@ -1161,7 +1152,6 @@ echo "CPPFLAGS............. ${CPPFLAGS}"
echo "CXX.................. ${CXX}"
echo "CXXFLAGS............. ${CXXFLAGS}"
echo "OPENMP_CFLAGS........ ${OPENMP_CFLAGS}"
-echo "ENABLE_DAP_NETCDF.... ${enable_dap_netcdf}"
echo "ENABLE_DAP........... ${enable_dap}"
echo "ENABLE_GSL........... ${enable_gsl}"
echo "HAVE_NETCDF4_H....... ${header_defines_nc_chunked}"
diff --git a/data/Makefile.am b/data/Makefile.am
index 28e9cf2..453db96 100644
--- a/data/Makefile.am
+++ b/data/Makefile.am
@@ -1,8 +1,8 @@
-# $Header: /cvsroot/nco/nco/data/Makefile.am,v 1.36 2014/04/01 21:44:24 pvicente Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/data/Makefile.am,v 1.38 2014/08/21 18:22:44 zender Exp $ -*-makefile-*-
test_data = big.nc in.nc in_rec_zero.nc
-test_data_netCDF4 = in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc cmip5.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc hdn.nc
+test_data_netCDF4 = in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc cmip5.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc hdn.nc mrd.nc
# netCDF build rules
%.nc : %.cdl
@@ -26,22 +26,18 @@ in_2.nc : in_2.cdl
in_grp_3.nc : in_grp_3.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
-
in_grp_4.nc : in_grp_4.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
in_grp_5.nc : in_grp_5.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
-
in_grp_6.nc : in_grp_6.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
-
in_grp_7.nc : in_grp_7.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
-
cmip5.nc : cmip5.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
@@ -51,6 +47,9 @@ dsm.nc : dsm.cdl
hdn.nc : hdn.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
+mrd.nc : mrd.cdl
+ - at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
+
obs.nc : obs.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
@@ -63,10 +62,9 @@ mdl_2.nc : mdl_2.cdl
mdl_3.nc : mdl_3.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
-
all: ${test_data} ${test_data_netCDF4}
-EXTRA_DIST = big.cdl dsm.cdl hdn.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl in_grp_3.cdl in_grp_4.cdl in_grp_5.cdl in_grp_6.cdl in_grp_7.cdl in_1.cdl in_2.cdl cmip5.cdl obs.cdl mdl_1.cdl buggy.cdl in_rec_zero.cdl ncap.in ncap.in2 ncap2.in tst.nco
+EXTRA_DIST = big.cdl dsm.cdl hdn.cdl mrd.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl in_grp_3.cdl in_grp_4.cdl in_grp_5.cdl in_grp_6.cdl in_grp_7.cdl in_1.cdl in_2.cdl cmip5.cdl obs.cdl mdl_1.cdl buggy.cdl in_rec_zero.cdl ncap.in ncap.in2 ncap2.in tst.nco
# Automake manual section 14:
# If configure built it, 'distclean' should delete it
@@ -74,7 +72,7 @@ EXTRA_DIST = big.cdl dsm.cdl hdn.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl
DISTCLEANFILES = foo*
# Build procedure produces these files:
-CLEANFILES = 85.nc 86.nc 87.nc 88.nc 89.nc big.nc foo.nc h0001.nc h0002.nc h0003.nc in.nc in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc in_grp_7.nc cmip5.nc hdn.nc dsm.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc buggy.nc in_rec_zero.nc ../src/nco_c++/in.nc
+CLEANFILES = 85.nc 86.nc 87.nc 88.nc 89.nc big.nc foo.nc h0001.nc h0002.nc h0003.nc in.nc in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc in_grp_7.nc cmip5.nc hdn.nc mrd.nc dsm.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc buggy.nc in_rec_zero.nc ../src/nco_c++/in.nc
MAINTAINERCLEANFILES = Makefile.in
diff --git a/data/Makefile.in b/data/Makefile.in
index 567dce2..3e9d0e5 100644
--- a/data/Makefile.in
+++ b/data/Makefile.in
@@ -14,7 +14,7 @@
@SET_MAKE@
-# $Header: /cvsroot/nco/nco/data/Makefile.in,v 1.115 2014/04/02 05:40:23 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/data/Makefile.in,v 1.116 2014/08/15 19:13:35 zender Exp $ -*-makefile-*-
VPATH = @srcdir@
am__is_gnu_make = test -n '$(MAKEFILE_LIST)' && test -n '$(MAKELEVEL)'
am__make_running_with_option = \
@@ -260,8 +260,8 @@ top_build_prefix = @top_build_prefix@
top_builddir = @top_builddir@
top_srcdir = @top_srcdir@
test_data = big.nc in.nc in_rec_zero.nc
-test_data_netCDF4 = in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc cmip5.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc hdn.nc
-EXTRA_DIST = big.cdl dsm.cdl hdn.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl in_grp_3.cdl in_grp_4.cdl in_grp_5.cdl in_grp_6.cdl in_grp_7.cdl in_1.cdl in_2.cdl cmip5.cdl obs.cdl mdl_1.cdl buggy.cdl in_rec_zero.cdl ncap.in ncap.in2 ncap2.in tst.nco
+test_data_netCDF4 = in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc cmip5.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc hdn.nc mrd.nc
+EXTRA_DIST = big.cdl dsm.cdl hdn.cdl mrd.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl in_grp_3.cdl in_grp_4.cdl in_grp_5.cdl in_grp_6.cdl in_grp_7.cdl in_1.cdl in_2.cdl cmip5.cdl obs.cdl mdl_1.cdl buggy.cdl in_rec_zero.cdl ncap.in ncap.in2 ncap2.in tst.nco
# Automake manual section 14:
# If configure built it, 'distclean' should delete it
@@ -269,7 +269,7 @@ EXTRA_DIST = big.cdl dsm.cdl hdn.cdl in.cdl in_grp.cdl in_grp_1.cdl in_grp_2.cdl
DISTCLEANFILES = foo*
# Build procedure produces these files:
-CLEANFILES = 85.nc 86.nc 87.nc 88.nc 89.nc big.nc foo.nc h0001.nc h0002.nc h0003.nc in.nc in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc in_grp_7.nc cmip5.nc hdn.nc dsm.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc buggy.nc in_rec_zero.nc ../src/nco_c++/in.nc
+CLEANFILES = 85.nc 86.nc 87.nc 88.nc 89.nc big.nc foo.nc h0001.nc h0002.nc h0003.nc in.nc in_grp.nc in_grp_1.nc in_grp_2.nc in_grp_3.nc in_grp_4.nc in_grp_5.nc in_grp_6.nc in_grp_7.nc cmip5.nc hdn.nc mrd.nc dsm.nc obs.nc mdl_1.nc mdl_2.nc mdl_3.nc buggy.nc in_rec_zero.nc ../src/nco_c++/in.nc
MAINTAINERCLEANFILES = Makefile.in
all: all-am
@@ -508,6 +508,9 @@ dsm.nc : dsm.cdl
hdn.nc : hdn.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
+mrd.nc : mrd.cdl
+ - at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
+
obs.nc : obs.cdl
- at PATH_TO_NCGEN@ -k netCDF-4 -o $@ $<
diff --git a/data/dsm.cdl b/data/dsm.cdl
index ba97caf..8f706b0 100644
--- a/data/dsm.cdl
+++ b/data/dsm.cdl
@@ -3,7 +3,7 @@
// Contains nested ensembles, metadata-only leaf groups, and "in-between data"
// Usage:
// ncgen -k netCDF-4 -b -o ~/nco/data/dsm.nc ~/nco/data/dsm.cdl
-// ncdismember ~/nco/data/dsm.nc /data/zender/nco/tmp cf 1.3 > ~/foo.txt 2>&1
+// ncdismember ~/nco/data/dsm.nc /data/zender/nco/tmp cf 1.5 > ~/foo.txt 2>&1
netcdf dsm {
@@ -19,6 +19,7 @@ netcdf dsm {
:metadata = "g2 group contains metadata and one variable but no shared dimensions";
variables:
float one;
+ one:long_name="the loneliest number";
data:
one=1;
} // g2
@@ -29,6 +30,7 @@ netcdf dsm {
lat=2;
variables:
float one_arr(lat);
+ one_arr:long_name="the loneliest array";
data:
one_arr=1,1;
} // g3
@@ -41,6 +43,7 @@ netcdf dsm {
:metadata = "g4g1 group contains one variable that depends on an inherited dimension";
variables:
float one_arr(lat);
+ one_arr:long_name="the loneliest array";
data:
one_arr=1,1;
} // g4g1
@@ -53,16 +56,48 @@ netcdf dsm {
lat=2;
variables:
float one_arr(lat);
+ one_arr:long_name="the loneliest array";
group: g5g1 {
:metadata = "g5g1 group contains one variable that depends on an inherited dimension";
variables:
float one_arr(lat);
+ one_arr:long_name="the loneliest array";
data:
one_arr=1,1;
} // g5g1
} // g5
+ group: g6 {
+ :metadata = "g6 group contains variables to test CF checkers";
+ dimensions:
+ time_like_2=2;
+ time_like_3=2;
+ variables:
+ int period;
+ period:units="second";
+ period:long_name="length of time between successive orbits";
+ byte time_like_1;
+ time_like_1:units="ns";
+ time_like_1:long_name="time as non-coordinate scalar";
+ byte time_like_2(time_like_2);
+ time_like_2:units="ns";
+ time_like_2:long_name="time is coordinate array";
+ byte time_like_3(time_like_3);
+ time_like_3:calendar="none";
+ time_like_3:units="ns";
+ time_like_3:long_name="time is coordinate array";
+ byte time_like_4(time_like_3);
+ time_like_4:units="ns";
+ time_like_4:long_name="time is non-coordinate array";
+ data:
+ period=1;
+ time_like_1=1b;
+ time_like_2=1b,2b;
+ time_like_3=1b,2b;
+ time_like_4=1b,2b;
+ } // g6
+
group: cesm {
group: cesm_01 {
@@ -76,7 +111,9 @@ netcdf dsm {
time=4;
variables:
float tas1(time);
- float tas2(time);
+ tas1:long_name="temperature";
+ float tas2(time);
+ tas2:long_name="temperature";
data:
tas1=272.1,272.1,272.1,272.1;
tas2=272.1,272.1,272.1,272.1;
@@ -94,10 +131,12 @@ netcdf dsm {
time=4;
variables:
float tas1(time);
- float tas2(time);
+ tas1:long_name="temperature";
+ float tas2(time);
+ tas2:long_name="temperature";
data:
tas1=272.2,272.2,272.2,272.2;
- tas2=272.2,272.2,272.2,272.2;
+ tas2=272.2,272.2,272.2,272.2;
} // cesm_02
@@ -116,7 +155,9 @@ netcdf dsm {
time=4;
variables:
float tas1(time);
- float tas2(time);
+ tas1:long_name="temperature";
+ float tas2(time);
+ tas2:long_name="temperature";
data:
tas1=273.1,273.1,273.1,273.1;
tas2=273.1,273.1,273.1,273.1;
@@ -134,11 +175,12 @@ netcdf dsm {
time=4;
variables:
float tas1(time);
+ tas1:long_name="temperature";
float tas2(time);
+ tas2:long_name="temperature";
data:
tas1=273.2,273.2,273.2,273.2;
tas2=273.2,273.2,273.2,273.2;
-
} // ecmwf_02
} // ecmwf
diff --git a/data/in.cdl b/data/in.cdl
index 1551741..0fd6812 100644
--- a/data/in.cdl
+++ b/data/in.cdl
@@ -60,7 +60,7 @@ variables:
:Conventions = "CF-1.0";
:history = "History global attribute.\nAttributes like this often have embedded newlines to enhance legibility.\nSuch newlines should serve as linebreaks on the screen, hence,\nfriendly CDL converters print a single NC_CHAR attribute as a comma-separated list of strings\nwhere each embedded delimiter marks a linebreak.\nOtherwise it would be harder for humans to read the CDL.";
:julian_day = 200000.04;
- :RCS_Header = "$Header: /cvsroot/nco/nco/data/in.cdl,v 1.187 2014/04/13 02:36:53 zender Exp $";
+ :RCS_Header = "$Header: /cvsroot/nco/nco/data/in.cdl,v 1.189 2014/08/21 20:39:01 zender Exp $";
int date_int(date_dmn);
date_int:long_name = "Date (as array of ints: YYYY,MM,DD,HH,MM)";
@@ -255,6 +255,22 @@ variables:
cnv_CF_crd:coordinates = "lat_gds lon_gds ";
cnv_CF_crd:reason = "Test whether coordinates attribute strings that end with a space break after nco_var_lst_crd_ass_add() call to nco_lst_prs_2d()";
+ float cnv_CF_ncl(time);
+ cnv_CF_ncl:long_name = "test CF ancillary_variables convention";
+ cnv_CF_ncl:standard_name = "specific_humidity";
+ cnv_CF_ncl:ancillary_variables = "cnv_CF_ncl_var_1 cnv_CF_ncl_var_2";
+ cnv_CF_ncl:purpose = "Main variable that has ancillary variables named cnv_CF_ncl_var_1 and cnv_CF_ncl_var_2";
+
+ float cnv_CF_ncl_var_1(time);
+ cnv_CF_ncl_var_1:long_name = "test CF ancillary_variables convention";
+ cnv_CF_ncl_var_1:standard_name = "specific_humidity standard_error";
+ cnv_CF_ncl_var_1:purpose = "Ancillary variable for cnv_CF_ncl. Other ancillary variable is cnv_CF_ncl_var_2.";
+
+ float cnv_CF_ncl_var_2(time);
+ cnv_CF_ncl_var_2:long_name = "test CF ancillary_variables convention";
+ cnv_CF_ncl_var_2:standard_name = "specific_humidity detection_limit";
+ cnv_CF_ncl_var_2:purpose = "Ancillary variable for cnv_CF_ncl. Other ancillary variable is cnv_CF_ncl_var_1.";
+
float PS(time,lat,lon);
PS:long_name = "surface pressure";
PS:units = "pascal";
@@ -985,7 +1001,6 @@ variables:
float txyz(time,lon,lat,lev);
txyz:long_name = "four dimensional record variable stored in txyz (time,lon,lat,lev) order";
-
float four_dmn_rec_var(time,lat,lev,lon);
four_dmn_rec_var:long_name = "four dimensional record variable";
four_dmn_rec_var:units = "watt meter-2";
@@ -1021,6 +1036,13 @@ variables:
var_nm-dash:long_name = "Variable and attribute names include dash characters";
var_nm-dash:att_nm-dash = 1.0e36f;
+ float vld_rng(time);
+ vld_rng:long_name = "Temperature";
+ vld_rng:purpose = "Array containing _FillValue at some locations, out-of-range values at other locations, and valid data in the remainder";
+ vld_rng:_FillValue = -999.0f;
+ vld_rng:valid_min = 180.f;
+ vld_rng:valid_max = 360.f;
+
// float var_nm.dot;
// var_nm.dot:long_name = "Variable and attribute names include dot characters";
// 20070102: Periods in attribute names choke OPeNDAP from FC7 RPM TODO nco911
@@ -1063,6 +1085,9 @@ data:
char_var_nul='\0';
char_var_space=" ";
cnv_CF_crd=273.1,273.2,273.3,273.4,273.5,273.6,273.7,273.8;
+ cnv_CF_ncl=1.,2.,3.,4.,5.,6.,7.,8.,9.,10.;
+ cnv_CF_ncl_var_1=11.,22.,23.,24.,25.,26.,27.,28.,29.,30.;
+ cnv_CF_ncl_var_2=21.,32.,33.,34.,35.,36.,37.,38.,39.,40.;
date_int=1964,3,12,12,9;
dgn=73;
dgn_var=73;
@@ -1559,6 +1584,9 @@ data:
// -99.5,74.5,75.5,76.5,77.5,78.5,79.5,-99.5;
time_udunits = 876012, 876018, 876024;
+
+ vld_rng= 273.,-999.,180.,179.,273.,360.,361.,1.0e36,-1.0e36,273.;
+
wnd_spd= -999,0.5,1.5,0.5,1.5,0.5,1.5,0.5,
0.5,-999,0.5,0.5,0.5,0.5,0.5,0.5,
0.5,1.5,-999,1.5,0.5,1.5,0.5,1.5,
diff --git a/data/mrd.cdl b/data/mrd.cdl
new file mode 100644
index 0000000..9e6b9bb
--- /dev/null
+++ b/data/mrd.cdl
@@ -0,0 +1,30 @@
+// -*-C++-*-
+
+// Purpose: Test Multiple Record Dimensions
+
+// Generate netCDF file with:
+// ncgen -k netCDF-4 -b -o ~/nco/data/mrd.nc ~/nco/data/mrd.cdl
+
+// Reproduce bug 20140815: ncrcat (not ncks) fails on variables with multiple record dimensions reported by rmla 20140619
+// ncrcat -O -d parameter,0,0 -d time,1,1 -d run,0,1 -d step,0,1 -d number,0,1 -d ngr,0,1 ${DATA}/hdf/71355.ecmf.1.nc ~/mrd.nc
+// ncrcat -O -h -d time,0 ~/nco/data/mrd.nc ~/foo.nc
+// ncdump ~/foo.nc
+
+netcdf mrd {
+dimensions:
+ time = UNLIMITED ; // (2 currently)
+ step = UNLIMITED ; // (2 currently)
+variables:
+ int var_mrd(time, step) ;
+ int time(time) ;
+
+data:
+
+ var_mrd =
+ {1,
+ 2},
+ {3,
+ 4} ;
+
+ time = 1, 2 ;
+}
diff --git a/doc/ANNOUNCE b/doc/ANNOUNCE
index 9c70080..7b551a1 100644
--- a/doc/ANNOUNCE
+++ b/doc/ANNOUNCE
@@ -1,121 +1,102 @@
-$Header: /cvsroot/nco/nco/doc/ANNOUNCE,v 1.717 2014/05/29 18:19:54 zender Exp $ -*-text-*-
+$Header: /cvsroot/nco/nco/doc/ANNOUNCE,v 1.730 2014/08/27 04:44:00 zender Exp $ -*-text-*-
-The netCDF Operators NCO version 4.4.4 are ready.
+The netCDF Operators NCO version 4.4.5 are ready.
http://nco.sf.net (Homepage)
http://dust.ess.uci.edu/nco (Homepage "mirror")
This release is mainly a bugfix and stability release.
A few new features improve some corner-cases:
-It includes workarounds that allow NCO to successfully work with
-some names that violate netCDF but not HDF rules.
-Users can now retain "orphaned" dimensions after variable subsetting.
-nces now works with hyperslabs that resolve to the same size.
-Group broadcasting by ncbo is more intelligent when differencing
-ensemble means (created by nces) from full datasets.
+NCO now supports longer lists of input files, DAP files on HTTPS
+servers, and the CF ancillary_variables convention.
-A potentially serious bug in ncwa --mask_condition has been fixed.
-Users of ncwa --mask_condition are encouraged to upgrade.
-
-Work on NCO 4.4.5 is underway, still focused on stability and speed.
-This includes more netCDF4 mop-up, improved group broadcasting
-algorithms, and, possibly, improved HDF4 support, and new chunking
-features.
+Work on NCO 4.4.6 is underway, still focused on stability and speed.
+This includes more netCDF4 mop-up and new chunking features.
Enjoy,
Charlie
NEW FEATURES (full details always in ChangeLog):
-A. NCO now contains automatic workarounds to handle element names that
- contain characters that are legal in HDF though are illegal in
- netCDF. For example, slashes and leading special characters are
- are legal in HDF and illegal in netCDF element (i.e., group,
- variable, dimension, and attribute) names. NCO converts these
- forbidden characters to underscores, and retains the original names
- of variables in automatically produced attributes named hdf_name.
- Two real-world examples: NCO translates the NASA CERES dimension
- "(FOV) Footprints" to "_FOV_ Footprints", and "Cloud & Aerosol,
- Cloud Only, Clear Sky w/Aerosol, and Clear Sky" (yes, that's really
- a dimension name) to "Cloud & Aerosol, Cloud Only, Clear Sky
- w_Aerosol, and Clear Sky".
- ncks CERES_MODIS.hdf CERES_MODIS.nc
- http://nco.sf.net/nco.html#hdf4
-
-B. ncks --rad to Retain all dimensions.
- When invoked with --rad, ncks copies each dimension in the input
- file to the output file, regardless of whether the dimension is
- utilized by any variables. Normally ncks discards "orphan
- dimensions", i.e., dimensions not referenced by any variables.
- This switch allows users to keep non-referenced dimensions.
- When invoked in printing mode, this causes orphaned dimensions to
- be printed (they are not printed by default).
- ncks -O -C -v lat,lon ~/nco/data/in.nc ~/foo.nc
- ncks --rad -O -x -v lat ~/foo.nc ~/foo2.nc
- ncks --rad --cdl ~/foo2.nc
- http://nco.sf.net/nco.html#rad
-
-C. nces now computes statistics on ensemble members whose specified
- hyperslabs resolve to the same size. nces has always worked well
- with identically shaped ensemble members, and on ensemble members
- whose record-dimension hyperslabs resolve to the same size.
- Now nces works well with ensemble members whose specified
- hyperslabs along any dimension resolve to the same size. The
- use-case that demanded this was a researcher who wished to compare
- a certain lat/lon region (stored in some regional files) with the
- same region stored in other global files (with the same grid).
- The regional files (e.g., Greenland only) are much smaller than
- global files so nces's new capability allows users to "get by" with
- regional files rather than always storing global files.
- nces -O --nsm_grp -d lat,0 -d lon,2 -d time,0 -p ~/nco/data grp1.nc grp2.nc ~/foo.nc
- http://nco.sf.net/nco.html#nces
+A. NCO now supports stdin input file lists up to ~50 MB long.
+ This applies to all NCO multi-file operators (ncra, ncea, ncrcat).
+ The previous limit was 10 MB. The new limit suffices for 30 years
+ of hourly datasets where each dataset name is 192 bytes long.
+ One NASA user is averaging 10 years of data, or 87600 files.
+ Who will be the first user to break the million file barrier?
+ http://nco.sf.net/nco.html#stdin
+
+B. NCO now supports the CF ancillary_variables convention described at
+ http://cfconventions.org/1.6.html#ancillary-data
+ This convention allows ancillary variables to be associated with
+ one or more primary variables. NCO attaches any such variables to
+ the extraction list along with the primary variable and its
+ coordinates and bounds, if any.
+ http://nco.sf.net/nco.html#ncl
+
+C. NCO now accesses DAP files on HTTPS servers. Previously NCO would
+ only test filenames beginning with "http://" for DAP access.
+ Now NCO also tests filenames beginning with "https://" for DAP.
+ If you use DAP servers with a protocol besides HTTP or HTTPS please
+ tell us so we can enable NCO for those services too.
+ http://nco.sf.net/nco.html#dap
+
+D. ncks --grp_xtr_var_xcl: Group Extraction Variable Exclusion
+ This new switch helps control variable and group extraction.
+ Normally NCO works in "intersection mode" where the objects
+ extracted are the intersection of arguments to -g and -v.
+ And the --union switch can be used to make their union.
+ As of 4.4.4 (June, 2014), ncks (alone) supports an option to
+ include specified groups yet exclude specified variables.
+ The --grp_xtr_var_xcl switch (with long option equivalent --gxvx
+ extracts all contents of groups given as arguments to
+ -g except for variables given as arguments to -v.
+ Use this when one or a few variables in hierarchical files are not
+ to be extracted, and all other variables are. This is useful when
+ coercing netCDF4 files into netCDF3 files such as with converting,
+ flattening, or dismembering files.
+ ncks --grp_xtr_var_xcl -g g1 -v v1 # Extract all of group g1 except v1
+ http://nco.sf.net/nco.html#gxvx
+
+E. New chunking policy r1d changes chunksize of 1-D record variables
+ (and no other variables) to specified (with --cnk_dmn) chunksize.
+ Any specified record dimension chunksizes will be applied to 1-D
+ record variables only. Other dimensions may be chunked with their
+ own --cnk_dmn options that will apply to all variables.
+ For example, ncks --cnk_plc=r1d --cnk_dmn=time,1000.
+ This sets time chunks to 1000 only in 1-D record variables.
+ Without the r1d policy, time chunks would change in all variables.
+ Not to be confused with chunking map rd1.
+ Thanks to James Adams for suggesting this.
+ http://nco.sf.net/nco.html#r1d
BUG FIXES:
-A. Fixed ncwa incorrect interpretation of some --mask_conditions.
- Lexer/Parser could return incorrect mask values for negative numbers.
- Thanks to Keith Lindsay for report, and to Henry Butowsky for fix.
- Prior to this fix, the ncwa lexer would drop the negative sign, if
- any, from the comparators appearing in the mask condition, e.g.,
- ncwa --mask_condition "lat < -20" was parsed as "lat < 20" not
- "lat < -20". Hence, users of ncwa --mask_condition (or -B) should
- upgrade. NB: The -m -M -T form of ncwa masking is/was not buggy.
- http://nco.sf.net#bug_ncwa_mask_condition
-
-B. Restore former tolerance of -x for non-existent elements.
- NCO normally requires that variables and groups specified with -v
- and -g must match the input file contents. The exception is when
- the -x flag tells NCO to exclude these elements. This exception
- was broken since NCO 4.2.x, and is now working again. Now excluding
- non-existent variables should one again work, e.g.,
- ncks -O -x -v no_such_variable ~/nco/data/in.nc ~/foo.nc
- Thanks to Keith Oleson for this bug report.
- http://nco.sf.net/nco.html#x
-
-C. Fix bug that caused CDL and XML printing to truncate trailing zeros
- of floating point exponents. Before this bugfix, ncks --cdl would
- print 1.100e-10 as 1.100e-1 instead of 1.1e-10. All CDL and XML
- printing prior to 4.4.4 mis-prints floating point numbers with
- exponents that end in zero (i.e., +/- 10, 20, 30 ... 200, 210...).
- Users of CDL and XML mode are urged to upgrade. This bug changed
- affected values by some multiple of 10 orders of magnitude.
- Hence it is likely that users affected by this bug would notice it
- when carefully performing any statistics, yet possible they would
- not for fields with large dynamic ranges. Thanks to Stubaan for report.
-
-D. Fix regression tests not to cause false negatives due to netCDF
- 4.3.2 record dimension chunk size changes
-
-E. ncdismember better handles whitespace in group names
-
-F. Fix numerous memory leaks and some corner-case segfaults
-
-KNOWN PROBLEMS:
+A. ncrename: fix unsafe pointer de-reference and improve diagnostics
+
+B. Fix problem introduced in 4.4.0 where sanitizing of filenames with
+ colons confused MS Windows interpretation of volume names, e.g.,
+ "C:\foo" became "C\:\foo" and caused write error. Workaround is to
+ use --no_tmp_fl or upgrade to 4.4.5. Thanks to James Adams for
+ reporting.
+
+C. Always send correct dimension sizes to chunker when hyperslabbing.
+ Fixes a bug reported where chunking and hyperslabbing played
+ cruelly together. Thanks to Parker Norton for reporting.
+ http://nco.sf.net#bug_cnk_hyp
+
+D. ncpdq: fix mishandling of dimension reversal arguments
+ Versions 4.3.2-4.4.4 of ncpdq could fail to correctly parse some
+ valid forms of the dimension reversal syntax. Failure resulted,
+ so no bad data was written. Solution is to upgrade to 4.4.5.
+ Thanks to Fan Fang for reporting.
+
+KNOWN PROBLEMS DUE TO NCO:
This section of ANNOUNCE reports and reminds users of the
existence and severity of known, not yet fixed, problems.
- These problems occur with NCO 4.4.4 built/tested with netCDF
- 4.3.3-rc1 on top of HDF5 hdf5-1.8.12 with these methods:
+ These problems occur with NCO 4.4.5 built/tested with netCDF
+ 4.3.3-rc1 on top of HDF5 hdf5-1.8.13 with these methods:
cd ~/nco;./configure --enable-netcdf4 # Configure mechanism -or-
cd ~/nco/bld;make dir;make allinone # Old Makefile mechanism
@@ -132,7 +113,33 @@ A. NOT YET FIXED (NCO problem)
Cause: NCO parsing of ncatted arguments is not sophisticated
enough to handle arrays of NC_STRINGS with embedded delimiters.
-B. NOT YET FIXED (netCDF library problem)
+B. NOT YET FIXED (NCO problem?)
+ ncra/ncrcat (not ncks) hyperslabbing can fail on variables with multiple record dimensions
+
+ Demonstration:
+ ncrcat -O -d time,0 ~/nco/data/mrd.nc ~/foo.nc
+
+ 20140826: Verified problem still exists
+ 20140619: Problem reported by rmla
+ Cause: Unsure. Maybe ncra.c loop structure not amenable to MRD?
+ Workaround: Convert to fixed dimensions then hyperslab
+
+C. NOT YET FIXED (NCO problem?)
+ Correctly handle stride argument on netCDF4 datasets
+ Specifying strided hyperslab on netCDF4 datasets leads
+ to enormous slowdown or failure with recent NCO versions.
+
+ Demonstration:
+ ncks -O -d time,0,,12 ~/ET_2000-01_2001-12.nc ~/foo.nc
+
+ 20140826: Verified problem still exists
+ 20140718: Problem reported by Parker Norton
+ Cause: Unclear. Interaction of stride and MSA?
+ Workaround: Convert file to netCDF3 first, then use stride
+
+KNOWN PROBLEMS DUE TO BASE LIBRARIES/PROTOCOLS:
+
+A. NOT YET FIXED (netCDF library problem)
Probe hidden attributes (chunking, compression) of HDF4 files
Demonstration:
@@ -145,7 +152,7 @@ B. NOT YET FIXED (netCDF library problem)
Bug report filed: netCDF #HZY-708311 ncdump/netCDF4 segfaults probing HDF4 file
Tracking tickets NCF-272, NCF-273
-C. NOT YET FIXED (would require DAP protocol change?)
+B. NOT YET FIXED (would require DAP protocol change?)
Unable to retrieve contents of variables including period '.' in name
Periods are legal characters in netCDF variable names.
Metadata are returned successfully, data are not.
@@ -160,7 +167,7 @@ C. NOT YET FIXED (would require DAP protocol change?)
Bug report filed: https://www.unidata.ucar.edu/jira/browse/NCF-47
-D. NOT YET FIXED (would require DAP protocol change)
+C. NOT YET FIXED (would require DAP protocol change)
Correctly read scalar characters over DAP.
DAP non-transparency: Works locally, fails through DAP server.
Problem, IMHO, is with DAP definition/protocol
diff --git a/doc/ChangeLog b/doc/ChangeLog
index a3da80c..ab20346 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,3 +1,128 @@
+2014-08-26 Charlie Zender <zender at uci.edu>
+
+ * NCO 4.4.5 release procedure:
+ Changes since nco-4_4_4: https DAP, gxvx, mk, ncl_var, dmn_cmn, ncpdq, C:
+ cd ~/nco;cvs tag -d nco-4_4_5;cvs tag -d nco-4_4_5-1
+ cd ~/nco;cvs commit -m "Preparing nco-4.4.5 release"
+ cvs tag -c nco-4_4_5;cvs tag -c nco-4_4_5-1
+
+2014-08-25 Charlie Zender <zender at uci.edu>
+
+ * Specify correct dmn_cmn[] information to nco_cnk_sz_set_trv()
+
+2014-08-22 Charlie Zender <zender at uci.edu>
+
+ * Sanitize filenames prior to shell use with nm2sng_fl() instead of nm2sng_cdl()
+ Fixes bug in MS Windows handling volume names like "C:\foo"
+
+2014-08-21 Charlie Zender <zender at uci.edu>
+
+ * Fix false negative regressions due to new chunking defaults
+
+ * Fix ncpdq mis-handling of dimension reversal arguments (introduced between 4.3.2--4.3.6)
+
+ * Fix inadvertent omission of --cnk_map switch in ncecat
+
+2014-08-15 Charlie Zender <zender at uci.edu>
+
+ * Change default chunking policy/map from g2d/rd1 to xst/xst (fxm: breaks some regressions)
+
+ * Add mrd.cdl to check compliance/performance for files/variables with Multiple Record Dimensions
+
+2014-08-14 Charlie Zender <zender at uci.edu>
+
+ * Add cnk_plc_r1d to only change chunking of specified 1-D record variables
+
+2014-08-13 Charlie Zender <zender at uci.edu>
+
+ * Tweak Makefile for rhea.ccs.ornl.gov
+
+2014-07-14 Charlie Zender <zender at uci.edu>
+
+ * Tidy ncks.c and nco_grp_utl.c for MPI work
+
+ * Clarify ncrcat packing issues in man page
+
+2014-07-11 Charlie Zender <zender at uci.edu>
+
+ * Change FL_LST_IN_MAX_LNG from 10 MB to 504576001 B per request of Christine Smit
+ Use case: 30 years of hourly data files each 192 characters long
+
+2014-07-10 Charlie Zender <zender at uci.edu>
+
+ * Deprecate ENABLE_PNETCDF from meaning exposed PnetCDF API
+ Soon it will mean that netCDF4 was built with --enable-pnetcdf
+
+2014-07-08 Charlie Zender <zender at uci.edu>
+
+ * Handle CF ancillary_variables like, well, ancillary variables
+
+2014-07-06 Charlie Zender <zender at uci.edu>
+
+ * Integrate netCDF4 MPI I/O calls in library, begin conversion with ncks
+
+ * Clean-up nco_get_prg_info(), make consistent with newer netCDF regression tests
+
+2014-07-05 Charlie Zender <zender at uci.edu>
+
+ * Remove Makefile cruft to simplify building parallel NCO
+
+2014-07-04 Charlie Zender <zender at uci.edu>
+
+ * Use -5 --fl_fmt=pnetcdf to create NC_FORMAT_CDF5 files
+
+ * Build simply when PNETCDF=Y
+
+2014-07-01 Charlie Zender <zender at uci.edu>
+
+ * Improve CF-compliance checking infrastructure for mabel/ICESat2
+
+2014-06-17 Charlie Zender <zender at uci.edu>
+
+ * Implement i18n in ncks, extend to es and fr
+
+2014-06-15 Charlie Zender <zender at uci.edu>
+
+ * Apply copyright notice changes to most source files
+
+2014-06-13 Charlie Zender <zender at uci.edu>
+
+ * Update and streamline project homepage
+
+2014-06-12 Charlie Zender <zender at uci.edu>
+
+ * Improve ncrename diagnostics, fix unset pointer de-reference
+
+2014-06-11 Charlie Zender <zender at uci.edu>
+
+ * Document --grp_xtr_var_xcl
+
+2014-06-10 Charlie Zender <zender at uci.edu>
+
+ * Utilize @verbatim environment in all nco.texi @examples
+
+2014-06-06 Charlie Zender <zender at uci.edu>
+
+ * Improve NCO compliance with NASA Reuse-Readiness Levels (RRLs)
+ Reorganize documentation on citation, authorship, copyright, and licensing
+
+ * Document NARR example of SLD statistics
+
+2014-06-05 Charlie Zender <zender at uci.edu>
+
+ * nc_set_log_level(nco_dbg_lvl) to quiet HDF logging messages for ncdismember
+
+2014-06-04 Charlie Zender <zender at uci.edu>
+
+ * Add pnetCDF token stubs. Build pnetCDF-enabled netCDF4 in /usr/local/parallel.
+
+ * Filenames that begin with https:// now trigger DAP access code path
+
+2014-05-31 Charlie Zender <zender at uci.edu>
+
+ * Mac OS X compatibility with bld/Makefile complete. No regressions!
+ Using MacPorts netCDF 4.3.1, Xcode 5.1, GNU coreutils (for cut)
+
2014-05-29 Charlie Zender <zender at uci.edu>
* NCO 4.4.4 release procedure:
@@ -11129,7 +11254,7 @@
* Created ncap_var_stretch() which generalizes var_conform_dim()
by including convolution of variables. ncap_var_stretch() appears
- to work as drop in replacement for var_conform_dim().
+ to work as drop in replacement for var_conform_dim().
Convolution is just a stub which does not do anything yet.
Realized that expansion might work by creating arbitrary variable
of convolution size and then separately calling var_conform_dim()
@@ -11148,7 +11273,7 @@
All of these machines have bison installed
Some of these builds require building getopt.o separately
Build fails on IBM because yacc does not understand pure_parser
-
+
2001-12-28 Charlie Zender <zender at uci.edu>
* More CEWI initializations
@@ -11158,7 +11283,7 @@
* Remove C++ comment characters that crept into various routines
Using // comments causes default to compilation to break on many
architectures (Linux being an exception)
-
+
* cvs tag -c nco-2_1_1
Changes since nco-2_1_0: ncap uses @ for attributes
Mixed rank handling improved but still broken
@@ -11177,12 +11302,12 @@
i.e var_nm at att_nm rather than var_nm:att_nm
* Changed ncap.y So that 1-D variables can be saved in an attribute
-
+
* Attempted to fix the rank problem. Added ncap_var_conform_dim() to
ncap_utl.c, Its not working correctly at the mo.
-
+
* Added att_lst_max to ncap.c
-
+
* Updated ncap.in
2001-12-02 Charlie Zender <zender at uci.edu>
@@ -11208,7 +11333,7 @@
2001-10-30 Charlie Zender <zender at uci.edu>
* Fixed getopt dependencies and included nco_netcdf.h nco.h in
- ncap stuff
+ ncap stuff
2001-10-28 Charlie Zender <zender at uci.edu>
@@ -11218,7 +11343,7 @@
* Use NC_REC_DMN_UNDEFINED instead of -1 where appropriate
- * Fix argument list to nco_inq_varid() call in ncap
+ * Fix argument list to nco_inq_varid() call in ncap
* Fix netCDF3 migration bug that could cause core dumps because
non-coordinate dimensions where being interpreted as coordinate
@@ -11228,7 +11353,7 @@
* Added VERSION infrastructure for recording build information in executable
- * Check rcd before Exit_Gracefully() in main() routines so
+ * Check rcd before Exit_Gracefully() in main() routines so
rcd does not generate "set but not used warnings"
2001-10-07 Charlie Zender <zender at uci.edu>
@@ -11240,7 +11365,7 @@
information-specific versions of inquire functions where
possible.
- * Verified nco-2_0_2 passes test suite
+ * Verified nco-2_0_2 passes test suite
* nco_typ_sng(): NC_CHAR is unsigned char, moved nco_typ_sng(),
c_type_nm(), fortran_typ_nm() to nco_netcdf library so that
@@ -11485,7 +11610,7 @@
* Added OpenMP critical regions to var_get() and var_refresh()
* Added OpenMP critical regions around thread-unsafe netCDF
- write calls in ncwa and ncra/ncea.
+ write calls in ncwa and ncra/ncea.
* Finally removed 1995--1996-era SGI enum workarounds from nc.h
SGI compiler on dataproc seems to behave sanely now
@@ -11500,7 +11625,7 @@
work either.
* Multi-threaded version of ncwa averages variables in T42 file
- correctly sometimes, but also incorrectly. Currently unpredictable
+ correctly sometimes, but also incorrectly. Currently unpredictable
what causes discrepancy.
* Removed arg_cnt from ncwa.c. ncwa.c now uses standard
@@ -11517,7 +11642,7 @@
2000-09-13 Charlie Zender <zender at uci.edu>
* Contrary to the documentation, ncflint has always processed
- coordinate variables. Perhaps fixing coordinate variables is a
+ coordinate variables. Perhaps fixing coordinate variables is a
better idea? Patched var_lst_divide() to fix all non-record
coordinate variable to ncflint. Not sure if I will release this
though. Perhaps it should be a switch?
@@ -11543,7 +11668,7 @@
* Added some clarifications to memory handling in the manual, and
additional examples provoked by John Sheldon's GFDL netCDF
- website.
+ website.
* Integrated ncvarid_or_die() and ncdimid_or_die() into ncrename
@@ -11554,7 +11679,7 @@
* Will all previous changes to nco_malloc(), nco_realloc(), and
memory management in general, make tst now seems to be well
behaved with Electric Fence, and duplicates answers without
- Electric Fence.
+ Electric Fence.
* Another nco_realloc() tweak to satisfy Electric Fence:
Now realloc() is never called when size == 0
@@ -11584,18 +11709,18 @@
2000-08-23 Charlie Zender <zender at uci.edu>
* Functionalized type conversion routines nco_cnv_var_dbl() and
- nco_cnv_dbl_var()
+ nco_cnv_dbl_var()
* Fixed x:y bug in opt arg of ncra.c introduced in 1.2
2000-08-14 Charlie Zender <zender at uci.edu>
- * Added this text to the license, provided by Steven G. Johnson
+ * Added this text to the license, provided by Steven G. Johnson
- "As a special exception to the terms of the GPL, you are permitted
- to link the NCO source code with the NetCDF and HDF libraries
- and distribute the resulting executables under the terms of the GPL,
- but in addition obeying the extra stipulations of the netCDF and
+ "As a special exception to the terms of the GPL, you are permitted
+ to link the NCO source code with the NetCDF and HDF libraries
+ and distribute the resulting executables under the terms of the GPL,
+ but in addition obeying the extra stipulations of the netCDF and
HDF library licenses."
This is intended to allow NCO to link to the non-GPL licenses of
@@ -11635,7 +11760,7 @@
2000-07-09 Charlie Zender <zender at uci.edu>
* Added section on Contributing/contributors to nco.texi
-
+
* Fixed case when missing value is first in min and max operators
* Added min, max, ttl cases to nco_tst.sh
@@ -11643,7 +11768,7 @@
* Added temporary variable to all low-level arithmetic routines
(e.g., var_add()) to store missing value in order to reduce
dereferencing of pointers to missing values. This may result in
- measurable speedups for all arithmetic operators.
+ measurable speedups for all arithmetic operators.
2000-07-08 Charlie Zender <zender at uci.edu>
@@ -11705,7 +11830,7 @@
* Tagged this as nco1_1_48
- * Found and fixed ncdiff bug in TODO #155.
+ * Found and fixed ncdiff bug in TODO #155.
Bug had been inserted in ncdiff 1.5 (nco-1.1.15, November 1998)
when I switched from using dimension IDs to using dimension names
to identify and compare dimensions in var_conform_dim(). Problem
@@ -11716,10 +11841,10 @@
out in ncdiff() so I was able to check that turning it back on
solves the problem. Now I have removed old commented-out block
from ncdiff (because it was confusing) and all logic is now local
- to var_conform_dim(). This fix increases the number of strstr()
+ to var_conform_dim(). This fix increases the number of strstr()
comparisons of dimension names because names must now be compared
- twice in var_conform_dim() for each variable being expanded.
- Oh well.
+ twice in var_conform_dim() for each variable being expanded.
+ Oh well.
2000-05-12 Charlie Zender <zender at uci.edu>
@@ -11729,8 +11854,8 @@
* Finished testing of feature allowing skipping of initial files
when lmt_typ = dim_idx. Seems to work. Now dim_idx and crd_val
- hyperslabs may have arbitrary numbers of superfluous files at
- beginning and end.
+ hyperslabs may have arbitrary numbers of superfluous files at
+ beginning and end.
* Added rec_skp_nsh member to lmt structure to support keeping
track of records skipped in superfluous initial files for lmt_typ
@@ -11750,13 +11875,13 @@
* Switched NCO from atof(), atol() to strtod(), strtol()
- * Added ability to skip superfluous trailing files to lmt_evl()
+ * Added ability to skip superfluous trailing files to lmt_evl()
when limits are coordinate values. Needs testing but appears to
work. Had to use a goto statement, icky. Fixes TODO #157?
2000-05-04 Charlie Zender <zender at uci.edu>
- * More fixes to fix problems with Electric Fence
+ * More fixes to fix problems with Electric Fence
2000-04-18 Charlie Zender <zender at uci.edu>
@@ -11785,9 +11910,9 @@
* Tagged this as nco-1_1_45
* Fix to PID length bug in fl_out_open() on SGIs
- Now use dynamically allocated string to hold PID
+ Now use dynamically allocated string to hold PID
Kudos to Juliana Rew for finding this bug
-
+
2000-01-16 Charlie Zender <zender at uci.edu>
* Changed all addresses except website to UCI ESS
@@ -11797,7 +11922,7 @@
2000-01-14 Charlie Zender <zender at uci.edu>
* Calling ncwa without arguments now causes operator to print
- usage and exit successfully
+ usage and exit successfully
* Print error message and hint when ncwa called with -a dim1 -a
dim2 instead of -a dim1,dim2
@@ -11839,7 +11964,7 @@
ncatted -O -h -a test,global,o,c,"NREL, NCAR" in.nc
because the new attribute value followed the comma delimiter used
internally by ncatted to delimit list elements
-
+
* Fixed so that setting strings to zero length with ncatted works,
e.g., ncatted -O -a history,global,o,c,"" in.nc
@@ -11852,10 +11977,10 @@
-DAIX on the IBM SP cluster environment
1999-10-21 Charlie Zender <zender at dust.ps.uci.edu>
-
+
* Defined MY_BLD_DIR in Makefile before it is used
Re-tagged this as nco1_1_41
-
+
1999-10-17 Charlie Zender <zender at dust.ps.uci.edu>
* Tagged this as nco1_1_41
@@ -11872,7 +11997,7 @@
* Fixed another bug in ncwa reported by Keith Lindsay.
The denominator in normalized averages did not always account for
missing values in the variable being averaged. This bug may have
- been introduced sometime during ncwa rewrites around 19981201.
+ been introduced sometime during ncwa rewrites around 19981201.
I'm sure it has not always been there.
1999-10-03 Charlie Zender <zender at dust.ps.uci.edu>
@@ -11881,10 +12006,10 @@
* Added test target in bld/Makefile. Now `make test' automatically
downloads a small (66 kb) file on which it performs a small
- battery of tests (bld/nco_tst.sh).
+ battery of tests (bld/nco_tst.sh).
* Revamped build procedure to use GNU make dependencies rather
- than makdep perl script.
+ than makdep perl script.
* All *.c files now build cleanly with gcc -Wall
@@ -11907,13 +12032,13 @@
* Added ncwa test #12 to nco_tst.sh. This tests for a bug
reported by Keith Lindsay where ncwa averaged a variable which is
completely missing_value to a value of 0.0 rather than
- missing_value.
+ missing_value.
* Removed C_ONLY token and made builds completely C-based by
default. Introduced new token USE_FORTRAN_ARITHMETIC to build
old style NCO with fortran arithmetic routines. Seems to work
- fine. Translated Fortran date routines newdate() and days2eom() to
- C as part of this.
+ fine. Translated Fortran date routines newdate() and days2eom() to
+ C as part of this.
1999-08-04 Charlie Zender <zender at dust.acd.ucar.edu>
@@ -11932,9 +12057,9 @@
multiple colons (which are legal in UNIX). Files with single
colons in their names, as opposed to rcp requests, still cause
core dumps and will continue to do so until I write a routine
- which determines whether to treat the filename as an rcp
+ which determines whether to treat the filename as an rcp
request based on some sort of valid hostname recognition
- algorithm.
+ algorithm.
1999-07-29 Charlie Zender <zender at dust.acd.ucar.edu>
@@ -12119,7 +12244,7 @@ Fri Dec 4 15:06:23 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
* Made sure ncwa weights were being masked when normalization was
invoked. Formerly, they were not. This was a bug. The bug is now
- fixed.
+ fixed.
* Rearranged normalization logic of ncwa
@@ -12130,7 +12255,7 @@ Fri Dec 4 15:06:23 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
* Allow hyperslab coordinate specification in exponential format
even when decimal point is missing, e.g., "-d lon,36e1" is valid
- * var_conform_dim() now checks dimension names rather than IDs
+ * var_conform_dim() now checks dimension names rather than IDs
Mon Nov 23 17:29:02 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
@@ -12157,13 +12282,13 @@ Sat Oct 31 14:56:33 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
triggering this bug. Solution was to make ncra, like ncrcat,
simply process ALL record variable even NC_CHAR and NC_BYTE,
though the averaging operation on these types is still
- ill-defined.
+ ill-defined.
Wed Aug 26 16:30:27 1998 Charlie Zender <zender at odin.cgd.ucar.edu>
* Fixed bld/nco_tst.sh to work again at NCAR. `make test' now
performs non-trivial tests of ncwa and ncdiff. Only works at
- NCAR (a necessary input file is rather large).
+ NCAR (a necessary input file is rather large).
Wed Aug 19 11:26:25 1998 Charlie Zender <zender at odin.cgd.ucar.edu>
@@ -12179,8 +12304,7 @@ Wed Aug 19 11:26:25 1998 Charlie Zender <zender at odin.cgd.ucar.edu>
* Added nco_vrs_prs() to parse NCO versions. NCO version is now
always printed with -r option.
- * Fixed bug where -n NINTAP list did not recognize `.cdf'
- suffixes.
+ * Fixed bug where -n NINTAP list did not recognize `.cdf' suffixes.
Mon Aug 10 21:53:34 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
@@ -12188,22 +12312,22 @@ Mon Aug 10 21:53:34 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
be avoided if desired.
* Fixed bug in ncrename where fl_in could be free()'d before it
- was malloc()'d in fl_nm_prs().
+ was malloc()'d in fl_nm_prs().
* Fixed bug in ncdiff where variables of same rank but different
types would cause core dump when being subtracted. Improved
- diagnostics for failures with ncdiff.
-
+ diagnostics for failures with ncdiff.
+
1998-07-07 Charlie Zender <zender at z.ppp.ucar.edu>
* Added -h option (suppresses history concatentation) to all
- operators. Changed existing ncks -h option to -m (for metadata).
+ operators. Changed existing ncks -h option to -m (for metadata).
Sun Jun 7 17:45:20 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
- * Added more descriptive error diagnostics to ncvarid() calls
+ * Added more descriptive error diagnostics to ncvarid() calls
to var_lst_mk() ncks to report the names of user-specified
- variables which do not exist in input files.
+ variables which do not exist in input files.
1998-05-16 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
@@ -12212,7 +12336,7 @@ Sun Jun 7 17:45:20 1998 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
1998-05-08 Charlie Zender <zender at sanitas-e0.cgd.ucar.edu>
* Added improved error diagnostics to ncks when -A fails.
- Added improved error diagnostics to fl_out_close() and fl_mv().
+ Added improved error diagnostics to fl_out_close() and fl_mv().
-r now prints library version for all operators.
-r and usg_prn() now prints NCO homepage URL.
@@ -12233,13 +12357,13 @@ Mon Feb 9 09:50:26 1998 Charlie Zender <zender at odin.cgd.ucar.edu>
loop over variables. This reduces peak memory consumption by a
factor of three and sustained memory by a factor of two to three.
ncwa performance should be noticeably enhanced by this. This
- problem affected, and this fix improves, only the ncwa operator.
-
+ problem affected, and this fix improves, only the ncwa operator.
+
Sun Feb 8 21:50:32 1998 Charlie Zender <zender at odin.cgd.ucar.edu>
* Downloaded and altered pvmgetarch from pvm3.4b6. This version
was returning SGI instead of CRAY on Ouray (=Cray J90 Unicos
- 10.0.0) because pvmgetarch thinks machines with /bin/4D are SGI.
+ 10.0.0) because pvmgetarch thinks machines with /bin/4D are SGI.
Distributing this customized version of pvmgetarch with NCO.
Also changed new pvmgetarch so it returns SUNMP on any Sun
multiprocessor, regardless of whether PVM_SHMEM is set to ON.
@@ -12295,19 +12419,19 @@ Fri Oct 17 12:53:54 1997 Charlie Zender <zender at odin.cgd.ucar.edu>
* Fixed fl_out_open() to abort after receiving more than 10
incorrect user responses. This fixes a bug where NCO would
crash in non-interactive shells when the -O or -A options were
- omitted.
+ omitted.
1997-10-07 Charlie Zender <zender at z.ppp.ucar.edu>
* Finished ncatted documentation. Cleaned up code to avoid
compilation errors with SGI on memcpy(). Touched up manual.
Releasing this as NCO Version 1.1.
-
+
Sun Sep 21 15:08:49 1997 Charlie Zender <zender at z.ppp.ucar.edu>
* Merged WIN32 modifications into distribution. Added WIN32 and
C_ONLY tokens to code. Relinked with netCDF 3.3.1, had no
- problems.
+ problems.
Tue Sep 16 23:53:44 1997 Charlie Zender <zender at z.ppp.ucar.edu>
@@ -12319,7 +12443,7 @@ Tue Sep 16 23:53:44 1997 Charlie Zender <zender at z.ppp.ucar.edu>
Thu Aug 28 17:07:50 1997 Charlie Zender <zender at heinlein.cgd.ucar.edu>
* Rewrote ncdiff documention, which had many errors and
- omissions.
+ omissions.
Sat Jun 28 23:26:40 1997 Charlie Zender <zender at z.ppp.ucar.edu>
@@ -12342,7 +12466,7 @@ Fri May 30 13:12:25 1997 Charlie Zender <zender at heinlein.cgd.ucar.edu>
* Added routines to process time variables in ARM files.
- * Added hyam,hybm,hyai,hybi to list of variables which will not
+ * Added hyam,hybm,hyai,hybi to list of variables which will not
be differenced by ncdiff.
* ncdiff now chooses mss_val from either file where it's valid,
@@ -12398,7 +12522,7 @@ Wed Mar 26 21:13:09 1997 Charlie Zender <zender at z.ppp.ucar.edu>
distribution
* Changed ncks -s option to accept full printf() style format
- strings
+ strings
* Fixed memory leak in var_get() in nc_utl.c which caused memory
to be allocated twice. This also fixed longstanding performance
@@ -12406,7 +12530,7 @@ Wed Mar 26 21:13:09 1997 Charlie Zender <zender at z.ppp.ucar.edu>
current record. Thanks to jps at GFDL.GOV (John Sheldon) for
discovering this bug.
- * General release of nco-0.9 on netCDF and CCM mailing lists
+ * General release of nco-0.9 on netCDF and CCM mailing lists
Thu Feb 8 23:01:04 MST 1996 Charlie Zender <zender at ncar.ucar.edu>
diff --git a/doc/LICENSE b/doc/LICENSE
index 94a9ed0..1927ef0 100644
--- a/doc/LICENSE
+++ b/doc/LICENSE
@@ -1,674 +1,16 @@
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-version or of any later version published by the Free Software
-Foundation. If the Program does not specify a version number of the
-GNU General Public License, you may choose any version ever published
-by the Free Software Foundation.
-
- If the Program specifies that a proxy can decide which future
-versions of the GNU General Public License can be used, that proxy's
-public statement of acceptance of a version permanently authorizes you
-to choose that version for the Program.
-
- Later license versions may give you additional or different
-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
-later version.
-
- 15. Disclaimer of Warranty.
-
- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- <one line to give the program's name and a brief idea of what it does.>
- Copyright (C) <year> <name of author>
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- <program> Copyright (C) <year> <name of author>
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-<http://www.gnu.org/licenses/>.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+All source code created by the NCO project and distributed with NCO is
+re-distributable under the terms of the GNU General Public License
+(GPL) Version 3. The full license text is at
+http://www.gnu.org/copyleft/gpl.html and in the file COPYING.
+Copyright information is in the file COPYRIGHT.
+
+As a special exception to the terms of the GPL, you are permitted
+to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
+libraries and to distribute the resulting executables under the terms
+of the GPL, but in addition obeying the extra stipulations of the
+HDF, netCDF, OPeNDAP, and UDUnits licenses.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+See the GNU General Public License for more details.
diff --git a/doc/MANIFEST b/doc/MANIFEST
index 5503493..d0d6750 100644
--- a/doc/MANIFEST
+++ b/doc/MANIFEST
@@ -1,4 +1,4 @@
-$Header: /cvsroot/nco/nco/doc/MANIFEST,v 1.65 2014/04/01 17:45:20 pvicente Exp $ -*-text-*-
+$Header: /cvsroot/nco/nco/doc/MANIFEST,v 1.70 2014/08/22 01:01:20 zender Exp $ -*-text-*-
This file enumerates the files in the NCO distribution and, where
appropriate, describes the purpose of the file.
@@ -7,8 +7,12 @@ Volatile files are created automatically (e.g., by invoking
./configure) and may not be present in pristine source trees.
Top-level files:
-COPYING NCO Software License: GPL3
+AUTHORS Whom to praise and blame
+CITATION How and why to cite NCO in your work
+COPYING GNU General Public License GPL3
+COPYRIGHT Copyright information
INSTALL Boilerplate instructions for ./configure
+LICENSE License details
acinclude.m4 NCO M4 macro definitions used by aclocal to generate aclocal.m4
aclocal.m4 M4 macros generated from acinclude.m4 by aclocal
autogen.sh Gather all autotools necessary to run autoconf
@@ -91,6 +95,7 @@ nco/data/cmip5.cdl CDL file to test ncbo functionality on groups
nco/data/dsm.cdl CDL file to test ncdismember
nco/data/mdl_1.cdl CDL file to test ensemble operations
nco/data/mdl_2.cdl CDL file to test ensemble operations
+nco/data/mrd.cdl CDL file to test multiple record dimensions
nco/data/obs.cdl CDL file to test group broadcasting
nco/data/in_rec_zero.cdl CDL file to test zero-record files
nco/data/ncap.in Sample ncap input script
@@ -117,28 +122,36 @@ nco/doc/TAG CVS tag for this version
nco/doc/TODO List of tasks for future releases
nco/doc/VERSION NCO version
nco/doc/beta.txt Availability of beta- or pre-release Debian packages
+nco/doc/build_hints.shtml Hints to build from source
nco/doc/debian.txt Creating and updating Debian NCO .deb packages
nco/doc/dir Example Info file to load nco.info
nco/doc/dods.sh Install OPeNDAP 3.4.X for NCO DAP-enabled clients
+nco/doc/doe.jpg DOE logo (JPG format)
+nco/doc/endorsements.txt Statements of support for NCO
nco/doc/help.txt Advertisement for help with NCO (outdated---from 2000)
+nco/doc/highlights_old.shtml Short summaries of old releases
nco/doc/index.shtml NCO website homepage
nco/doc/logo_srl.png NCO spiral logo PNG raster format
nco/doc/logo_srl.svg NCO spiral logo Scalable Vector Graphic format
nco/doc/logo_srl.xcf NCO spiral logo GIMP format
+nco/doc/milestones_old.shtml Milestones in old releases
nco/doc/mpi.txt MPI Environments for NCO
nco/doc/my-bib-macros.texi TeXInfo bibliography macros for nco.texi
+nco/doc/nasa.png NASA logo (PNG format)
nco/doc/ncap.txt Description of the ncap operator (not yet used)
nco/doc/nco.dvi(v) NCO User's Guide: DVI format
nco/doc/nco.html(v) NCO User's Guide: HTML format
nco/doc/nco.info(v) NCO User's Guide: Info format
nco/doc/nco.pdf(v) NCO User's Guide: Portable Document Format
+nco/doc/nco.png NCO Webpage icon (PNG format)
nco/doc/nco.ps(v) NCO User's Guide: Postscript format
nco/doc/nco.texi NCO User's Guide: TeXInfo format
-nco/doc/nco.png NCO Webpage icon (PNG format)
nco/doc/nco_news.shtml NCO news archive
nco/doc/netcdf4.sh Install latest netcdf4 and HDF libraries for NCO
+nco/doc/nsf.png NSF logo (PNG format)
nco/doc/opendap.sh Install OPeNDAP 3.5.X for NCO DAP-enabled clients
-nco/doc/surfit.txt Summer research project advertisement
+nco/doc/problems_old.shtml Summaries of old bugs
+nco/doc/surfit.txt Summer research project advertisement for UCI
nco/doc/tags_doc.sh Generate Emacs tags for all NCO documents
nco/doc/valgrind.txt Valgrind suppressions file for debugging NCO
@@ -164,6 +177,15 @@ nco/man/ncwa.1 ncwa man page
Object directory:
nco/obj/README Description of object directory
+Portable Object Template directory:
+nco/po/nco.pot Portable Object Template file for NCO
+
+Portable Object Spanish directory:
+nco/po/es/nco.po Portable Object Spanish translations for NCO
+
+Portable Object French directory:
+nco/po/fr/nco.po Portable Object French translations for NCO
+
Source code directories:
nco/src/nco Source for base NCO library and operators
nco/src/nco_c++ Source for libnco_c++ C++ interface to netCDF API
diff --git a/doc/TAG b/doc/TAG
index e501165..de12b9f 100644
--- a/doc/TAG
+++ b/doc/TAG
@@ -1 +1 @@
-$Name: nco-4_4_4 $
+$Name: nco-4_4_5 $
diff --git a/doc/TODO b/doc/TODO
index 592418b..fb864f6 100644
--- a/doc/TODO
+++ b/doc/TODO
@@ -1,4 +1,4 @@
-$Header: /cvsroot/nco/nco/doc/TODO,v 1.1265 2014/05/27 02:55:26 zender Exp $
+$Header: /cvsroot/nco/nco/doc/TODO,v 1.1267 2014/08/27 04:44:01 zender Exp $
# Purpose: TODO items for NCO
@@ -653,7 +653,15 @@ nco1106. autoconvert netCDF4 string variable to netCDF3 nc_char type. requires d
nco1109. broadcast degenerate dimensions in nco_var_cnf_dmn()/ncap_var_cnf_dmn(): helps ncap/ncwa/ncbo/ncflint
nco1110. ncap2: allow type specification as per christine smit (GSFC) request 20140407
nco1111. ncrcat/ncecat check consistency of packing attributes across files (requested by ocehugo 20140522)
-nco1112.
+nco1112. nco: nintap double iterator rqs by dave allured 20140813
+nco1113. nco: rsp parker norton help srd slowdown issue help 20140718
+ Slowdown occurs only when using srd
+ time ncks -O ~/ET_2000-01_2001-12.nc ~/foo.nc # works 1m38s
+ time ncks -O -d time,0 ~/ET_2000-01_2001-12.nc ~/foo.nc # works 0m03s
+ time ncks -O -d time,0,0,12 ~/ET_2000-01_2001-12.nc ~/foo.nc # borken after 6m13s, numerous HDF Errors
+ time ncks -O -L 0 -d time,0,0,12 ~/ET_2000-01_2001-12.nc ~/foo.nc # borken after 6m13s, numerous HDF Errors
+ time ncks -O -d time,0,,12 ~/ET_2000-01_2001-12.nc ~/foo.nc # borken after 6m13s, numerous HDF Errors
+nco1114.
qrk
************************************************************************
End ncoXXX TODOs
diff --git a/doc/VERSION b/doc/VERSION
index f15ec04..5f70498 100644
--- a/doc/VERSION
+++ b/doc/VERSION
@@ -1 +1 @@
-4.4.4
\ No newline at end of file
+4.4.5
\ No newline at end of file
diff --git a/doc/build_hints.shtml b/doc/build_hints.shtml
new file mode 100644
index 0000000..7bdd2bb
--- /dev/null
+++ b/doc/build_hints.shtml
@@ -0,0 +1,313 @@
+<!-- $Header: /cvsroot/nco/nco/doc/build_hints.shtml,v 1.1 2014/06/15 16:45:40 zender Exp $
+
+Purpose: Build_Hints archive
+
+URL:
+http://nco.sf.net/build_hints.shtml
+http://dust.ess.uci.edu/nco/build_hints.shtml
+file:///home/zender/nco/doc/build_hints.shtml
+
+Usage:
+/usr/bin/scp ~/nco/doc/build_hints.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+scp -p ~/nco/doc/build_hints.shtml dust.ess.uci.edu:/var/www/html/nco
+-->
+
+<!doctype html public "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+ <title>NCO Homepage</title>
+ <meta name="GENERATOR" content="Mozilla/3.04Gold (X11; I; Linux 2.0.0 i686) [Netscape]">
+ <meta name="Author" content="Charles S. Zender">
+ <meta name="Keywords" content="NCO Homepage, netCDF, netCDF operator, GCM, HDF, scientific data">
+</head>
+<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
+
+<dt><a name="Makefile"></a></dt> <!-- http://nco.sf.net#Makefile -->
+<dt><a name="hnt"></a></dt> <!-- http://nco.sf.net#hnt -->
+<dt><a name="bld_hnt"></a></dt> <!-- http://nco.sf.net#bld_hnt -->
+<h2>Hints to Build-from-Source:</h2>
+
+<ul><b>Generic Build Hints:</b>
+
+<a name="bld_cnf"></a> <!-- http://nco.sf.net#bld_cnf -->
+<li><i>The two NCO build mechanisms:</i>
+NCO has two build mechanisms: (1) GNU configure and
+(2) a custom Makefile (<tt>nco/bld/Makefile</tt>)
+designed for hand-editing.
+Try the traditional GNU <tt>configure</tt> method first, i.e.,
+<tt>./configure;make;make check;make install</tt>.
+This method involves no hand-editing of makefiles, but trouble-free
+builds with it are less common than we would like.
+The file <tt>nco/configure.eg</tt> contains a table which describes the
+success you can expect building NCO with the <tt>configure</tt>
+mechanism.
+If the simple <tt>configure</tt> recipe above does not work, savvy
+users may find it straightforward to modify and use the following, more
+advanced <tt>configure</tt> recipe:
+<tt>
+<pre class="example">
+# gcc/g++ Sysadmins use/modify this to install/update NCO in /usr/local, based on netCDF4 also in /usr/local (works on givre 20100727):
+export GNU_TRP=`~/nco/autobld/config.guess`
+cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
+CPPFLAGS='-DHAVE_NETCDF4_H -I/usr/local/include' LDFLAGS='-L/usr/local/lib' ./configure --prefix='/usr/local' --enable-ncap2 --enable-netcdf4 > nco.configure.${GNU_TRP}.foo 2>&1
+/bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
+/bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
+make clean;make > nco.make.${GNU_TRP}.foo 2>&1
+make check >> nco.make.${GNU_TRP}.foo 2>&1
+sudo make install >> nco.make.${GNU_TRP}.foo 2>&1
+</pre>
+</tt>
+This is the recipe that the developers use to test <tt>configure</tt>
+on their machines.
+Please contribute patches required to get the <tt>configure</tt>
+mechanism working properly for NCO on your platform.
+The <a href="http://dust.ess.uci.edu/nco/rgr">regressions archive</a>
+contains gory details of successful (and failed) builds for many platforms.
+Plaform-specific build hints (CentOS, Mac OS X, RHEL, Solaris)
+are listed <a href="#bld_plt_spc">below</a>.
+<br>
+
+All platforms continue to work fine with the <tt>nco/bld/Makefile</tt>
+method:
+<tt>
+<pre class="example">
+export MY_BIN_DIR='/home/username/bin' # Executables installed here
+export MY_OBJ_DIR='/home/username/obj' # Object files placed here
+export MY_LIB_DIR='/home/username/lib' # Libraries built here
+mkdir -p ${MY_BIN_DIR} ${MY_OBJ_DIR} ${MY_LIB_DIR}
+cd ~/nco/bld
+make dir
+make all
+make ncap2
+make test
+</pre>
+</tt>
+Disadvantages are that <tt>nco/bld/Makefile</tt> (1) Usually requires
+editing to fix your platforms paths; (2) Does not support shared
+libraries; and (3) Requires a degree from Hogwarts to understand.
+</li>
+
+<!-- http://nco.sf.net#dpl_sym -->
+<a name="dpl_sym"></a>
+<li><i>Duplicate symbols errors:</i>
+When building NCO with the netCDF4 library and headers, some compilers
+emit errors due to duplicate symbol definitions.
+This arises because of the complexity of the build system.
+Essentially, NCO has to define some netCDF API prototypes itself
+to handle the corner case where the netCDF4 distribution is used
+to build netCDF3 libraries.
+We have tried to address this issue using <tt>autoconf/configure</tt>
+but it is beyond our abilities.
+The fix is to manually tell NCO that the netCDF4 header
+file <tt>netcdf.h</tt> is in fact being used so that NCO should
+not attempt to define these prototypes.
+Do this, e.g., with <tt>CPPFLAGS='-DHAVE_NETCDF4_H'</tt> or
+<tt>USR_TKN='-DHAVE_NETCDF4_H'</tt> if you use <tt>configure</tt>.
+</li>
+
+<!-- http://nco.sf.net#bld_chn -->
+<a name="bld_chn"></a>
+<li><i>Build Chain Version Incompatibilities:</i>
+NCO requires GNU <tt>make</tt> version ≥ 3.78.1 to support target-specific variable values in <tt>bld/Makefile</tt>.
+NCO most often fails to build because <tt>ncap</tt> fails to build.
+Two of the most common reasons that <tt>ncap</tt> fails to build are
+(1) GNU <tt>bison</tt> is out-of-date (upgrade <tt>bison</tt>)
+and (2) <tt>--enable-optimize-*</tt> is specified to
+<tt>configure</tt> (do not specify it).<br>
+</li>
+
+<!-- http://nco.sf.net#bld_c99 -->
+<a name="bld_c99"></a>
+<li><i>C99-compliance & old compilers:</i>
+NCO versions ≥ 2.9.8 require the compiler to
+support the 1999 ISO C-Standard called C99.
+NCO takes advantage of two C99 features, restricted pointers and
+designated initializers.
+To build NCO versions ≥ 2.9.8 without a C99-compliant
+compiler, simply undefine the <tt>restrict</tt> type qualifier
+before compiling NCO.
+Do this, e.g., with <tt>CPPFLAGS='-Drestrict='</tt>.
+More details on C99 compatibility are in the header file
+<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco.h"><tt>nco/src/nco/nco.h</tt></a>.<br>
+</li>
+
+<!-- http://nco.sf.net#bld_netcdf -->
+<a name="bld_netcdf"></a>
+<li><i>Old netCDF libraries:</i>
+NCO versions ≥ 3.0.0 require netCDF versions
+≥ 3.6 to take advantage of the new 64-bit offset file type.
+The library <i>and</i> include directories (e.g., <tt>/usr/lib</tt> and
+<tt>/usr/include</tt>, respectively) for netCDF version ≥ 3.6
+must be on the path searched by the compiler, and must precede the
+locations of any older netCDF installations.
+To build NCO versions ≥ 3.0.0 with older netCDF versions
+< 3.6, simply define the pre-processor token
+<tt>NC_64BIT_OFFSET</tt> to <tt>0</tt> before compiling NCO.
+Do this, e.g., with <tt>CPPFLAGS='-DNC_64BIT_OFFSET=0'</tt> or
+<tt>USR_TKN='-DNC_64BIT_OFFSET=0'</tt> if you use <tt>configure</tt>
+or <tt>bld/Makefile</tt>, respectively.
+Users attempting to build NCO with OPeNDAP versions ≤ 3.6.x may
+need this workaround because OPeNDAP did not fully support netCDF
+version 3.6.x functionality until OPeNDAP versions ≥ 3.7.0.
+(The indicator for this problem is a build error like
+<tt>"nco_fl_utl.c", line 30.20: 1506-045 (S) Undeclared identifier
+NC_64BIT_OFFSET</tt>.)
+All modern NCO versions require netCDF versions ≥ 3.5.0 to
+support <tt>nc_type NC_NAT</tt> in NCO source code.
+NCO versions 3.9.0 and greater (May, 2007) require netCDF versions
+≥ 3.6.0 to resolve the <tt>nc_inq_format()</tt> function.
+</li>
+
+<!-- http://nco.sf.net#bld_ncap -->
+<a name="bld_ncap"></a>
+<li><i><tt>ncap</tt> build hints:</i>
+<tt>ncap</tt> is a sophisticated and somewhat fragile program.
+<tt>ncap</tt> requires <tt>flex</tt> to build correctly.
+AT&T <tt>lex</tt> will not work because it does not understand
+<tt>EOF</tt> rules used in <tt>ncap_lex.l</tt>.
+<tt>bison</tt> version 1.29 (the default version on early
+Mac OS X) is buggy and does not parse <tt>ncap_yacc.y</tt>
+correctly; previous and later <tt>bison</tt>'s work
+correctly.
+<tt>bison</tt> version 1.25 will not build <tt>ncap</tt> on Solaris.
+Please upgrade <tt>bison</tt> to the latest version (e.g., 1.875+)
+before reporting <tt>ncap</tt> build problems.
+If <tt>ncap</tt> keeps you from building NCO, and you do not need
+<tt>ncap</tt>, configure with <tt>--disable-ncap</tt> (and know that
+<tt>ncwa</tt> will fail to build as a result).
+</li>
+
+<!-- http://nco.sf.net#bld_GSL -->
+<a name="bld_gsl"></a><a name="bld_GSL"></a>
+<li><i>Build Hints with GSL:</i><br>
+NCO versions 3.9.6— support automatic building and linking
+for <a href="http://www.gnu.org/software/gsl">GSL</a>
+versions 1.4—.
+Earlier GSL versions are not supported.<br>
+</li>
+
+<!-- http://nco.sf.net#bld_DAP -->
+<a name="bld_dap"></a><a name="bld_DAP"></a><a name="bld_DODS"></a><a name="bld_OPeNDAP"></a>
+<li><i>Build Hints with DAP:</i><br>
+NCO versions 3.9.9— support automatic building and linking
+for DAP supplied from <a href="http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/DAP-Support.html">libnetcdf</a> versions 4.1-beta1 and beyond<br>
+NCO versions 3.1.3— support automatic building and linking
+for <a href="http://opendap.org">OPeNDAP</a> versions 3.6.x and
+GCC versions 4.0+.<br>
+NCO versions 3.0.1—3.1.2 support automatic building and linking
+for <a href="http://opendap.org">OPeNDAP</a> versions 3.5.x and
+GCC versions 3.4+.<br>
+NCO versions 2.8.5—3.0.0 support automatic building and linking
+for <a href="http://opendap.org">OPeNDAP</a> versions 3.4.x and
+GCC versions 3.3+.<br>
+NCO versions ?.?.?—2.8.4 support automatic building and linking
+for <a href="http://opendap.org">DODS</a> versions 3.2.x and
+GCC versions 3.2+.<br>
+No other version combinations are supported.
+</li>
+
+<!-- http://nco.sf.net#bld_nco_c++ -->
+<a name="bld_nco_c++"></a>
+<li><i><tt>libnco_c++</tt> build hints:</i>
+<tt>libnco_c++</tt> requires a good C++ compiler to build correctly.
+Few people need <tt>libnco_c++</tt>, so the workaround is not to build it.
+This is done by configuring with <tt>--disable-nco_cplusplus</tt>.
+</li>
+
+</ul>
+
+<!-- http://nco.sf.net#bld_plt_spc -->
+<a name="bld_plt_spc"></a>
+<ul><b>Platform-Specific Build Hints:</b>
+<!-- http://nco.sf.net#bld_aix -->
+<a name="bld_aix"></a>
+<li><i>AIX build hints:</i>
+NCO versions 2.8.7+ do not build with autotools under AIX when
+<tt>--enable-optimize-*</tt> is selected.
+The workaround is to not use <tt>--enable-optimize-*</tt>.
+NCO versions 2.9.7+ do not build shared libraries with AIX xlc
+compilers because of silly AIX library dependencies activated
+by OpenMP directives.
+The workaround is to configure with <tt>--disable-shared</tt>.
+</li>
+
+<!-- http://nco.sf.net#bld_irix -->
+<a name="bld_irix"></a>
+<li><i>IRIX build hints:</i>
+The most common problem with building on SGI IRIX is an out-of-date toolchain.
+</li>
+
+<!-- http://nco.sf.net#bld_osx -->
+<a name="bld_osx"></a>
+<li><i>Mac OS X build hints:</i>
+Mac OS X users report success building NCO without patches so
+long as they (1) Install the latest version of <tt>bison</tt>,
+(2) Disable shared libraries and (3) Disable extended regular
+expressions. This is done with
+<tt>./configure --disable-regex --disable-shared</tt>
+
+Building NCO with shared libraries on Mac OS X on may be possible.
+To try, first re-build and re-install the netCDF library using
+<tt>CFLAGS=-fno-common</tt>.
+Apparently netCDF, unlike most codes, does not set this automatically.
+Then build NCO normally.
+
+Mac OS X ships with a broken version of the POSIX <tt>cut</tt>
+utility which causes many NCO regression tests to appear to fail.
+In fact the NCO commands succeed, but the <tt>cut</tt> output fails.
+The workaround is not to heed the regression tests, or to install a
+working <tt>cut</tt>, e.g., from the GNU <tt>coreutils</tt> package.
+</li>
+
+<!-- http://nco.sf.net#bld_rhel -->
+<a name="bld_rhel"></a>
+<a name="bld_centos"></a> <!-- http://nco.sf.net#bld_centos -->
+<li><i>RHEL build hints:</i>
+Scripts for generating executables for recent (4.0.x, ~2011) versions of NCO for RedHat Enterprise Linux 5 (RHEL5) and CentOS5 platforms are described <a href="http://sf.net/projects/nco/forums/forum/9830/topic/4089501">here</a>.
+Older information on building x86_64 RPMs is available <a href="http://dust.ess.uci.edu/wangd/s9y">here</a>.
+</li>
+
+<!-- http://nco.sf.net#bld_slr -->
+<a name="bld_slr"></a>
+<li><i>Solaris build hints:</i>
+All recent NCO versions build with autotools on Solaris 2.7—2.9.
+The most common problem with building on Solaris with
+<tt>cc</tt>/<tt>CC</tt> is that <tt>bison</tt> may be out-of-date.
+Install an up-to-date <tt>bison</tt> (e.g., 1.875+).
+Solaris 2.10, i.e., Solaris10, had the audacity to change the
+prototype of the <tt>ctime_r()</tt> function and so does not build
+NCO 3.0.1.
+The fix is to upgrade to the current NCO version.
+</li>
+
+<!-- http://nco.sf.net#bld_sx -->
+<a name="bld_sx"></a>
+<li><i>SX build hints:</i>
+NEC SX does not understand the <tt>S_ISLNK</tt> macro,
+preferring instead the (non-POSIX) <tt>S_IFLNK</tt> macro.
+This macro appears in the file
+<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco_fl_utl.c"><tt>nco_fl_utl.c</tt></a>.
+The patch I wrote for this may be broken.
+Will someone with NEC SX please send us a working patch?
+</li>
+
+<!-- http://nco.sf.net#bld_wnd -->
+<a name="bld_wnd"></a>
+<li><i>Windows build hints:</i>
+Building on Microsoft Windows is possible with Cygwin.
+The resulting executables will behave normally on local files,
+but will not have some (most?) of NCO's network functionality
+(e.g., <tt>scp</tt>, <a href="http://opendap.org">OPeNDAP</a>).
+See the <a href="http://nco.sf.net/nco.html#wnd">User's Guide</a>
+for more details.
+</li>
+
+<!--Qt/MSVC -->
+<li><i>Windows build with Qt/MSVC:</i>
+As of NCO 4.2.0, you may build NCO from source using MSVC and Qt, please see the <a href="nco_qt_msvc.shtml">NCO Qt/MSVC build</a> page.
+</li>
+</ul>
+<hr></p>
+
+</body>
+</html>
diff --git a/doc/debian.txt b/doc/debian.txt
index 6dd0a17..620563d 100644
--- a/doc/debian.txt
+++ b/doc/debian.txt
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/doc/debian.txt,v 1.202 2014/05/01 19:05:39 zender Exp $ -*-text-*-
+# $Header: /cvsroot/nco/nco/doc/debian.txt,v 1.203 2014/05/29 18:36:54 zender Exp $ -*-text-*-
# Purpose: Debian information for NCO netCDF Operators project
# Notes describe procedure to manipulate Debian-specific distribution
@@ -29,19 +29,19 @@ apt-get install dh-make debhelper devscripts fakeroot gnupg debian-policy develo
2. Debian build procedure recommends placing entire package source in
subdirectory of main package.
- For starters, we wish to create .debs of tagged releases, e.g., nco-4.4.4
- First we create a clean source distribution of nco and place it in nco-4.4.4
- Once automated, we will use cvs co -rnco-4_4_4 to get source
+ For starters, we wish to create .debs of tagged releases, e.g., nco-4.4.5
+ First we create a clean source distribution of nco and place it in nco-4.4.5
+ Once automated, we will use cvs co -rnco-4_4_5 to get source
Until we know what is necessary, however, we just copy a snapshot
2.1 Clean all build files from development directory
cd ~/nco;make distclean;cd bld;make clean;cd ~
tar cvzf ./nco/nco.tar.gz ./nco/*
-cd ~/nco;tar xvzf nco.tar.gz;mv nco nco-4.4.4
-/bin/rm nco.tar.gz;tar cvzf nco-4.4.4.tar.gz ./nco-4.4.4/*
-cd ~/nco/nco-4.4.4
-dh_make -e zender at uci.edu -f ../nco-4.4.4.tar.gz
+cd ~/nco;tar xvzf nco.tar.gz;mv nco nco-4.4.5
+/bin/rm nco.tar.gz;tar cvzf nco-4.4.5.tar.gz ./nco-4.4.5/*
+cd ~/nco/nco-4.4.5
+dh_make -e zender at uci.edu -f ../nco-4.4.5.tar.gz
2.2 The preceding steps created template debian files for a .deb,
Those files now reside in ~/nco/debian.
@@ -56,7 +56,7 @@ dh_make -e zender at uci.edu -f ../nco-4.4.4.tar.gz
from previous build
cd ~/nco;/bin/rm *.gz
- cd ~/nco/nco-4.4.4
+ cd ~/nco/nco-4.4.5
dpkg-buildpackage -rfakeroot > foo 2>&1
dpkg-buildpackage -rsudo > foo 2>&1
@@ -85,12 +85,12 @@ patch -p0 < nco_X.Y.Z-3.diff # Patch destination with Debian diff
make tags
# Put cute version-specific string in nco_ctl.c:nco_nmn_get()
# Install correct version numbers before updating Debian
-# tags-query replace 4_4_4 with X_Y_Z+1
-# tags-query replace 4.4.4 with X.Y.Z+1
+# tags-query replace 4_4_5 with X_Y_Z+1
+# tags-query replace 4.4.5 with X.Y.Z+1
# If tags-query replace does not work, be sure to manually change
# versions in configure.ac, debian/files, doc/ANNOUNCE, doc/debian.txt,
# doc/index.shtml, doc/nco.texi, bld/nco_dst.pl, doc/VERSION
- cd ~/nco/debian;dch -b --force-distribution --distribution=unstable -v 4.4.4-1 # Update changelog (-b forces this version number)
+ cd ~/nco/debian;dch -b --force-distribution --distribution=unstable -v 4.4.5-1 # Update changelog (-b forces this version number)
emacs ~/nco/bld/nco.spec # Update changelog
# For unknown reason rules file may lose its executable bit
chmod a+x ~/nco/debian/rules
@@ -98,22 +98,22 @@ patch -p0 < nco_X.Y.Z-3.diff # Patch destination with Debian diff
cd ~/nco;aclocal;autoheader;automake --foreign;autoconf
# Save all files in emacs before tagging
# Tag CVS code after changing files in ~/nco/debian
- cd ~/nco;cvs commit -m "Preparing nco-4.4.4 release";cvs tag -c nco-4_4_4
- ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4_4_4
+ cd ~/nco;cvs commit -m "Preparing nco-4.4.5 release";cvs tag -c nco-4_4_5
+ ${HOME}/nco/bld/nco_dst.pl --dbg=2 --bld --cln nco-4_4_5
# Upload tarball to SF https://sourceforge.net/projects/nco/files
- cd;scp dust.ess.uci.edu:/var/www/html/nco/src/nco-4.4.4.tar.gz .
+ cd;scp dust.ess.uci.edu:/var/www/html/nco/src/nco-4.4.5.tar.gz .
7. Ubuntu PPA
https://help.launchpad.net/Packaging/PPA
-dput NCO nco_4.4.4-2~ppa1_source.changes
+dput NCO nco_4.4.5-2~ppa1_source.changes
sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com
# Location of build diagnostics for mentors to help
-http://dust.ess.uci.edu/nco/src/nco_4.4.4-1.dpkg-buildpackage.txt
-http://dust.ess.uci.edu/nco/src/nco_4.4.4-1.dsc
-http://dust.ess.uci.edu/nco/src/nco_4.4.4-1_i386.changes
-http://dust.ess.uci.edu/nco/src/nco_4.4.4-1_i386.deb
-http://dust.ess.uci.edu/nco/src/nco_4.4.4.orig.tar.gz
+http://dust.ess.uci.edu/nco/src/nco_4.4.5-1.dpkg-buildpackage.txt
+http://dust.ess.uci.edu/nco/src/nco_4.4.5-1.dsc
+http://dust.ess.uci.edu/nco/src/nco_4.4.5-1_i386.changes
+http://dust.ess.uci.edu/nco/src/nco_4.4.5-1_i386.deb
+http://dust.ess.uci.edu/nco/src/nco_4.4.5.orig.tar.gz
# Becoming a Debian developer
http://www.debian.org/devel/join/newmaint
@@ -167,31 +167,31 @@ Matej Vela <vela at debian.org>, Daniel Baumann <daniel at debian.org>, Warren Turkal
# export LD_LIBRARY_PATH=/usr/lib:/lib:/usr/X11R6/lib
# sudo aptitude install antlr bison flex gsl-bin libgsl0-dev libantlr-dev netcdf-bin libnetcdfc7 libnetcdf-dev texinfo libcurl4-gnutls-dev libexpat1-dev libxml2-dev udunits-bin libudunits2-0 libudunits2-dev
cd ~/nco;cvc
-sudo /bin/rm -rf ${DATA}/nco-4.4.4 ${DATA}/nco_4.4.4* ${DATA}/debian # Cleanup last build. sudo necessary for removal because dpkg-buildpackage uses sudo?
-# cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_4-1 -d nco-4.4.4 nco # Export based on tag
-cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -D "1 second ago" -d nco-4.4.4 nco # Export most recent
-tar cvzf ./nco_4.4.4.orig.tar.gz --exclude='nco-4.4.4/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.4
-/bin/rm -rf ${DATA}/nco-4.4.4 # Remove cvs-exported directory
-tar xvzf ./nco_4.4.4.orig.tar.gz # Untar to get directory without excluded files
-mkdir -p ${DATA}/nco-4.4.4/debian/source;cd ~/nco/debian;/bin/cp changelog compat control convert copyright doc-base files info rules ${DATA}/nco-4.4.4/debian;cd ~/nco/debian/source;/bin/cp format ${DATA}/nco-4.4.4/debian/source # Replace debian directory with _CURRENT_ (main trunk) settings
+sudo /bin/rm -rf ${DATA}/nco-4.4.5 ${DATA}/nco_4.4.5* ${DATA}/debian # Cleanup last build. sudo necessary for removal because dpkg-buildpackage uses sudo?
+# cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_5-1 -d nco-4.4.5 nco # Export based on tag
+cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -D "1 second ago" -d nco-4.4.5 nco # Export most recent
+tar cvzf ./nco_4.4.5.orig.tar.gz --exclude='nco-4.4.5/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.5
+/bin/rm -rf ${DATA}/nco-4.4.5 # Remove cvs-exported directory
+tar xvzf ./nco_4.4.5.orig.tar.gz # Untar to get directory without excluded files
+mkdir -p ${DATA}/nco-4.4.5/debian/source;cd ~/nco/debian;/bin/cp changelog compat control convert copyright doc-base files info rules ${DATA}/nco-4.4.5/debian;cd ~/nco/debian/source;/bin/cp format ${DATA}/nco-4.4.5/debian/source # Replace debian directory with _CURRENT_ (main trunk) settings
#export DEB_BUILD_OPTIONS='disable-dap-netcdf disable-netcdf4 disable-udunits2'; # Disable optional packages based on available Debian support
-#cd ${DATA}/nco-4.4.4;dpkg-buildpackage -rsudo -uc -us > ~/foo.nco 2>&1 # -uc -us: Do not sign changes or source files
-#cd ${DATA}/nco-4.4.4;dpkg-buildpackage -rsudo -sa > ~/foo.nco 2>&1 # -sa: Include _orig.tar.gz in .changes
-cd ${DATA}/nco-4.4.4;dpkg-buildpackage -rsudo > ~/foo.nco 2>&1
+#cd ${DATA}/nco-4.4.5;dpkg-buildpackage -rsudo -uc -us > ~/foo.nco 2>&1 # -uc -us: Do not sign changes or source files
+#cd ${DATA}/nco-4.4.5;dpkg-buildpackage -rsudo -sa > ~/foo.nco 2>&1 # -sa: Include _orig.tar.gz in .changes
+cd ${DATA}/nco-4.4.5;dpkg-buildpackage -rsudo > ~/foo.nco 2>&1
sudo dpkg --remove nco
-sudo dpkg --install ${DATA}/nco_4.4.4-1_*.deb
+sudo dpkg --install ${DATA}/nco_4.4.5-1_*.deb
cd ~/nco/bld;MY_BIN_DIR=/usr/bin ../bm/nco_bm.pl --regress
# http://lintian.debian.org/full/zender@uci.edu.html
-lintian ${DATA}/nco_4.4.4-1_*.deb
-ls -l ${DATA}/nco_4.4.4*
+lintian ${DATA}/nco_4.4.5-1_*.deb
+ls -l ${DATA}/nco_4.4.5*
m ~/foo.nco
# Upload Ubuntu (rather than Debian) packages to websites
-scp ${DATA}/nco_4.4.4* dust.ess.uci.edu:/var/www/html/nco/src
-scp ${DATA}/nco_4.4.4* zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
+scp ${DATA}/nco_4.4.5* dust.ess.uci.edu:/var/www/html/nco/src
+scp ${DATA}/nco_4.4.5* zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
# NB: Make sure RPMs build before uploading to debian, since changing
# Debian versions is a PITA
# NB: Only upload pbuilder Debian Sid (not personal Ubuntu) .deb builds to Debian mentors
-# cd ${DATA};dupload -t mentors nco_4.4.4-1_*.changes
+# cd ${DATA};dupload -t mentors nco_4.4.5-1_*.changes
bsrc # Reset shell environment for regular development
# New build system #2
@@ -205,52 +205,52 @@ DIST=sid sudo pbuilder update # Update chroot before building package in it
# dget http://ftp.debian.org/debian/pool/main/n/nco/nco_3.9.0-1.dsc
# dget http://ftp.debian.org/debian/pool/main/n/netcdf/netcdf_3.6.1-1.dsc
# apt-get source nco # Get package source
-sudo /bin/rm /var/cache/pbuilder/result/nco_4.4.4* # Cleanup prior build
+sudo /bin/rm /var/cache/pbuilder/result/nco_4.4.5* # Cleanup prior build
# To pass DEB_BUILD_OPTIONS to pbuilder while using sudo, one must first
# modify sudoers with visudo to prevent sudo from resetting environment
#export DEB_BUILD_OPTIONS='disable-dap-netcdf disable-netcdf4 disable-udunits2'; # Disable optional packages based on available Debian support
-cd ${DATA};DIST=sid sudo pbuilder build nco_4.4.4-1.dsc > ~/foo.nco.pbuilder 2>&1
-cd /var/cache/pbuilder/result;debsign -k6F635D10 nco_4.4.4-1_*.changes
-lintian /var/cache/pbuilder/result/nco_4.4.4-1_*.deb
+cd ${DATA};DIST=sid sudo pbuilder build nco_4.4.5-1.dsc > ~/foo.nco.pbuilder 2>&1
+cd /var/cache/pbuilder/result;debsign -k6F635D10 nco_4.4.5-1_*.changes
+lintian /var/cache/pbuilder/result/nco_4.4.5-1_*.deb
sudo dpkg --remove nco
-sudo dpkg --install /var/cache/pbuilder/result/nco_4.4.4-1_*.deb
+sudo dpkg --install /var/cache/pbuilder/result/nco_4.4.5-1_*.deb
cd ~/nco/bld;MY_BIN_DIR=/usr/bin ../bm/nco_bm.pl --regress
# NB: Upload pbuilder Debian Sid packages to Debian mentors, but not
# to personal or NCO websites since most people use Ubuntu not Debian
# NB: Debian versions are a PITA, ensure RPMs build before uploading to Debian
-cd /var/cache/pbuilder/result;dupload -t mentors nco_4.4.4-1_*.changes
+cd /var/cache/pbuilder/result;dupload -t mentors nco_4.4.5-1_*.changes
# RPM builds as root
export rpm_root='/usr/src/redhat'
# export sudo_sng='' # sudo not-necessary when builing in user directories
export sudo_sng='sudo' # sudo necessary when building in system directories
cd ~/nco;cvc;cvu
-/bin/rm -rf ${DATA}/nco-4.4.4 ${DATA}/nco-4.4.4* # Cleanup last build
+/bin/rm -rf ${DATA}/nco-4.4.5 ${DATA}/nco-4.4.5* # Cleanup last build
${sudo_sng} /bin/rm -r -f \
-${rpm_root}/BUILD/nco-4.4.4 \
-${rpm_root}/RPMS/i386/nco-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-debuginfo-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-devel-4.4.4-?.i386.rpm \
-${rpm_root}/SOURCES/nco-4.4.4.tar.gz \
-${rpm_root}/SPECS/nco-4.4.4.spec \
-${rpm_root}/SRPMS/nco-4.4.4-?.src.rpm
-cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_4-1 -d nco-4.4.4 nco # Export based on tag
-${sudo_sng} ln -s ${HOME}/nco/bld/nco.spec ${rpm_root}/SPECS/nco-4.4.4.spec
-tar cvzf ./nco-4.4.4.tar.gz --exclude='nco-4.4.4/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.4
-${sudo_sng} /bin/cp ${DATA}/nco-4.4.4.tar.gz ${rpm_root}/SOURCES
+${rpm_root}/BUILD/nco-4.4.5 \
+${rpm_root}/RPMS/i386/nco-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-debuginfo-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-devel-4.4.5-?.i386.rpm \
+${rpm_root}/SOURCES/nco-4.4.5.tar.gz \
+${rpm_root}/SPECS/nco-4.4.5.spec \
+${rpm_root}/SRPMS/nco-4.4.5-?.src.rpm
+cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_5-1 -d nco-4.4.5 nco # Export based on tag
+${sudo_sng} ln -s ${HOME}/nco/bld/nco.spec ${rpm_root}/SPECS/nco-4.4.5.spec
+tar cvzf ./nco-4.4.5.tar.gz --exclude='nco-4.4.5/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.5
+${sudo_sng} /bin/cp ${DATA}/nco-4.4.5.tar.gz ${rpm_root}/SOURCES
cd ${rpm_root}/SPECS
-${sudo_sng} rpmbuild -ba --sign nco-4.4.4.spec > ~/foo.nco 2>&1
+${sudo_sng} rpmbuild -ba --sign nco-4.4.5.spec > ~/foo.nco 2>&1
scp \
-${rpm_root}/RPMS/i386/nco-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-debuginfo-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-devel-4.4.4-?.i386.rpm \
-${rpm_root}/SRPMS/nco-4.4.4-?.src.rpm \
+${rpm_root}/RPMS/i386/nco-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-debuginfo-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-devel-4.4.5-?.i386.rpm \
+${rpm_root}/SRPMS/nco-4.4.5-?.src.rpm \
dust.ess.uci.edu:/var/www/html/nco/src
scp \
-${rpm_root}/RPMS/i386/nco-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-debuginfo-4.4.4-?.i386.rpm \
-${rpm_root}/RPMS/i386/nco-devel-4.4.4-?.i386.rpm \
-${rpm_root}/SRPMS/nco-4.4.4-?.src.rpm \
+${rpm_root}/RPMS/i386/nco-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-debuginfo-4.4.5-?.i386.rpm \
+${rpm_root}/RPMS/i386/nco-devel-4.4.5-?.i386.rpm \
+${rpm_root}/SRPMS/nco-4.4.5-?.src.rpm \
zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
# RPM builds as user
@@ -259,33 +259,33 @@ zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
export rpm_root="${DATA}/rpm/nco"
#cd ~/nco;cvc;cvu # This risks committing unwanted *.[ch]pp files
mkdir -p ${DATA}/rpm/nco/TMP ${DATA}/rpm/nco/BUILD
-/bin/rm -rf ${DATA}/nco-4.4.4 ${DATA}/nco-4.4.4* # Cleanup last build
+/bin/rm -rf ${DATA}/nco-4.4.5 ${DATA}/nco-4.4.5* # Cleanup last build
/bin/rm -r -f \
-${rpm_root}/nco-4.4.4-?.src.rpm \
-${rpm_root}/nco-4.4.4.spec \
-${rpm_root}/nco-4.4.4.tar.gz \
-${rpm_root}/*/nco-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-debuginfo-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-devel-4.4.4-?.*.rpm
-# cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_4-1 -d nco-4.4.4 nco # Export based on tag
-cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -D "1 second ago" -dnco-4.4.4 nco # Export most recent and build as 4.4.4-1
-tar cvzf ./nco-4.4.4.tar.gz --exclude='nco-4.4.4/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.4
-/bin/cp ${DATA}/nco-4.4.4.tar.gz ${rpm_root}
+${rpm_root}/nco-4.4.5-?.src.rpm \
+${rpm_root}/nco-4.4.5.spec \
+${rpm_root}/nco-4.4.5.tar.gz \
+${rpm_root}/*/nco-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-debuginfo-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-devel-4.4.5-?.*.rpm
+# cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -r nco-4_4_5-1 -d nco-4.4.5 nco # Export based on tag
+cd ${DATA};cvs -d zender at nco.cvs.sf.net:/cvsroot/nco export -kkv -D "1 second ago" -dnco-4.4.5 nco # Export most recent and build as 4.4.5-1
+tar cvzf ./nco-4.4.5.tar.gz --exclude='nco-4.4.5/debian*' --exclude='.cvsignore' --exclude='ncap_lex.c' --exclude='ncap_yacc.[ch]' ./nco-4.4.5
+/bin/cp ${DATA}/nco-4.4.5.tar.gz ${rpm_root}
ln -s ${HOME}/nco/bld/nco.spec ${rpm_root}/nco.spec
cd ${rpm_root}
rpmbuild -ba --sign nco.spec > ~/foo.nco 2>&1
-rpmlint ${rpm_root}/*/nco-4.4.4-?.*.rpm
+rpmlint ${rpm_root}/*/nco-4.4.5-?.*.rpm
sudo yum remove nco
-sudo yum install ${rpm_root}/*/nco-4.4.4-?.*.rpm
+sudo yum install ${rpm_root}/*/nco-4.4.5-?.*.rpm
scp \
-${rpm_root}/*/nco-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-debuginfo-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-devel-4.4.4-?.*.rpm \
-${rpm_root}/nco-4.4.4-?.*.src.rpm \
+${rpm_root}/*/nco-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-debuginfo-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-devel-4.4.5-?.*.rpm \
+${rpm_root}/nco-4.4.5-?.*.src.rpm \
dust.ess.uci.edu:/var/www/html/nco/src
scp \
-${rpm_root}/*/nco-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-debuginfo-4.4.4-?.*.rpm \
-${rpm_root}/*/nco-devel-4.4.4-?.*.rpm \
-${rpm_root}/nco-4.4.4-?.*.src.rpm \
+${rpm_root}/*/nco-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-debuginfo-4.4.5-?.*.rpm \
+${rpm_root}/*/nco-devel-4.4.5-?.*.rpm \
+${rpm_root}/nco-4.4.5-?.*.src.rpm \
zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
diff --git a/doc/endorsements.txt b/doc/endorsements.txt
new file mode 100644
index 0000000..b13c6d3
--- /dev/null
+++ b/doc/endorsements.txt
@@ -0,0 +1,151 @@
+Received fxm:
+
+************************************************************************
+Received 20140613:
+
+NCO benefits my research in dynamic global vegetation models and
+climate change research by allowing me to easily modify and analyze
+climate data and vegetation simulation data.
+
+--
+John B. Kim
+PNW Research Station & WWETAC, US Forest Service
+jbkim at fs.fed.us 541-750-7287 (o) 541-286-5546 (m)
+
+************************************************************************
+Received 20120720:
+
+I installed NCO in Windows 7 and have crosschequed the results of ncra
+with ArcGIS, and they match perfectly. NCO Works like a champ. it
+takes only a fraction of a second to average over 10 million records
+(argis takes over 10 minutes). I am curious how can this be even
+possible but what it matters is that the results are correct.
+Thanks,
+Camilo Mora
+************************************************************************
+Received 20110325:
+
+Dear Prof. Zender,
+
+I am composing this email to express my strongest endorsement for the
+NCO software and its development. I am an assistant professor in
+Department of Atmospheric, Oceanic, and Space Sciences at the
+University of Michigan. My research area is in understanding various
+issues associated with radiative transfer, water vapor, clouds, and
+their interactions via diagnosis analysis of observations and GCM
+outputs. I have been using NCO operators since 2006. As my group and I
+have to constantly deal with large amount of data sets of reanalysis,
+GCM simualtions, and satellite data products, we benefit enormously
+from using NCO. It saves a great amount of our time in programming and
+preprocessing data, and it greatly simplifies such coding tasks. For
+our day-to-day research work, NCO software is as important as Matlab,
+Fortran, and Perl. It has already become an inseparable and critical
+component in data analysis and our research. And I know many
+researchers share the same view with me regarding the technical
+importance of NCO. Therefore, I endorse the development of NCO without
+any reservation.
+
+ Sincerely,
+
+ Xianglei Huang
+
+
+-------------------------------------------------------------------
+Xianglei Huang
+Assistant Professor
+Department of Atmospheric, Oceanic, and Space Sciences
+College of Engineering, University of Michigan
+2455 Hayward St, Ann Arbor, MI 48109
+Phone: 734-936-0491 FAX: 734-936-0503
+xianglei at umich.edu
+-------------------------------------------------------------------
+
+************************************************************************
+Received 20040809:
+
+Prof Zender,
+
+I'm writing in support of the recent NSF proposal [1] to improve the
+"NCO" suite of NetCDF/HDF data analysis tools. Our group:
+
+ http://paoc.mit.edu/cmi/
+ http://mitgcm.org/
+
+and many of our collaborators are steadily moving toward the use of both
+hierarchical data formats (such as NetCDF and HDF) and multi-terabyte
+data sets. Under these circumstances, tools such as NCO become
+increasingly useful and important for our work.
+
+I am impressed with the capabilities offered by current NCO releases and
+would very much like to see it extended (per the above proposal) to take
+fuller advantage of parallel systems. I believe that such a free, open,
+and extensible set of parallel analysis tools would be an important
+resource for the GFD community. While nearly all ocean and atmospheric
+models have evolved to take advantage of parallel execution, it seems
+that many of the data analysis tools have lagged. Thus, for many
+researchers, it is the pre- and post-processing steps that consume the
+most time and can be the greatest barrier to experimental progress.
+
+Thus, I look forward to parallel versions of the NCO tools that will
+take better advantage of both our SMP (threaded) and cluster (MPI-based)
+computing resources.
+
+Best regards,
+Ed Hill
+
+ [1] SEI(GEO): Scientific Data Operators Optimized for
+ Distributed Interactive and Batch Analysis of Tera-Scale
+ Geophysical Data, Dr. Charles S. Zender, Department of
+ Earth System Science, University of California at Irvine
+
+
+-- Edward H. Hill III, PhD office: MIT Dept. of EAPS; Rm 54-1424; 77
+ Massachusetts Ave. Cambridge, MA 02139-4307 emails: eh3 at mit.edu
+ ed at eh3.com URLs: http://web.mit.edu/eh3/ http://eh3.com/ phone:
+ 617-253-0098 fax: 617-253-4464
+
+************************************************************************
+Received 20040611:
+
+The best netCDF processing software I have ever used. NCO is
+indispensible in my work.
+Good luck!
+
+Haijun
+
+--------------------------------------------
+Haijun Yang, Associate Professor
+Department of Atmospheric Science
+School of Physics, Peking University
+209 Chengfu Road, Beijing, China 100871
+Tel: 86-10-62767436
+Fax: 86-10-62751094
+Email: hjyang at pku.edu.cn
+--------------------------------------------
+************************************************************************
+Received 20040430:
+
+I find the NCO operators to be indispensable in my work, and
+many of my colleagues would say the same. Their usefulness
+is perhaps best captured by the surprise of some people to whom
+I have introduced NCO when they learned that it is a separate
+entity from the NETCDF library.
+
+The developers of NCO have always replied promptly to my help
+requests and have on occasion even added new functionality
+that I had requested.
+
+In my opinion, the advantages of NCO compared to mathematically more
+comprehensive packages reading NETCDF files are that it is fast, very
+concise, free of charge, runs on almost any platform, and can be
+easily integrated into shell or other kinds of scripts. And with
+the evolution of the ncap utility, the capabilities of NCO are
+becoming sufficient for tasks of greater numerical complexity.
+
+------------------------------------------------------------
+Dr. Maxwell Kelley
+Laboratoire des Sciences du Climat et de l'Environnement
+L'Orme des Merisiers CEA Saclay
+91191 Gif sur Yvette cedex mkelley at lsce.saclay.cea.fr
+France +33 1 69 08 27 02
+------------------------------------------------------------
diff --git a/doc/highlights_old.shtml b/doc/highlights_old.shtml
new file mode 100644
index 0000000..a99af41
--- /dev/null
+++ b/doc/highlights_old.shtml
@@ -0,0 +1,239 @@
+<!-- $Header: /cvsroot/nco/nco/doc/highlights_old.shtml,v 1.1 2014/06/13 19:43:50 zender Exp $
+
+Purpose: Highlights archive
+
+URL:
+http://nco.sf.net/highlights_old.shtml
+http://dust.ess.uci.edu/nco/highlights_old.shtml
+file:///home/zender/nco/doc/highlights_old.shtml
+
+Usage:
+/usr/bin/scp ~/nco/doc/highlights_old.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+scp -p ~/nco/doc/highlights_old.shtml dust.ess.uci.edu:/var/www/html/nco
+-->
+
+<!doctype html public "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+ <title>NCO Homepage</title>
+ <meta name="GENERATOR" content="Mozilla/3.04Gold (X11; I; Linux 2.0.0 i686) [Netscape]">
+ <meta name="Author" content="Charles S. Zender">
+ <meta name="Keywords" content="NCO Homepage, netCDF, netCDF operator, GCM, HDF, scientific data">
+</head>
+<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
+
+<dt><a name="News"></a></dt>
+<h2>Release Highlights from 2000–2012 (versions 1.1.47–4.2.3)</h2>
+
+<li><b>NCO 4.2.3</b>:
+Group Path Editing (GPE);
+<tt>ncecat</tt> <a href="#bug_ncecat_nintap">bugfix</a></li>
+<li><b>NCO 4.2.2</b>:
+<tt>ncks</tt>, <tt>ncecat</tt> support groups;
+<tt>--hdr_pad</tt> all operators;
+<tt>ncks</tt> prints underscores;
+fixes to <tt>--[mk/fix]_rec_dmn</tt>;
+<tt>ncpdq</tt> fix;
+<tt>ncwa</tt> on Windows;</li>
+<li><b>NCO 4.2.1</b>:
+<tt>--ram_all</tt> for <a href="http://nco.sf.net/nco.html#diskless">diskless files</a>;
+<tt>--no_tmp_fl</tt> to <a href="http://nco.sf.net/nco.html#no_tmp_fl">bypass</a> temporary files;
+Negative indices for <a href="http://nco.sf.net/nco.html#hyp">hyperslabs</a>;
+<tt>ncpdq</tt> unpacks coordinate variables;
+<tt>ncra/ncrcat</tt> SSC/MRO <a href="http://nco.sf.net/nco.html#ssc">options</a>;
+<tt>ncra/ncrcat</tt> rebase <a href="http://nco.sf.net/nco.html#rbs">bounds</a>;</li>
+<li><b>NCO 4.2.0</b>:
+<tt>ncecat</tt> "fixes" auxiliary coordinates and bounds;
+<tt>ncks</tt> uses <tt>nc__open</tt>, format <tt>NC_INT</tt> with <tt>%i</tt>;
+<tt>ncra -y ttl</tt> fix;
+<tt>ncrcat</tt> UDUnits fix;
+<tt>ncwa</tt> and <tt>ncap2</tt> limited NaN support;
+Microsoft Visual Studio support;</li>
+<li><b>NCO 4.1.0</b>:
+MD5 digests;
+<tt>ncap2</tt> sorts & maps;
+<tt>ncks</tt> MM3 <a href="#bug_mm3">workaround</a>;
+<tt>ncrename/ncatted</tt> chmods;
+<tt>ncatted</tt> NaN support</li>
+<li><b>NCO 4.0.9</b>:
+Fix over-zealous <tt>ncap2</tt> packing;
+Fix <tt>nces -y ttl</tt>;
+Fix/improve <tt>ncap2 print, array()</tt>;
+Warn when appending variables of suspicious record length;
+Warn when <tt>NC_MAX_ATTRS</tt> exceeded</li>
+<li><b>NCO 4.0.8</b>:
+Support <a href="http://nco.sf.net/nco.html#hpss">HPSS</a>;
+Workaround netCDF <tt>NOFILL</tt> <a href="#bug_nofill">bug</a> (<i>upgrade recommended</i>);
+Support CF <tt>bounds</tt>;
+CF <tt>noleap</tt> not <tt>no_leap</tt>;
+Fix <tt>ncatted</tt> overwrite-mode;
+Fix <tt>NC_BYTE</tt> printing</li>
+<li><b>NCO 4.0.7</b>:
+Fix degenerate hyperslab <a href="#bug_hyp_dgn">bug</a> (<i>upgrade recommended</i>)</li>
+<li><b>NCO 4.0.6</b>:
+<tt>clang</tt>-compliance;
+Fix <tt>ncra</tt> YYYYMMDD-<tt>date</tt> <a href="#bug_ncra_cf_YYYYMMDD_date">bug</a>;
+Extract all associated coordinates;
+Tighten <tt>ncbo</tt> warnings;
+<tt>ncpdq</tt> warns when _FillValue outside packing range</li>
+<li><b>NCO 4.0.5</b>:
+Fix <tt>ncks</tt> <a href="#bug_ncks_nc4_nc4_hyp_fix">hyperslabbing bug</a>;
+Fix <tt>ncra</tt> <a href="#bug_ncra_cf_crd_rec_crd">CF "coordinate" bug</a></li>
+<li><b>NCO 4.0.4</b>:
+Chunking in all operators; preserve deflation; <tt>ncks</tt> print formatting;
+Fix <tt>ncrename</tt> <a href="#bug_ncrename_dot">bug</a>;
+Do not pack coordinate variables</li>
+<li><b>NCO 4.0.3</b>:
+Fix <tt>configure</tt> for ncap2, netCDF4, UDUnits2, netCDF-DAP;
+Fix <tt>ncbo</tt> <a href="#bug_ncbo_rfr">bug</a> under AIX xlC;
+Fix <tt>ncra</tt> <a href="#bug_ncra_date">bug</a> for some CF-compliant dates.</li>
+<li><b>NCO 4.0.2</b>:
+Consistent deflation, chunking with <tt>netCDF4_classic</tt>;
+Fix <tt>ncap2</tt> RAM vars, 1-D arrays;
+Fix <tt>ncatted</tt> appending <tt>NUL</tt>s.</li>
+<li><b>NCO 4.0.1</b>:
+Easily create/remove record dimensions with <tt>ncks --mk_rec_dmn</tt>, <tt>--fix_rec_dmn</tt>;</li>
+<li><b>NCO 4.0.0</b>:
+Bilinear interpolation, GSL fitting;
+Chunking improvements;
+Better support CF <tt>calendar</tt> and <tt>coordinate</tt> attributes</li>
+<li><b>NCO 3.9.9</b>:
+netCDF4 chunking and <tt>NC_STRING</tt> support;
+GSL statistics, interpolation functions;
+UDUnits2 <tt>time-since</tt> support;
+<tt>ncrcat</tt> re-basing</li>
+<li><b>NCO 3.9.8</b>:
+<tt>ncap2</tt> supports <tt>sort()</tt>, <tt>array()</tt>;
+better DAP/libnetcdf and UDUnits2 builds;
+GSL distribution/RNG functions</li>
+<li><b>NCO 3.9.7</b>:
+Improve GSL-build support;
+<tt>ncap2</tt> threading improvements;
+<tt>ncks --no_dmn_var_nm</tt> printing</li>
+<li><b>NCO 3.9.6</b>:
+Fix OpenMP MSA <a href="#bug_thr_msa">bug</a> (<i>upgrade highly recommended</i>);
+Memory management to improve threading;
+<tt>ncatted</tt> workaround for netCDF4 <tt>_FillValue</tt>;
+disable OpenMP with netCDF4/HDF;
+no math on type <tt>NC_CHAR</tt>;
+<tt>ncap2</tt> <a href="http://nco.sf.net/nco.html#ncap2">documentation</a>,
+better missing value propagation,
+<tt>#include</tt> files,
+<a href="http://nco.sf.net/nco.html#gsl">GSL</a> math functions</li>
+<li><b>NCO 3.9.5</b>:
+Multi-slabbing (MSA) and <tt>-X</tt> everywhere;
+<tt>ncecat -M</tt>;
+netCDF4-enabled builds on Cygwin;
+<tt>ncap2</tt> builds on Solaris</li>
+<li><b>NCO 3.9.4</b>:
+File consanguinity;
+<tt>ncks</tt>: CF auxiliary coords, LZ stats;
+<tt>ncap2</tt>: masks, index arrays, print attributes, OpenMP, <tt>atan2()</tt>, <tt>pow()</tt></li>
+<li><b>NCO 3.9.3</b>:
+SWAMP release;
+<tt>ncecat -u</tt>;
+<tt>wget</tt> URLs;
+GCC 4.2;
+<tt>ncap2</tt> OpenMP</li>
+<li><b>NCO 3.9.2</b>:
+<tt>_FillValue</tt> supplants <tt>missing_value</tt>;
+<tt>UDUnits2 support</tt>;
+<tt>ncap2</tt> type-conversion support and printing;
+netCDF4 <tt>configure</tt> fixes;
+Change licenses to GPL3 and FDL1.2</li>
+<li><b>NCO 3.9.1</b>:
+<a href="http://nco.sf.net/nco.html#deflate">Support</a> lossless netCDF4/HDF deflation;
+Improve Intel compiler support;
+<tt>ncap2</tt> for/while loops;
+various and sundry build fixes</li>
+<li><b>NCO 3.9.0</b>:
+<a href="http://nco.sf.net/nco.html#nco4">Support netCDF4</a> types (<tt>ubyte</tt>, <tt>ushort</tt>, <tt>uint</tt>, <tt>int64</tt>, and <tt>uint64</tt>);
+Control <tt>ncks</tt> metadata <a href="http://nco.sf.net/nco.html#prn">copying</a>;
+Fix <tt>ncbo</tt> packed valued <a href="#bug_ncbo_pck">bug</a> (<i>upgrade recommended</i>);
+Improve IRIX 6.5 support</li>
+<li><b>NCO 3.2.0</b>: More forgiving exclusion list (<tt>-x -v <i>var_nm</i></tt>) <a href="http://nco.sf.net/nco.html#xcl">handling</a>; Fix <tt>rmssdn</tt> normalization; Support Mac OS X on Intel; Documentation bugfixes</li>
+<li><b>NCO 3.1.9</b>: <tt>ncap2</tt> in RPM packages; Quieter output; AIX <tt>configure</tt> supports <tt>ncap2</tt>; Update to DAP for netCDF 3.6.2; Fix <tt>nc[erw]a</tt> for coordinate min/max/ttl; <tt>ncecat</tt> allows files to differ in record dimension size</li>
+<li><b>NCO 3.1.8</b>: Support <tt>_FillValue</tt> with compile-time switch; Debian package synchronized, includes <tt>ncap2</tt></li>
+<li><b>NCO 3.1.7</b>: <tt>ncap2</tt> “double-parsing”, array initialization, supercedes <tt>ncap</tt></li>
+<li><b>NCO 3.1.6</b>: Support <a href="http://nco.sf.net/nco.html#srd">stride</a> in all hyperslabbing operators; change more WARNINGs to INFOs</li>
+<li><b>NCO 3.1.5</b>: New <tt>ncap2</tt> array and hyperslab features; change some WARNINGs to INFOs, add Pathscale and update PGI and Intel compiler support</li>
+<li><b>NCO 3.1.4</b>: Fix <tt>ncbo</tt> memory problem; report timer results</li>
+<li><b>NCO 3.1.3</b>: <tt>ncap2</tt> automatically <a href="http://nco.sf.net/nco.html#att_prp">propagates</a> attributes to new/derived variables; NCO handles record variables with zero records; <a href="http://nco.sf.net/nco.html#cnv_CF_crd">support</a> CF <tt>coordinates</tt> convention; <tt>ncwa -b</tt> <a href="http://nco.sf.net/nco.html#ncwa">retains</a> degenerate dimensions; build fixes for Cray T3E, Solaris, Cygwin.</li>
+<li><b>NCO 3.1.2</b>: <tt>ncap2</tt> control structures (conditionals, loops, etc.); keep non-processed data <a href="bug_pack_fix">packed</a> in output file; binary operators <tt>ncbo</tt> and <tt>ncflint</tt> work when only one variable has <tt>missing_value</tt> attribute; change <tt>ncra</tt> and <tt>nces</tt> to always average coordinate variables</li>
+<li><b>NCO 3.1.1</b>: NCO builds (again) with C++ compilers; ncap2 development code; server-side extensions</li>
+<li><b>NCO 3.1.0</b>: MPI operators are bug-free; fix <t>./configure</t> for MPI and netCDF4; MRV algorithm speeds up <tt>ncwa</tt> 5—10 times; <tt>ncap</tt> random number generator <tt>rnd_nbr()</tt></li>
+<li><b>NCO 3.0.3</b>: Eliminate all critical read regions (accelerates all SMP operators); builds with netCDF4 alpha; read <t>NETCDF4_CLASSIC</t> (i.e., HDF) files automatically; write <t>NETCDF4</t> files <a href="http://nco.sf.net/nco.html#netcdf4">on request</a>; <a href="http://nco.sf.net#BM">benchmark results</a> quantify parallelism.</li>
+<li><b>NCO 3.0.2</b>: Fewer critical read regions; all known memory leaks plugged; better Intel compiler support; <tt>SFTP</tt> protocol support; FTP protocol supports <tt>.netrc</tt>-based passwords; better model grid-property-awareness (e.g., <tt>lat_bnds</tt>); <tt>ncatted</tt> <tt>ncks</tt>, <tt>ncrename</tt> support metadata header padding with <tt>--hdr</tt>; <tt>ncbo</tt> supports heterogeneous variable ordering; <tt>ncatted</tt> bugfix</li>
+ <li><b>NCO 3.0.1</b>: benchmarks; <tt>ncks</tt> printing tweaks; memory cleanup; <tt>ncap</tt> double-parse speedup and <a href="bug_ncap_cmt">exponentiation bugfix</a>; thread operators by default</li>
+ <li><b>NCO 3.0.0</b>: New <tt>ncks -P</tt> print switch; <tt>ncap</tt> optimizations; <tt>-Z</tt> option supports 64-bit offsets (requires netCDF 3.6); NEC SX build improvements; support GCC 3.4.X; <tt>nco_put_vara()</tt> overloads in <tt>libnco_c++</tt></li>
+<li><b>NCO 2.9.9</b>: <tt>ncpdq</tt> packs/unpacks entire files; <tt>ncbo</tt> is threaded</li>
+<li><b>NCO 2.9.8</b>: <a href="./nco.html#ncpdq"><tt>ncpdq</tt></a> released; <tt>ncwa --msk_sng</tt> consolidated mask switch; C99 compiler required</li>
+<li><b>NCO 2.9.7</b>: Read input file lists from <tt>stdin</tt>; write <tt>nco_input_file_list</tt> attributes; add <tt>nco_put_att<int,short,long></tt> functions to libnco_c++; large file support (LFS); write <tt>nco_openmp_thread_number</tt> attribute</li>
+<li><b>NCO 2.9.6</b>: Support <tt>-o fl_out</tt> syntax; 64-bit ABI for x86_64; <a href="http://www.debian.org">Debian</a> builds libnco_c++</li>
+<li><b>NCO 2.9.5</b>: <tt>ncflint</tt> handles <tt>missing_value</tt> data better, is commutative when weights are equal</li>
+<li><b>NCO 2.9.4</b>: <tt>ncecat</tt> works on pure scalar files; change to <tt>cvs.sf.net</tt>; AIX GCC builds</li>
+<li><b>NCO 2.9.3</b>: <tt>ncra</tt> and <tt>nces</tt> now <a name="bug_mss_val_zro_ncra">work correctly</a> when <tt>missing_value</tt> equals zero or any intermediate sums</li>
+<li><b>NCO 2.9.2</b>: <tt>ncap</tt> <tt>S/V</tt>, <tt>S%V</tt>, and <tt>S^V</tt> <a href="#bug_ncap_cmt">operations fixed</a> (<tt>S</tt> = scalar, <tt>V</tt> = variable)</li>
+<li><b>NCO 2.9.1</b>: <tt>ncwa</tt> works again on packed <tt>NC_FLOAT</tt> data (<a href="#bug_pck_ncwa">broke when?</a>)</li>
+<li><b>NCO 2.9.0</b>: Complete <tt>ncap</tt> modulo operator (<tt>V%S</tt>) and generic exponentiation (<tt>V^S</tt>), scalar divided by variable (<tt>S/V</tt>); workaround stack memory problem with GCC extensions; fix <tt>make check</tt></li>
+<li><b>NCO 2.8.8</b>: <tt>--enable-[optimize/debug]-custom</tt> options for GCC work again (broke in 2.8.6)</li>
+<li><b>NCO 2.8.7</b>: <tt>ncap</tt> packing works again (<a href="#bug_pck">broke in 2.8.4</a>); Cygwin builds work again</li>
+<li><b>NCO 2.8.6</b>: AIX and IRIX builds work again; custom GCC builds with <tt>-Werror</tt></li>
+<li><b>NCO 2.8.5</b>: Solaris <tt>make install</tt> works; <tt>ncap</tt> changes attribute values correctly; <a href="#bld_DODS">Support DODS 3.4+, deprecate 3.3-</a>; add <tt>--enable-[optimize/debug]-custom</tt> options to <tt>./configure</tt></li>
+<li><b>NCO 2.8.4</b>: Index-based hyperslabs work again (<a href="#bug_idx_hyp">broke in 2.7.3</a>, <i>upgrade highly recommended</i>); <tt>ncap</tt> peak memory usage reduced still more; support for AMD Opteron x86_64 architecture</li>
+<li><b>NCO 2.8.3</b>: Fix big <tt>ncap</tt> memory leak; fix regressions; remove scary packing warnings</li>
+<li><b>NCO 2.8.2</b>: <tt>ncbo</tt> handles distinct <tt>missing_value</tt>s correctly; improve error diagnostics</li>
+<li><b>NCO 2.8.1</b>: <a href="./nco.html#rx">“Variable wildcarding”</a>—extended regular expressions in <tt>-v var,...</tt> lists—support in all operators</li>
+<li><b>NCO 2.8.0</b>: New “binary” operator <a href="./nco.html#ncbo"><tt>ncbo</tt></a>, obsoletes <tt>ncdiff</tt>; <a href="http://www.debian.org">Debian</a> integration</li>
+<li><b>NCO 2.7.4</b>: Autotools build support for AIX; fix UDUnits confusion with floating point hyperslab specifications</li>
+<li><b>NCO 2.7.3</b>: Support <a href="http://www.unidata.ucar.edu/packages/udunits">UDUnits</a> (and some <a href="http://www.cgd.ucar.edu/cms/eaton/cf-metadata/CF-working.html">CF</a>) conventions, e.g., <tt>ncks -d wvl "1 picometer","1 furlong" -d time,"2001-03-19 06:00:0.0","2001-03-19 18:00:0.0"</tt></li>
+<li><b>NCO 2.7.2</b>: Printing (<tt>ncks -H</tt>) plays well with multi-slabbing</li>
+<li><b>NCO 2.7.1</b>: (Packaged) Fallback to B. Sittler's <tt>getopt()</tt> for long option support; store fixed, packed variables correctly with <tt>ncap</tt>.</li>
+<li><b>NCO 2.7.0</b>: Support for GNU/POSIX long options; <tt>ncks</tt> introduces <i>multi-slabbing</i> (= multiple hyperslabs) capability</li>
+<li><b>NCO 2.6.6</b>: Fix and document <tt>ncrename</tt> attribute renaming; add type conversion functions to <tt>ncap</tt></li>
+<li><b>NCO 2.6.5</b>: Cray, Sun build improvements</li>
+<li><b>NCO 2.6.4</b>: Mac OS X, NEC, SGI build improvements</li>
+<li><b>NCO 2.6.3</b>: Mac OS X builds work seamlessly; documentation fixed</li>
+<li><b>NCO 2.6.2</b>: Major improvements in autotools support; <tt>ncap</tt> supports user-defined dimensions</li>
+<li><b>NCO 2.6.1</b>: Minor fix to unpacking support</li>
+<li><b>NCO 2.6.0</b>: All arithmetic operators (<tt>ncap</tt>, <tt>ncdiff</tt>, <tt>nces</tt>, <tt>ncflint</tt>, <tt>ncra</tt>) support unpacking</li>
+<li><b>NCO 2.5.6</b>: Handle <tt>missing_value</tt> correctly for integer variables in <tt>ncra</tt>, merge <tt>autoconf</tt> build</li>
+<li><b>NCO 2.5.5</b>: Handle files without existing global “<tt>History</tt>” attribute correctly</li>
+<li><b>NCO 2.5.4</b>: Add support NEC-SX support; update Cray support; small build changes</li>
+<li><b>NCO 2.5.3</b>: Fix native builds under MS Windows with Cygwin <tt>ncap</tt>; hint to <tt>ncwa</tt></li>
+<li><b>NCO 2.5.2</b>: Add math functions to <tt>ncap</tt>; hint to <tt>ncwa</tt></li>
+<li><b>NCO 2.5.1</b>: <tt>ncatted</tt> deletes all attributes of <tt>att_var</tt> when <tt>att_nm</tt> not specified</li>
+<li><b>NCO 2.5.0</b>: man(1) pages from <a href="http://www.debian.org">Debian</a> distribution</li>
+<li><b>NCO 2.4.6</b>: Free (speech) sort routines</li>
+<li><b>NCO 2.4.5</b>: Arithmetic speedups</li>
+<li><b>NCO 2.4.4</b>: 64-bit AIX builds</li>
+<li><b>NCO 2.4.3</b>: Handle non-standard “History” attributes</li>
+<li><b>NCO 2.4.2</b>: <tt>ncap</tt> supports nesting files with <tt>#include</tt></li>
+<li><b>NCO 2.4.0</b>: <tt>ncks</tt> supports writing native binary output with <tt>-b</tt> switch</li>
+<li><b>NCO 2.3.1</b>: <tt>ncap</tt> builds on all Unices</li>
+<li><b>NCO 2.3.0</b>: Library redesign</li>
+<li><b>NCO 2.2.4</b>: <tt>ncap</tt> fully supports packing and unpacking variables</li>
+<li><b>NCO 2.2.3</b>: <tt>ncap</tt> supports manually unpacking variables stored with <tt>scale_factor</tt> and <tt>add_offset</tt></li>
+<li><b>NCO 2.2.2</b>: fix rare <tt>ncwa</tt> crash with weights</li>
+<li><b>NCO 2.2.1</b>: fix <tt>ncap</tt> divide and <tt>fmodf</tt> bugs</li>
+<li><b>NCO 2.2.0</b>: (RPM available) <a href="./nco_news.shtml#20020203">20020203</a>: <tt>ncap</tt> public debut (has division error, please upgrade)</li>
+<li><b>NCO 2.1.3</b>: <tt>ncap</tt> implements LHS casting</li>
+<li><b>NCO 2.1.2</b>: C++ API to netcdf; libnco_c++ open for business</li>
+<li><b>NCO 2.1.0</b>: <tt>ncap</tt> full lexer/parser operational</li>
+<li><b>NCO 2.0.3</b>: small fixes to 2.0.0 (e.g., <tt>ncks</tt> printing)</li>
+<li><b>NCO 2.0.2</b>: Add packing/unpacking capabilities based on <tt>scale_factor</tt> and <tt>add_offset</tt> convention</li>
+<li><b>NCO 2.0.1</b>: Add user-configurable multi-threaded capability to arithmetic-intensive operators <tt>ncwa</tt>, <tt>nces</tt>, and <tt>ncra</tt></li>
+<li><b>NCO 2.0.0</b>: (RPM available) <a href="./nco_news.shtml#20010507">20010507</a>: Switched all internal calls to netCDF 3.x API</li>
+<li><b>NCO 1.2.2</b>: <a href="./nco_news.shtml#20010211">20010211</a>: Allow weights with
+<tt>ncwa</tt> in min/max/ttl operations; easier building with HDF4.
+<tt>ncrename</tt> can now work on specific variables rather than whole file.
+<tt>ncks</tt> has <tt>-q</tt> option for cleaner printing</li>
+<li><b>NCO 1.2.1</b>: <a href="./nco_news.shtml#20000828">20000828</a>: Added type-conversion of integers to floating point before arithmetic; fixed broken <tt>-v</tt> option</li>
+<li><b>NCO 1.2</b>: <a href="./nco_news.shtml#20000730">20000730</a>: Added non-linear operations to <tt>ncra/nces</tt> and <tt>ncwa</tt>: min,max,total,rms,rmssdn,sqrt. Added <a href="http://opendap.org">DODS</a> compliance.</li>
+<li><b>NCO 1.1.48</b>: <a href="./nco_news.shtml#20000515">20000515</a>: Potentially serious bugfix to <tt>ncdiff</tt>, recommend upgrade</li>
+<li><b>NCO 1.1.47</b>: <a href="./nco_news.shtml#20000510">20000510</a>: Improved <tt>ncra</tt> and <tt>ncrcat</tt> to allow lazier specifications of input files</li>
+</ul>
+<hr></p>
+
+</body>
+</html>
diff --git a/doc/index.shtml b/doc/index.shtml
index 8ea386d..a01e9ec 100644
--- a/doc/index.shtml
+++ b/doc/index.shtml
@@ -1,4 +1,4 @@
-<!-- $Header: /cvsroot/nco/nco/doc/index.shtml,v 1.883 2014/05/29 18:19:54 zender Exp $
+<!-- $Header: /cvsroot/nco/nco/doc/index.shtml,v 1.917 2014/08/27 04:44:01 zender Exp $
Purpose: NCO homepage
URL:
@@ -7,7 +7,9 @@ http://dust.ess.uci.edu/nco/index.shtml
file:///home/zender/nco/doc/index.shtml
Usage:
-/usr/bin/scp ~/nco/doc/index.shtml ~/nco/doc/logo_cog.png ~/nco/doc/logo_cog_nmr.png ~/nco/doc/logo_nco_stk.png ~/nco/doc/logo_pch.png ~/nco/doc/logo_srl.png ~/nco/doc/nasa.png ~/nco/doc/nco.png ~/nco/doc/nsf.png zender,nco at web.sf.net:/home/project-web/nco/htdocs
+/usr/bin/scp ~/nco/doc/index.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+scp -p ~/nco/doc/index.shtml dust.ess.uci.edu:/var/www/html/nco
+/usr/bin/scp ~/nco/doc/doe.jpg ~/nco/doc/index.shtml ~/nco/doc/logo_cog.png ~/nco/doc/logo_cog_nmr.png ~/nco/doc/logo_nco_stk.png ~/nco/doc/logo_pch.png ~/nco/doc/logo_srl.png ~/nco/doc/nasa.png ~/nco/doc/nco.png ~/nco/doc/nsf.png zender,nco at web.sf.net:/home/project-web/nco/htdocs
scp -p ~/nco/doc/index.shtml ~/nco/doc/logo_cog.png ~/nco/doc/logo_cog_nmr.png ~/nco/doc/logo_nco_stk.png ~/nco/doc/logo_pch.png ~/nco/doc/logo_srl.png ~/nco/doc/nasa.png ~/nco/doc/nco.png ~/nco/doc/nsf.png dust.ess.uci.edu:/var/www/html/nco
scp -p ~/nco/doc/.htaccess zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
scp -p ~/nco/doc/.htaccess dust.ess.uci.edu:/var/www/html/nco/src
@@ -48,14 +50,14 @@ Try to disable Spammers' machines:
<a href="http://sf.net/projects/nco/forums/forum/9829">Discussion</a> /
<a href="http://sf.net/projects/nco/forums/forum/9830">Help</a> /
<a href="#RTFM">Manual</a> /
-<a href="http://nco.sf.net">Homepage</a> /
<a href="http://sf.net/projects/nco">Project</a> /
<a href="http://nco.cvs.sf.net/nco/nco/src/nco">Source</a> /
</td>
<td align="right" valign="top">
+[<a href="https://acme-climate.atlassian.net/wiki/display/ACME/ACME+Home">ACME</a>]
[<a href="http://www.antlr.org">ANTLR</a>]
-[<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/latest-cf-conventions-document-1">CF</a>]
+[<a href="http://cfconventions.org/1.6.html">CF</a>]
[<a href="https://wiki.earthdata.nasa.gov/display/ESDSWG/Dataset+Interoperability+Working+Group">DIWG</a>]
[<a href="http://www.gnu.org/software/gsl">GSL</a>]
[<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a>]
@@ -68,7 +70,7 @@ Try to disable Spammers' machines:
<p><h1 align="center">Welcome to the netCDF Operator (NCO) Homepage</h1>
<p><h2>
-Current NCO version is 4.4.4 last updated on <!--#flastmod file="VERSION"-->
+Current NCO version is 4.4.5 last updated on <!--#flastmod file="VERSION"-->
</h2>
<table border=0 width=100%>
@@ -80,15 +82,15 @@ Current NCO version is 4.4.4 last updated on <!--#flastmod file="VERSION"-->
<li><a href="#Contribute">Contributing</a></li>
<li><a href="#prp_sei">NCO→SDO Project</a></li>
<li><a href="#Publications">Publications</a></li>
-<li><a href="#Version">Version Summary</a></li>
+<li><a href="#Highlights">Release Highlights</a></li>
<li><a href="#Binaries">Binaries</a></li>
<li><a href="#RTFM">Documentation</a></li>
<li><a href="#FAQ">FAQ</a></li>
<li><a href="#README/ChangeLog/TODO">README/ChangeLog/TODO</a></li>
<li><a href="#Source">Source Code</a></li>
<li><a href="#bld">Compiling</a></li>
-<li><a href="#NCAR">UCI and NCAR</a></li>
-<li><a href="#BM">Benchmarks</a></li>
+<li><a href="#NCAR">Supercomputers</a></li>
+<!-- <li><a href="#BM">Benchmarks</a></li> -->
<li><a href="#bug">Known Problems</a></li>
<li><a href="#People">People</a></li>
<li><a href="#Contact">Contact us</a></li>
@@ -116,14 +118,14 @@ Keep the size <250×250 pixels.<br>
-->
</td>
-NCO manipulates data stored in
+The NCO toolkit manipulates and analyzes data stored in
<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a>-accessible
formats, including
<a href="http://opendap.org">DAP</a>,
<a href="http://hdfgroup.org/products/hdf4">HDF4</a>, and
<a href="http://hdfgroup.org/HDF5">HDF5</a>.
-It also exploits the geophysical expressivity of many
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/latest-cf-conventions-document-1">CF</a>
+It exploits the geophysical expressivity of many
+<a href="http://cfconventions.org/1.6.html">CF</a>
(Climate & Forecast) metadata conventions,
the flexible description of physical dimensions translated by
<a href="http://www.unidata.ucar.edu/packages/udunits">UDUnits</a>,
@@ -144,97 +146,37 @@ and
<!-- http://nco.sf.net#news -->
<dt><a name="News"></a><a name="news"></a></dt>
<dt><a name="Milestones"></a><a name="milestones"></a></dt>
-<h2>NCO Milestones</h2>
+<h2>Recent Releases & Milestones</h2>
<ul>
-<li>2014 Jun ??: NCO 4.4.5 (<i>In progress</i>)
-<li>2014 May 29: NCO 4.4.4 (Stability)
-<li>2014 Apr 02: NCO 4.4.3 (Stability)
-<li>2014 Mar 27: NCO <a href="http://dust.ess.uci.edu/smn/smn_nco_gsfc_201403.pdf">Talk</a> at NASA GSFC, Greenbelt, Maryland</li>
-<li>2014 Mar 25: NCO <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201403.pdf">Poster</a> for NASA ESDSWG, Greenbelt, Maryland</li>
-<li>2014 Feb 20: NCO 4.4.2 (Stability)
-<li>2014 Jan 29: NCO 4.4.1 (Stability)
-<li>2014 Jan 09: NCO 4.4.0 (Stability)
-<li>2013 Dec 13: NCO <a href="http://dust.ess.uci.edu/smn/smn_nco_agu_201312.pdf">Talk</a> at Fall AGU, San Francisco, California</li>
-<li>2013 Dec 02: NCO 4.3.9 (new operator, <tt>nces</tt>)
-<li>2013 Nov 06: NCO 4.3.8 (<tt>ncatted</tt> groups)
-<li>2013 Oct 17: NCO 4.3.7 (HDF4, XML, <tt>ncrename</tt> groups)
-<li>2013 Oct 02: NCO <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201310.pdf">Poster</a> for NASA ESDSWG, Greenbelt, Maryland</li>
-<li>2013 Sep 27: NCO 4.3.6 (<tt>--dbl</tt> default, <tt>ncdismember</tt>)
-<li>2013 Sep 20: NCO 4.3.5 (<tt>nces</tt>, <tt>ncra</tt>, <tt>ncrcat</tt> groups)
-<li>2013 Aug 01: NCO 4.3.4 (<tt>ncpdq</tt> bugfix, HDF unpacking)
-<li>2013 Jul 24: NCO 4.3.3 (<tt>ncrename</tt>, <tt>ncwa</tt> groups, CDL, XML)
-<li>2013 Jul 05: NCO 4.3.2 (<tt>ncflint</tt>, <tt>ncpdq</tt> groups)</li>
+<li>2014 Sep ??: 4.4.6 (<i>In progress</i>)
+<li>2014 Aug 26: 4.4.5
+<li>2014 Jul 01: NASA ACCESS 2013 <a href="#prp_axs">project</a> commences</li>
+<li>2014 May 29: 4.4.4 (Stability)
+<li>2014 Apr 02: 4.4.3 (Stability)
+<li>2014 Mar 27: <a href="http://dust.ess.uci.edu/smn/smn_nco_gsfc_201403.pdf">Talk</a> at NASA GSFC, Greenbelt, Maryland</li>
+<li>2014 Mar 25: <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201403.pdf">Poster</a> for NASA ESDSWG, Greenbelt, Maryland</li>
+<li>2014 Feb 20: 4.4.2 (Stability)
+<li>2014 Jan 29: 4.4.1 (Stability)
+<li>2014 Jan 09: 4.4.0 (Stability)
+<li>2013 Dec 13: <a href="http://dust.ess.uci.edu/smn/smn_nco_agu_201312.pdf">Talk</a> at Fall AGU, San Francisco, California</li>
+<li>2013 Dec 02: 4.3.9 (new operator, <tt>nces</tt>)
+<li>2013 Nov 06: 4.3.8 (<tt>ncatted</tt> groups)
+<li>2013 Oct 17: 4.3.7 (HDF4, XML, <tt>ncrename</tt> groups)
+<li>2013 Oct 02: <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201310.pdf">Poster</a> for NASA ESDSWG, Greenbelt, Maryland</li>
+<li>2013 Sep 27: 4.3.6 (<tt>--dbl</tt> default, <tt>ncdismember</tt>)
+<li>2013 Sep 20: 4.3.5 (<tt>nces</tt>, <tt>ncra</tt>, <tt>ncrcat</tt> groups)
+<li>2013 Aug 01: 4.3.4 (<tt>ncpdq</tt> bugfix, HDF unpacking)
+<li>2013 Jul 24: 4.3.3 (<tt>ncrename</tt>, <tt>ncwa</tt> groups, CDL, XML)
+<li>2013 Jul 05: 4.3.2 (<tt>ncflint</tt>, <tt>ncpdq</tt> groups)</li>
<li>2013 Jun 03: Submitted NASA ACCESS 2013 <a href="http://dust.ess.uci.edu/prp/prp_axs/prp_axs.pdf">proposal</a></li>
-<li>2013 May 01: NCO 4.3.1 (Group broadcasting)</li>
-<li>2013 Mar 28: NCO 4.3.0 (<tt>ncbo</tt> groups)</li>
-<li>2013 Mar 19: NCO 4.2.6</li>
-<li>2013 Jan 28: NCO 4.2.5</li>
-<li>2013 Jan 21: NCO 4.2.4</li>
-<li>2012 Dec 05: NCO <a href="http://dust.ess.uci.edu/smn/smn_nco_agu_201212.pdf">Talk</a> at Fall AGU, San Francisco, California</li>
-<li>2012 Nov 28: NCO <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201211.pdf">Poster</a> at NASA ESDSWG, Annapolis, Maryland</li>
-<li>2012 Nov 13: NCO 4.2.3 (GPE)</li>
-<li>2012 Oct 29: NCO 4.2.2 (<tt>ncks, ncecat</tt> Groups)</li>
-<li>2012 Aug 02: NCO 4.2.1 (RAM disks)</li>
-<li>2012 Jun 12: NCO 4.2.0 (Windows support)</li>
-<li>2012 Apr 23: Received funding for NASA ACCESS 2011 <a href="#prp_access">project</a></li>
-<li>2012 Mar 29: NCO 4.1.0 (MD5 support, MM3)</li>
-<li>2012 Feb 13: NCO 4.0.9</li>
-<li>2011 Jun 03: Submitted NASA ACCESS 2011 <a href="http://dust.ess.uci.edu/prp/prp_access/prp_access.pdf">proposal</a></li>
-<li>2011 Apr 28: NCO 4.0.8 (HPSS support, NOFILL workaround, <i>upgrade recommended</i>)</li>
-<li>2011 Feb 21: NCO 4.0.7 (<i>upgrade recommended</i>)</li>
-<li>2011 Jan 15: NCO 4.0.6</li>
-<li>2010 Oct 13: NCO 4.0.5</li>
-<li>2010 Sep 24: NCO 4.0.4 (chunking everywhere)</li>
-<li>2010 Sep 02: NCO 4.0.3</li>
-<li>2010 Jun 27: NCO 4.0.2</li>
-<li>2010 Apr 05: NCO 4.0.1</li>
-<li>2010 Jan 05: NCO 4.0.0 (bilinear interpolation, calendar attributes)</li>
-<li>2009 Jul 15: NCO 3.9.9 (chunking, re-basing, GSL stats/interp)</li>
-<li>2009 Apr 29: NCO 3.9.8 (GSL RNG/PDF functions)</li>
-<li>2009 Mar 18: NCO 3.9.7</li>
-<li>2009 Jan 22: NCO 3.9.6 (GSL special functions) (<i>upgrade highly recommended</i>)</li>
-<li>2008 Sep 24: <tt>ncap2</tt> <a href="http://nco.sf.net/nco.html#ncap2">documentation</a></li>
-<li>2008 Aug 31: <a href="http://www.nsf.gov">NSF</a> funding ends</a></li>
-<li>2008 Aug 08: NCO <a href="http://nco.wiki.sf.net">Wiki</a>!</li>
-<li>2008 May 22: SWAMP <a href="http://dust.ess.uci.edu/ppr/smn_WZJ08_ccgrid_200805.pdf">Talk</a> at CCGRID08 in Lyon, France</li>
-<li>2008 May 11: NCO 3.9.5</li>
-<li>2008 Apr 28: NCO <a href="http://dust.ess.uci.edu/ppr/ppr_Zen08.pdf">overview</a> paper in EMS</li>
-<li>2008 Mar 04: NCO 3.9.4</li>
-<li>2007 Dec 10: SWAMP <a href="http://dust.ess.uci.edu/ppr/pst_WZJ074.pdf">Poster</a> at Fall AGU, San Francisco, California</li>
-<li>2007 Dec 07: NCO 3.9.3 (SWAMP!)</li>
-<li>2007 Dec 04: NCO <a href="http://dust.ess.uci.edu/ppr/ppr_ZeM07.pdf">scaling paper</a> in IJHPCA</li>
-<li>2007 Aug 29: NCO 3.9.2 (<tt>_FillValue</tt>s)</li>
-<li>2007 Aug 27: <a href="http://swamp.googlecode.com">SWAMP site</a> spins-off from NCO</li>
-<li>2007 Jun 29: NCO 3.9.1 (netCDF4 deflation)</li>
-<li>2007 May 26: NCO 3.9.0 (netCDF4 atomic types)</li>
-<li>2007 May 02: SWAMP <a href="http://dust.ess.uci.edu/smn/smn_WZJ07_gpc_200705.pdf">Talk</a> at GPC, Paris, France</li>
-<li>2007 Apr 20: NCO 3.2.0</li>
-<li>2007 Mar 29: NCO 3.1.9 x86_64 RPMs</li>
-<li>2007 Mar 10: NCO 3.1.9 (i386/x86_64 debs and i386 RPMs)</li>
-<li>2007 Feb 22: SWAMP <a href="http://dust.ess.uci.edu/smn/smn_WZJ07_opendap_200702.pdf">Talk</a> at OPeNDAP Developer's Workshop, Boulder, Colorado</li>
-<li>2007 Jan 15: <a href="http://dust.ess.uci.edu/smn/smn_nco_ams_200701.pdf">Talk</a> and <a href="http://dust.ess.uci.edu/ppr/abs_xtn_ZeW07.pdf">Extended Abstract</a> on NCO Scaling at AMS IIPS, San Antonio, Texas</li>
-<li>2007 Jan 09: <a href="http://dust.ess.uci.edu/ppr/pst_ZMW06.pdf">Poster</a> on NCO Scaling at Fall AGU, San Francisco, California</li>
-<li>2006 Dec 09: <a href="http://dust.ess.uci.edu/ppr/pst_WZJ06.pdf">Poster</a> on SWAMP at Fall AGU, San Francisco, California</li>
-<li>2006 Dec 06: NCO 3.1.8</li>
-<li>2006 Nov 11: NCO 3.1.7</li>
-<li>2006 Sep 18: NCO 3.1.6</li>
-<li>2006 Aug 29: NCO 3.1.5</li>
-<li>2006 Jun 07: NCO 3.1.4</li>
-<li>2006 May 30: NCO 3.1.3</li>
-<li>2006 Apr 21: NCO 3.1.2</li>
-<li>2006 Jan 30: NCO 3.1.1</li>
-<li>2005 Dec 02: NCO 3.1.0 (MPI!)</li>
-<li>2005 Oct 28: NCO 3.0.3</li>
-<li>2005 Oct 17: <a href="#BM">NCO parallel benchmarks</a></li>
-<li>2005 Aug 22: NCO 3.0.2</li>
-<li>2005 Jun 10: NCO 3.0.1</li>
-<li>2005 Mar 24: NCO 3.0.0</li>
-<li>2004 Sep 07: NCO 2.9.9 (<tt>ncpdq</tt> packs data quietly)</li>
-<li>2004 Sep 01: Funding for NSF <a href="#prp_sei">SEI Project</a> begins</li>
-<li>2004 Aug 07: NCO 2.9.8 (<a href="./nco.html#ncpdq"><tt>ncpdq</tt></a> re-orders dimensions)</li>
-<li>2004 Mar 04: Submit NSF <a href="http://dust.ess.uci.edu/prp/prp_sei/prp_sei.pdf">SEI proposal</a></li>
-<li><a href="./nco_news.shtml">Ancient NCO News & Announcements</a></li>
+<li>2013 May 01: 4.3.1 (Group broadcasting)</li>
+<li>2013 Mar 28: 4.3.0 (<tt>ncbo</tt> groups)</li>
+<li>2013 Mar 19: 4.2.6</li>
+<li>2013 Jan 28: 4.2.5</li>
+<li>2013 Jan 21: 4.2.4</li>
+<li><a href="./milestones_old.shtml">Milestones from 2003–2012 (versions 2.8.4–4.2.3)</a></li>
+<li><a href="./nco_news.shtml">News and Announcements from 1998–2003 (version 1.1.0–2.8.3) and earlier</a></li>
</ul>
<hr></p>
@@ -243,21 +185,48 @@ and
<h2>What is NCO?</h2>
<p>The netCDF Operators (NCO) comprise a dozen standalone,
command-line programs that take
-<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a> or
-<a href="http://hdfgroup.org">HDF</a>
-files as input, then operate (e.g., derive new data, average, print,
-hyperslab, manipulate metadata) and output the results to screen or
-files in text, binary, or netCDF formats.
-NCO aids manipulation and analysis of gridded scientific data.
+<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a>,
+<a href="http://hdfgroup.org">HDF</a>, and/or
+<a href="http://opendap.org">DAP</a>
+files as input, then operate (e.g., derive new data, compute
+statistics, print, hyperslab, manipulate metadata) and output the
+results to screen or files in text, binary, or netCDF formats.
+NCO aids analysis of gridded scientific data.
The shell-command style of NCO allows users to manipulate and analyze
-files interactively, or with simple scripts that avoid some overhead
-(and power) of higher level programming environments.
-The <a href="./nco.html">NCO User's Guide</a> illustrates their use
-with examples of climate data analysis:
+files interactively, or with expressive scripts that avoid some
+overhead of higher-level programming environments.
+</p>
+
+<p>
+Traditional geoscience data analysis requires users to work with
+numerous flat (data in one level or namespace) files.
+In that paradigm instruments or models produce, and then repositories
+archive and distribute, and then researchers request and analyze,
+collections of flat files.
+NCO works well with that paradigm, yet it also embodies the necessary
+algorithms to transition geoscience data analysis from relying solely
+on traditional (or “flat”) datasets to allowing newer
+hierarchical (or “nested”) datasets.
+</p>
+
+<p>
+The next logical step is to support and enable combining all
+datastreams that meet user-specified criteria into a
+single or small number of files that hold <i>all</i> the
+science-relevant data organized in hierarchical structures.
+NCO (and no other software to our knowledge) can do this now.
+We call the resulting data storage, distribution, and analysis
+paradigm Group-Oriented Data Analysis and Distribution
+(<a href="http://nco.sf.net/nco.html#godad">GODAD</a>).
+GODAD lets the scientific question organize the data, not the
+<i>ad hoc</i> granularity of all relevant datasets.
+The <a href="./nco.html">User Guide</a> illustrates
+<a href="http://nco.sf.net/nco.html#godad">GODAD</a>
+techniques for climate data analysis:
<ul>
<li><a href="./nco.html#ncap2"><tt>ncap2</tt></a> netCDF Arithmetic Processor (<a href="./nco.html#xmp_ncap">examples</a>)</li>
<li><a href="./nco.html#ncatted"><tt>ncatted</tt></a> netCDF ATTribute EDitor (<a href="./nco.html#xmp_ncatted">examples</a>)</li>
-<li><a href="./nco.html#ncbo"><tt>ncbo</tt></a> netCDF Binary Operator (includes <tt>ncadd</tt>, <tt>ncsubtract</tt>, <tt>ncmultiply</tt>, <tt>ncdivide</tt>) (<a href="./nco.html#xmp_ncbo">examples</a>)</li>
+<li><a href="./nco.html#ncbo"><tt>ncbo</tt></a> netCDF Binary Operator (addition, multiplication...) (<a href="./nco.html#xmp_ncbo">examples</a>)</li>
<li><a href="./nco.html#nces"><tt>nces</tt></a> netCDF Ensemble Statistics (<a href="./nco.html#xmp_nces">examples</a>)</li>
<li><a href="./nco.html#ncecat"><tt>ncecat</tt></a> netCDF Ensemble conCATenator (<a href="./nco.html#xmp_ncecat">examples</a>)</li>
<li><a href="./nco.html#ncflint"><tt>ncflint</tt></a> netCDF FiLe INTerpolator (<a href="./nco.html#xmp_ncflint">examples</a>)</li>
@@ -272,9 +241,9 @@ with examples of climate data analysis:
<p>
Note that the <a href="./nco.html#averagers">“averagers”</a>
(<tt>ncra</tt> and <tt>ncwa</tt>) are misnamed because they perform
-many non-linear operations as well, e.g., total, minimum, maximum, RMS.
+many non-linear statistics as well, e.g., total, minimum, RMS.
Moreover, <tt>ncap2</tt> implements a powerful domain language which
-handles arbitrarily complex operations.
+handles arbitrarily complex algebra, calculus, and statistics (using GSL).
The operators are as general as
<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a>
itself: there are no restrictions on the contents of input file(s).
@@ -284,30 +253,58 @@ NCO is designed to be used both interactively and with large batch jobs.
The default operator behavior is often sufficient for everyday needs,
and there are numerous command line (i.e., run-time) options, for
special cases.
-NCO works well and is used on most modern operating systems.
</p>
<p><hr width="100%"></p>
<!-- http://nco.sf.net#Contribute -->
<dt><a name="Contribute"></a></dt>
-<h2>How to Contribute</h2>
+<h2>How to Contribute: Volunteer, Endorse, or Donate</h2>
<p>In March, 2000, NCO became an Open Source project hosted by
<a href="http://sf.net">SourceForge.net</a>.
This facilitates collaboration, code contributions, and support.
-There is a <a href="./TODO">TODO list</a> about 200 items long!
+There is a <a href="./TODO">TODO list</a> hundreds of items long!
No matter what your programming background there is a task you can help with.
From re-organizing the TODO list itself, to improving this cheesy
webpage, to documentation, to designing and implementing new features
and interfaces, we need your help!
-The <a href="http://sf.net/projects/nco">NCO project homepage</a>
+The <a href="http://sf.net/projects/nco">project homepage</a>
contains mailing lists, discussion forums, and instructions to make
contributing to NCO easy.
-<p>As of June, 2003, you may easily donate your hard-earned money to NCO.
-Send your donation to NCO developers as a reward for good behavior,
-or as an incentive to tackle more <a href="./TODO"><tt>TODO</tt></a>
-items.
+<dt><a name="Endorsements"></a></dt> <!-- http://nco.sf.net#Endorsements -->
+<dt><a name="endorsement"></a></dt> <!-- http://nco.sf.net#endorsement -->
+<dt><a name="ndr"></a></dt> <!-- http://nco.sf.net#ndr -->
+<dt><a name="Endorsement"></a></dt> <!-- http://nco.sf.net#Endorsement -->
+<dt><a name="endorse"></a></dt> <!-- http://nco.sf.net#endorse -->
+<p>Many users feel unable to volunteer their time.
+An equally effective contribution in the long-run would be your
+<a href="#ndr">endorsement</a>, which may make the difference
+between a declined and an accepted proposal.
+An endorsement can be a few sentences that describes how NCO benefits your work or research.
+E-mail your endorsement to
+<a href="mailto:surname at uci.edu">Charlie “my surname is zender” Zender</a>
+with Subject: “NCO Proposal Endorsement”.
+This information is useful advocating for more NCO support.
+“What future proposals?” you ask, “Aren't you already funded?”
+Yes, in 2012 NASA funded us to implement netCDF4 groups and HDF support,
+and in 2014 NASA funded us to improve SLD handling.
+These funds are/were primarily for development and maintainance of
+specific features.
+To realize our grander ambition, i.e., to shift geoscience data
+analysis from a flat- to a hierarchical-paradigm
+(<a href="http://nco.sf.net/nco.html#godad">GODAD</a>),
+will require a sustained effort and software ecosystem that
+understands and implement hierarchical dataset concepts.
+And it's hard to sell a federal agency on the wisdom of investing in a paradigm shift!
+Other more prosaic tasks that need work are, for example,
+I/O parallelization (!!!), user-defined and non-atomic types, more CF conventions,
+cloud-services, JSON back-end, and user-defined <tt>ncap2</tt> functions.
+If you send an endorsement, please include (at least) your Name, Title, and Institutional affiliation.</p>
+
+Lastly, as of June, 2003, if you're more strapped for time than money
+and want to contribute something back, consider a monetary donation.
+This may incentivize us to tackle your favorite <a href="./TODO"><tt>TODO</tt></a> items.
<form action="https://www.paypal.com/cgi-bin/webscr" method="post">
<input type="hidden" name="cmd" value="_xclick">
<input type="hidden" name="business" value="zender at uci.edu">
@@ -321,88 +318,105 @@ items.
Inspired by President Obama's plan to bring more transparency to
government investment, these homepage donation counters track the
influence of your monetary donations on NCO development:
-<dt>Donations received between 20030624 and 20120301: US$144.55. Thank you, donors!</dt>
+<dt>Donations received between 20030624 and 20140615: US$144.55. Thank you, donors!</dt>
<dt>NCO features “incentivized” by these donations: More emoticons in the documentation :)</dt>
<hr></p>
<a name="nasa"></a> <!-- http://nco.sf.net#nasa -->
<a name="access"></a> <!-- http://nco.sf.net#access -->
+<dt><a name="prp_axs"></a></dt> <!-- http://nco.sf.net#prp_axs -->
+<h2>NASA ACCESS 2013 Project</h2>
+<img src="nasa.png" height=180 width=180 align=right>
+<p>
+The National Aeronautics and Space Administration (NASA) Cooperative
+Agreement <a href="NNX14AH55A">NNX14AH55A</a>
+funds our
+<a href="http://dust.ess.uci.edu/prp/prp_axs/prp_axs.pdf">project</a>,
+“Easy Access to and Analysis of NASA and Model Swath-like Data”
+from 20140701–20160630 as part of the
+Advancing Collaborative Connections for Earth System Science
+(<a href="http://science.nasa.gov/earth-science/earth-science-data/access">ACCESS</a>)
+program.
+This URL,
+<a href="http://nco.sf.net#prp_axs"><tt>http://nco.sf.net#prp_axs</tt></a>,
+points to the most up-to-date information on the ACCESS 2013 project.</p>
+
+<p>This ACCESS project provides resources to implement support in NCO
+for Swath-like data (SLD), i.e., dataset with non-rectangular and/or
+time-varying spatial grids in which one or more coordinates are multi-dimensional.
+It is often challenging and time-consuming to work with SLD,
+including all NASA Level 2 satellite-retrieved data, non-rectangular
+subsets of Level 3 data, and model data (e.g., CMIP5) that are
+increasingly stored on non-rectangular grids.
+Spatially intelligent software tools is a key component of the
+Group-Oriented Data Analysis and Distribution
+(<a href="http://nco.sf.net/nco.html#godad">GODAD</a>) paradigm we
+are developing for geoscience data analysis.</p>
+
+<p>We are currently recruiting a programmer (aka software engineer)
+or postdoc based at UCI for at least two years, to accomplish our
+ACCESS objectives.
+As described in the proposal, this person will be responsible for
+incorporating geospatial features and parallelism into NCO.
+See the ads for more details.
+(<a href="http://dust.ess.uci.edu/hire/prg_anl_06_adv.pdf">PDF</a>,
+ <a href="http://dust.ess.uci.edu/hire/prg_anl_06_adv.txt">TXT</a>).
+
<dt><a name="prp_access"></a></dt> <!-- http://nco.sf.net#prp_access -->
-<h2>NASA ACCESS Project</h2>
+<h2>NASA ACCESS 2011 Project</h2>
<img src="nasa.png" height=180 width=180 align=right>
<p>
-The National Aeronautics and Space Administration Cooperative Agreement (CA)
-<a href="fxm 11-ACCESS11-32">NASA 11-ACCESS11-32</a>
+The National Aeronautics and Space Administration (NASA) Cooperative
+Agreement <a href="NNX12AF48A">NNX12AF48A</a>
funded our
-<a href="http://dust.ess.uci.edu/prp/prp_access/prp_access.pdf">ACCESS Project</a>,
+<a href="http://dust.ess.uci.edu/prp/prp_access/prp_access.pdf">project</a>,
“Simplifying and accelerating model evaluation by NASA satellite data”
from 20120208–20140207 as part of the
-<a href="http://science.nasa.gov/earth-science/earth-science-data/access">Advancing Collaborative Connections for Earth System Science (ACCESS)</a> program.
+Advancing Collaborative Connections for Earth System Science
+(<a href="http://science.nasa.gov/earth-science/earth-science-data/access">ACCESS</a>)
+program.
We appreciate the proposal reviewers for and the staff of the
-<a href="http://science.nasa.gov/researchers/sara/division-corner/earth-science-division-corner">Earth Science Division (ESD) Research and Analysis (R\&A)</a>
-in the
-<a href="http://science.nasa.gov/about-us/organization-and-leadership">Science Mission Directorate (SMD)</a>.
+Earth Science Division
+(<a href="http://science.nasa.gov/researchers/sara/division-corner/earth-science-division-corner">ESD</a>)
+in the Science Mission Directorate
+(<a href="http://science.nasa.gov/about-us/organization-and-leadership">SMD</a>)
+Earth Science Data Systems (ESDS) Office.
NCO development was completely voluntary and without
institutional support from August, 2008–February, 2012.
This NASA support dramatically changed the scale and pace of NCO development.
This URL,
<a href="http://nco.sf.net#prp_access"><tt>http://nco.sf.net#prp_access</tt></a>,
-points to the most up-to-date information on the ACCESS proposal.</p>
+points to the most up-to-date information on the ACCESS 2011 project.</p>
-<p>The ACCESS project provides the human resources to implement support
+<p>This ACCESS project provided human resources to implement support
in NCO for hierarchical group features in netCDF4 files and for NCO to
-process (using wrappers) HDF-EOS files.
-Groups are a powerful HDF feature that some NASA satellite datasets
-(e.g., HIRDLS) exploit, and that sources of netCDF data (e.g., the
-CMIP5 archive of climate simulations for IPCC AR5) could better
-exploit.
-By supporting groups in a generic fashion, NCO hopes to remove one of
-the barriers to more widespread adoption of netCDF4 features.</p>
-
-<p>We recruited (i.e., these positions have been filled) two
-personnel, a programmer (aka software engineer)
+process HDF files.
+Groups are a powerful HDF feature that many NASA satellite datasets
+exploit, and that sources of netCDF data (e.g., the CMIP5 archive of
+climate simulations for IPCC AR5) could better exploit.
+By supporting groups in a generic fashion, NCO helps make possible
+more widespread adoption of hierarchical data analysis, aka
+Group-Oriented Data Analysis and Distribution
+(<a href="http://nco.sf.net/nco.html#godad">GODAD</a>).</p>
+
+<p>We recruited two personnel, a programmer (aka software engineer)
and a graduate student (scientific specialist) both based at UCI for
at least two years, to accomplish our ACCESS objectives.
As described in the proposal, the responsibilities of positions are
roughly segregated as follows:
The
<a href="http://dust.ess.uci.edu/hire/prg_anl_05_adv.pdf">programmer</a>
-is re-factoring the code-base to support groups, writing wrappers for
-NCO, an improving the build system (e.g., now we have native Windows builds!).
+helped re-factor the code-base to support groups and improved the
+build system so that now we have native Windows builds.
The
<a href="http://dust.ess.uci.edu/hire/sdn_grd_03_adv.pdf">graduate student researcher</a>
is analyzing and intercomparing snow cover and snow albedo datasets
from NASA MODIS and MISR datasets (in HDF format) and CMIP5
simulations (in netCDF format).
-Her analysis informs the development of NCO commands and wrappers for
-HDF atasets so that we solve the most important problems real-world
-researchers encounter in evaluating GCMs against NASA data.</p>
-
-<p>We continue to encourage you to e-mail NCO endorsements to
-<a href="mailto:surname at uci.edu">Charlie “my surname is zender” Zender</a>
-with Subject: “NCO Proposal Endorsement”.
-An endorsement can be a sentence or a page, describing how NCO
-benefits your work or research.
-The information in your endorsement will be used to create supplementary documents to NSF and NASA for future NCO proposal advocacy.
-“What future proposals?” you ask, “Didn't you just get funded?”
-Yes, we are funded to implement netCDF4 groups and HDF-EOS wrappers in NCO.
-Our ambition is get one more grant funded to fully support netCDF4
-capabilities in NCO.
-For example, user-defined types, multiple record coordinates, and some
-more CF conventions.
-Need I say more?
-If you send an endorsement, remember to include (at least) your Name, Title, and Institutional affiliation in the body.</p>
+Her analysis informs the development of GODAD so that NCO can solve
+the most important problems real-world researchers encounter in
+evaluating GCMs against satellite data.</p>
</ul>
-
-<a href="xmp_cesm.html">Pre-ACCESS CMIP5/MODIS analysis scripts</a>
-<!-- Copy files from http://glace.ess.uci.edu
-/usr/bin/scp /home/pvicente/nco/doc/index.shtml pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/nco/doc/xmp_cesm.html pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/nco/doc/cesm-eg.fig1.png pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/nco/doc/cesm-eg.fig2.png pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/nco/doc/cesm-eg.fig3.png pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
--->
-
<hr></p>
<a name="nsf"></a> <!-- http://nco.sf.net#nsf -->
@@ -418,14 +432,17 @@ funded our
<a href="http://dust.ess.uci.edu/prp/prp_sei/prp_sei.pdf">SEI Project</a>,
“SEI(GEO): Scientific Data Operators Optimized for Efficient Distributed Interactive and Batch Analysis of Tera-Scale Geophysical Data”
from 20040901–20080831 as part of the
-<a href="http://www.cise.nsf.gov/funding/pgm_display.cfm?pub_id=9473&div=iis">Science
- and Engineering Informatics (SEI)</a> program.
+Science and Engineering Informatics
+(<a href="http://www.cise.nsf.gov/funding/pgm_display.cfm?pub_id=9473&div=iis">SEI</a>)
+program.
We appreciate the proposal reviewers for and staff of the Divisions of
-<a href="http://www.cise.nsf.gov/div/index.cfm?div=iis">Information and Intelligent Systems (IIS)</a>
+Information and Intelligent Systems
+(<a href="http://www.cise.nsf.gov/div/index.cfm?div=iis">IIS</a>)
and
-<a href="http://www.cise.nsf.gov/div/index.cfm?div=sci">Shared Cyberinfrastructure (SC)</a>
-in the
-<a href="http://www.nsf.gov/home/cise">Directorate for Computer and Information Science and Engineering (CISE)</a>.
+Shared Cyberinfrastructure
+(<a href="http://www.cise.nsf.gov/div/index.cfm?div=sci">SC</a>) in the
+Directorate for Computer and Information Science and Engineering
+(<a href="http://www.nsf.gov/home/cise">CISE</a>).
Until September 2004, NCO development was completely voluntary and without institutional support.
This NSF support dramatically changed the scale and pace of NCO development.
This URL,
@@ -454,36 +471,24 @@ Another graduate student helped us design, implement, and release major
code changes.</p>
<p>On the institutional and hardware side, this project connected the
-<a href="http://www.ess.uci.edu/esmf">Earth System Modeling Facility</a> (ESMF)
-to the
-<a href="http://www.calit2.net">California Institute for Telecommunications and Information Technology</a> (Cal-IT2)
+Earth System Modeling Facility
+(<a href="http://www.ess.uci.edu/esmf">ESMF</a>) to the
+California Institute for Telecommunications and Information Technology
+(<a href="http://www.calit2.net">Cal-IT2</a>)
<a href="http://www.optiputer.net">OptIPuter</a> at the
-<a href="http://sdsc.ucsd.edu">San Diego Supercomputer Center</a>.
+San Diego Supercomputer Center
+(<a href="http://sdsc.ucsd.edu">SDSC</a>).
These supercomputers dedicated a TB of storage each to
<a href="http://www.opendap.org">OPeNDAP</a>-served climate simulation
datasets for DDRA.
After the proof-of-concept NCO DDRA was complete, we attempted a DDRA
intercomparison of the internationally distributed
-<a href="http://www.ccsm.ucar.edu/experiments/ccsm3.0">global climate change simulations</a>
-that reside on the
-<a href="http://www.earthsystemgrid.org">Earth System Grid</a>.
+CMIP3 global climate change simulations that reside on the
+Earth System Grid
+(<a href="http://www.earthsystemgrid.org">ESG</a>).
Our techniques tremendously accelerated the analysis of different
climate prediction scenarios for the same model, and among different
climate models (see <a href="#pub">publications</a>).</p>
-
-<p>We encourage you to e-mail NCO endorsements to
-<a href="mailto:surname at uci.edu">Charlie “my surname is zender” Zender</a>
-with Subject: “NCO Proposal Endorsement”.
-An endorsement can be a sentence or a page, describing how NCO
-benefits your work or research.
-The information in your endorsement will be used to create supplementary documents to NSF and NASA for future NCO proposal advocacy.
-“What future proposals?” you ask, “Didn't you just get funded?”
-Yes, we are funded to optimize and “grid-enable” NCO.
-There are still many desirable and unexplored methods for distributed data analysis
-and reduction (DDRA) that would benefit geosciences.
-For example, have you tried analyzing multiple NASA satellite datasets in HDF5 format?
-Need I say more?
-If you send an endorsement, remember to include (at least) your Name, Title, and Institutional affiliation in the body.</p>
</ul>
<hr></p>
@@ -493,9 +498,12 @@ If you send an endorsement, remember to include (at least) your Name, Title, and
<dt><a name="Publications"></a><a name="pub"></a><a name="pubs"></a></dt>
<h2>Publications and Presentations</h2>
<ul>
+<li><!-- Zen14 --> <a name="Zen14"></a> <!--http://www.ess.uci.edu/~zender#Zen14 -->
+Zender, C. S. (2014): <i>Use Hierarchical Storage and Analysis to Exploit Intrinsic Parallelism</i>. Presented to the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC), Goddard Space Flight Center, Greenbelt, MD, March 27, 2014.
+<a href="http://dust.ess.uci.edu/smn/smn_nco_gsfc_201403.pdf">PDF</a> (© 2014 by me)</a></li>
-<li><!-- ZVW13 --> <a name="ZVW12"></a> <!--http://www.ess.uci.edu/~zender#ZVW13 -->
-Zender, C. S., P. Vicente and W. Wang (2012): <i>Use Hierarchical Storage and Analysis to Exploit Intrinsic Parallelism</i>. Presented at the Fall Meeting of the American Geophysical Union, San Francisco, CA, December 9–13, 2013. <i>Eos Trans. AGU</i>, <b>93</b>(53), Fall Meet. Suppl., Abstract IN52A-06.
+<li><!-- ZVW13 --> <a name="ZVW13"></a> <!--http://www.ess.uci.edu/~zender#ZVW13 -->
+Zender, C. S., P. Vicente and W. Wang (2013): <i>Use Hierarchical Storage and Analysis to Exploit Intrinsic Parallelism</i>. Presented at the Fall Meeting of the American Geophysical Union, San Francisco, CA, December 9–13, 2013. <i>Eos Trans. AGU</i>, <b>93</b>(53), Fall Meet. Suppl., Abstract IN52A-06.
<a href="http://dust.ess.uci.edu/smn/smn_nco_agu_201312.pdf">PDF</a> (© 2013 by me)</a></li>
<li><!-- ZVW13 --> <a name="ZVW13"></a> <!--http://www.ess.uci.edu/~zender#ZVW13 -->
@@ -612,22 +620,31 @@ San Francisco, CA, December 5–9, 2006.
</ul>
<hr></p>
-<!-- http://nco.sf.net#vrs -->
-<dt><a name="Version"></a><a name="vrs"></a></dt>
-<h2>Version Summary</h2>
+<!-- http://nco.sf.net#hgh -->
+<dt><a name="Version"></a><a name="hgh"></a></dt>
+<h2>Release Highlights</h2>
Releases receive unique CVS tags and their tarballs are stored
<a href="http://nco.sf.net/src">here</a> on SourceForge and
<a href="http://dust.ess.uci.edu/nco/src">here</a> on our server at UCI.
You can also retrieve the source of tagged versions directly
<a name="#Source">with CVS</a>.
<ul>
-<li><b>NCO 4.4.6</b>: (<i>Future</i>)
+<li><b>NCO 4.4.7</b>: (<i>Future</i>)
extensive hashing?;
netCDF4 compound types?;
Optimize diskless files?;</li>
-<li><b>NCO 4.4.5</b>: (<i>In Progress, features completed or being worked on include</i>)
+<li><b>NCO 4.4.6</b>: (<i>In Progress, features completed or being worked on include</i>)
Chunking <tt>cnk_map=rew</tt>;
-<a href="http://nco.sf.net/nco.html#cnk">Chunking</a> bytes not elements, caching;</li>
+<a href="http://nco.sf.net/nco.html#cnk">Chunking</a> bytes not elements, caching</li>
+<li><b>NCO 4.4.5</b>: (<i>Current Stable Release</i>)
+DAP on <a href="http://nco.sf.net/nco.html#dap">HTTPS</a>;
+<tt>ancillary_variables</tt> for <a href="http://nco.sf.net/nco.html#ncl">CF</a>;
+<tt>ncks --grp_xtr_var_xcl</tt> <a href="http://nco.sf.net/nco.html#gxvx">subsetting</a>
+Chunking <tt>cnk_plc=r1d</tt>;
+Default chunking policy/map is <tt>xst/xst</tt>;
+Fix <tt>ncpdq</tt> dimension-reversal parsing;
+Chunking while hyperslabbing <a href="#bug_cnk_hyp">bugfix</a>;
+Correctly parse MS Windows volume names like <tt>C:\foo</tt></li>
<li><b>NCO 4.4.4</b>: (<i>Current Stable Release</i>)
netCDF'ize non-compliant element names;
<tt>-x var</tt> tolerates non-existence;
@@ -716,216 +733,10 @@ Intersection/union <a href="http://nco.sf.net/nco.html#unn">modes</a>;
<tt>ncrename</tt> global att. handling;
<tt>nces</tt> <a href="#bug_nces_rec_var">bugfix</a>;
<tt>ncra</tt> <a href="#bug_ncra_flg_bfr_nrm">bugfix</a></li>
-<li><b>NCO 4.2.3</b>:
-Group Path Editing (GPE);
-<tt>ncecat</tt> <a href="#bug_ncecat_nintap">bugfix</a></li>
-<li><b>NCO 4.2.2</b>:
-<tt>ncks</tt>, <tt>ncecat</tt> support groups;
-<tt>--hdr_pad</tt> all operators;
-<tt>ncks</tt> prints underscores;
-fixes to <tt>--[mk/fix]_rec_dmn</tt>;
-<tt>ncpdq</tt> fix;
-<tt>ncwa</tt> on Windows;</li>
-<li><b>NCO 4.2.1</b>:
-<tt>--ram_all</tt> for <a href="http://nco.sf.net/nco.html#diskless">diskless files</a>;
-<tt>--no_tmp_fl</tt> to <a href="http://nco.sf.net/nco.html#no_tmp_fl">bypass</a> temporary files;
-Negative indices for <a href="http://nco.sf.net/nco.html#hyp">hyperslabs</a>;
-<tt>ncpdq</tt> unpacks coordinate variables;
-<tt>ncra/ncrcat</tt> SSC/MRO <a href="http://nco.sf.net/nco.html#ssc">options</a>;
-<tt>ncra/ncrcat</tt> rebase <a href="http://nco.sf.net/nco.html#rbs">bounds</a>;</li>
-<li><b>NCO 4.2.0</b>:
-<tt>ncecat</tt> "fixes" auxiliary coordinates and bounds;
-<tt>ncks</tt> uses <tt>nc__open</tt>, format <tt>NC_INT</tt> with <tt>%i</tt>;
-<tt>ncra -y ttl</tt> fix;
-<tt>ncrcat</tt> UDUnits fix;
-<tt>ncwa</tt> and <tt>ncap2</tt> limited NaN support;
-Microsoft Visual Studio support;</li>
-<li><b>NCO 4.1.0</b>:
-MD5 digests;
-<tt>ncap2</tt> sorts & maps;
-<tt>ncks</tt> MM3 <a href="#bug_mm3">workaround</a>;
-<tt>ncrename/ncatted</tt> chmods;
-<tt>ncatted</tt> NaN support</li>
-<li><b>NCO 4.0.9</b>:
-Fix over-zealous <tt>ncap2</tt> packing;
-Fix <tt>nces -y ttl</tt>;
-Fix/improve <tt>ncap2 print, array()</tt>;
-Warn when appending variables of suspicious record length;
-Warn when <tt>NC_MAX_ATTRS</tt> exceeded</li>
-<li><b>NCO 4.0.8</b>:
-Support <a href="http://nco.sf.net/nco.html#hpss">HPSS</a>;
-Workaround netCDF <tt>NOFILL</tt> <a href="#bug_nofill">bug</a> (<i>upgrade recommended</i>);
-Support CF <tt>bounds</tt>;
-CF <tt>noleap</tt> not <tt>no_leap</tt>;
-Fix <tt>ncatted</tt> overwrite-mode;
-Fix <tt>NC_BYTE</tt> printing</li>
-<li><b>NCO 4.0.7</b>:
-Fix degenerate hyperslab <a href="#bug_hyp_dgn">bug</a> (<i>upgrade recommended</i>)</li>
-<li><b>NCO 4.0.6</b>:
-<tt>clang</tt>-compliance;
-Fix <tt>ncra</tt> YYYYMMDD-<tt>date</tt> <a href="#bug_ncra_cf_YYYYMMDD_date">bug</a>;
-Extract all associated coordinates;
-Tighten <tt>ncbo</tt> warnings;
-<tt>ncpdq</tt> warns when _FillValue outside packing range</li>
-<li><b>NCO 4.0.5</b>:
-Fix <tt>ncks</tt> <a href="#bug_ncks_nc4_nc4_hyp_fix">hyperslabbing bug</a>;
-Fix <tt>ncra</tt> <a href="#bug_ncra_cf_crd_rec_crd">CF "coordinate" bug</a></li>
-<li><b>NCO 4.0.4</b>:
-Chunking in all operators; preserve deflation; <tt>ncks</tt> print formatting;
-Fix <tt>ncrename</tt> <a href="#bug_ncrename_dot">bug</a>;
-Do not pack coordinate variables</li>
-<li><b>NCO 4.0.3</b>:
-Fix <tt>configure</tt> for ncap2, netCDF4, UDUnits2, netCDF-DAP;
-Fix <tt>ncbo</tt> <a href="#bug_ncbo_rfr">bug</a> under AIX xlC;
-Fix <tt>ncra</tt> <a href="#bug_ncra_date">bug</a> for some CF-compliant dates.</li>
-<li><b>NCO 4.0.2</b>:
-Consistent deflation, chunking with <tt>netCDF4_classic</tt>;
-Fix <tt>ncap2</tt> RAM vars, 1-D arrays;
-Fix <tt>ncatted</tt> appending <tt>NUL</tt>s.</li>
-<li><b>NCO 4.0.1</b>:
-Easily create/remove record dimensions with <tt>ncks --mk_rec_dmn</tt>, <tt>--fix_rec_dmn</tt>;</li>
-<li><b>NCO 4.0.0</b>:
-Bilinear interpolation, GSL fitting;
-Chunking improvements;
-Better support CF <tt>calendar</tt> and <tt>coordinate</tt> attributes</li>
-<li><b>NCO 3.9.9</b>:
-netCDF4 chunking and <tt>NC_STRING</tt> support;
-GSL statistics, interpolation functions;
-UDUnits2 <tt>time-since</tt> support;
-<tt>ncrcat</tt> re-basing</li>
-<li><b>NCO 3.9.8</b>:
-<tt>ncap2</tt> supports <tt>sort()</tt>, <tt>array()</tt>;
-better DAP/libnetcdf and UDUnits2 builds;
-GSL distribution/RNG functions</li>
-<li><b>NCO 3.9.7</b>:
-Improve GSL-build support;
-<tt>ncap2</tt> threading improvements;
-<tt>ncks --no_dmn_var_nm</tt> printing</li>
-<li><b>NCO 3.9.6</b>:
-Fix OpenMP MSA <a href="#bug_thr_msa">bug</a> (<i>upgrade highly recommended</i>);
-Memory management to improve threading;
-<tt>ncatted</tt> workaround for netCDF4 <tt>_FillValue</tt>;
-disable OpenMP with netCDF4/HDF;
-no math on type <tt>NC_CHAR</tt>;
-<tt>ncap2</tt> <a href="http://nco.sf.net/nco.html#ncap2">documentation</a>,
-better missing value propagation,
-<tt>#include</tt> files,
-<a href="http://nco.sf.net/nco.html#gsl">GSL</a> math functions</li>
-<li><b>NCO 3.9.5</b>:
-Multi-slabbing (MSA) and <tt>-X</tt> everywhere;
-<tt>ncecat -M</tt>;
-netCDF4-enabled builds on Cygwin;
-<tt>ncap2</tt> builds on Solaris</li>
-<li><b>NCO 3.9.4</b>:
-File consanguinity;
-<tt>ncks</tt>: CF auxiliary coords, LZ stats;
-<tt>ncap2</tt>: masks, index arrays, print attributes, OpenMP, <tt>atan2()</tt>, <tt>pow()</tt></li>
-<li><b>NCO 3.9.3</b>:
-SWAMP release;
-<tt>ncecat -u</tt>;
-<tt>wget</tt> URLs;
-GCC 4.2;
-<tt>ncap2</tt> OpenMP</li>
-<li><b>NCO 3.9.2</b>:
-<tt>_FillValue</tt> supplants <tt>missing_value</tt>;
-<tt>UDUnits2 support</tt>;
-<tt>ncap2</tt> type-conversion support and printing;
-netCDF4 <tt>configure</tt> fixes;
-Change licenses to GPL3 and FDL1.2</li>
-<li><b>NCO 3.9.1</b>:
-<a href="http://nco.sf.net/nco.html#deflate">Support</a> lossless netCDF4/HDF deflation;
-Improve Intel compiler support;
-<tt>ncap2</tt> for/while loops;
-various and sundry build fixes</li>
-<li><b>NCO 3.9.0</b>:
-<a href="http://nco.sf.net/nco.html#nco4">Support netCDF4</a> types (<tt>ubyte</tt>, <tt>ushort</tt>, <tt>uint</tt>, <tt>int64</tt>, and <tt>uint64</tt>);
-Control <tt>ncks</tt> metadata <a href="http://nco.sf.net/nco.html#prn">copying</a>;
-Fix <tt>ncbo</tt> packed valued <a href="#bug_ncbo_pck">bug</a> (<i>upgrade recommended</i>);
-Improve IRIX 6.5 support</li>
-<li><b>NCO 3.2.0</b>: More forgiving exclusion list (<tt>-x -v <i>var_nm</i></tt>) <a href="http://nco.sf.net/nco.html#xcl">handling</a>; Fix <tt>rmssdn</tt> normalization; Support Mac OS X on Intel; Documentation bugfixes</li>
-<li><b>NCO 3.1.9</b>: <tt>ncap2</tt> in RPM packages; Quieter output; AIX <tt>configure</tt> supports <tt>ncap2</tt>; Update to DAP for netCDF 3.6.2; Fix <tt>nc[erw]a</tt> for coordinate min/max/ttl; <tt>ncecat</tt> allows files to differ in record dimension size</li>
-<li><b>NCO 3.1.8</b>: Support <tt>_FillValue</tt> with compile-time switch; Debian package synchronized, includes <tt>ncap2</tt></li>
-<li><b>NCO 3.1.7</b>: <tt>ncap2</tt> “double-parsing”, array initialization, supercedes <tt>ncap</tt></li>
-<li><b>NCO 3.1.6</b>: Support <a href="http://nco.sf.net/nco.html#srd">stride</a> in all hyperslabbing operators; change more WARNINGs to INFOs</li>
-<li><b>NCO 3.1.5</b>: New <tt>ncap2</tt> array and hyperslab features; change some WARNINGs to INFOs, add Pathscale and update PGI and Intel compiler support</li>
-<li><b>NCO 3.1.4</b>: Fix <tt>ncbo</tt> memory problem; report timer results</li>
-<li><b>NCO 3.1.3</b>: <tt>ncap2</tt> automatically <a href="http://nco.sf.net/nco.html#att_prp">propagates</a> attributes to new/derived variables; NCO handles record variables with zero records; <a href="http://nco.sf.net/nco.html#cnv_CF_crd">support</a> CF <tt>coordinates</tt> convention; <tt>ncwa -b</tt> <a href="http://nco.sf.net/nco.html#ncwa">retains</a> degenerate dimensions; build fixes for Cray T3E, Solaris, Cygwin.</li>
-<li><b>NCO 3.1.2</b>: <tt>ncap2</tt> control structures (conditionals, loops, etc.); keep non-processed data <a href="bug_pack_fix">packed</a> in output file; binary operators <tt>ncbo</tt> and <tt>ncflint</tt> work when only one variable has <tt>missing_value</tt> attribute; change <tt>ncra</tt> and <tt>nces</tt> to always average coordinate variables</li>
-<li><b>NCO 3.1.1</b>: NCO builds (again) with C++ compilers; ncap2 development code; server-side extensions</li>
-<li><b>NCO 3.1.0</b>: MPI operators are bug-free; fix <t>./configure</t> for MPI and netCDF4; MRV algorithm speeds up <tt>ncwa</tt> 5—10 times; <tt>ncap</tt> random number generator <tt>rnd_nbr()</tt></li>
-<li><b>NCO 3.0.3</b>: Eliminate all critical read regions (accelerates all SMP operators); builds with netCDF4 alpha; read <t>NETCDF4_CLASSIC</t> (i.e., HDF) files automatically; write <t>NETCDF4</t> files <a href="http://nco.sf.net/nco.html#netcdf4">on request</a>; <a href="http://nco.sf.net#BM">benchmark results</a> quantify parallelism.</li>
-<li><b>NCO 3.0.2</b>: Fewer critical read regions; all known memory leaks plugged; better Intel compiler support; <tt>SFTP</tt> protocol support; FTP protocol supports <tt>.netrc</tt>-based passwords; better model grid-property-awareness (e.g., <tt>lat_bnds</tt>); <tt>ncatted</tt> <tt>ncks</tt>, <tt>ncrename</tt> support metadata header padding with <tt>--hdr</tt>; <tt>ncbo</tt> supports heterogeneous variable ordering; <tt>ncatted</tt> bugfix</li>
- <li><b>NCO 3.0.1</b>: benchmarks; <tt>ncks</tt> printing tweaks; memory cleanup; <tt>ncap</tt> double-parse speedup and <a href="bug_ncap_cmt">exponentiation bugfix</a>; thread operators by default</li>
- <li><b>NCO 3.0.0</b>: New <tt>ncks -P</tt> print switch; <tt>ncap</tt> optimizations; <tt>-Z</tt> option supports 64-bit offsets (requires netCDF 3.6); NEC SX build improvements; support GCC 3.4.X; <tt>nco_put_vara()</tt> overloads in <tt>libnco_c++</tt></li>
-<li><b>NCO 2.9.9</b>: <tt>ncpdq</tt> packs/unpacks entire files; <tt>ncbo</tt> is threaded</li>
-<li><b>NCO 2.9.8</b>: <a href="./nco.html#ncpdq"><tt>ncpdq</tt></a> released; <tt>ncwa --msk_sng</tt> consolidated mask switch; C99 compiler required</li>
-<li><b>NCO 2.9.7</b>: Read input file lists from <tt>stdin</tt>; write <tt>nco_input_file_list</tt> attributes; add <tt>nco_put_att<int,short,long></tt> functions to libnco_c++; large file support (LFS); write <tt>nco_openmp_thread_number</tt> attribute</li>
-<li><b>NCO 2.9.6</b>: Support <tt>-o fl_out</tt> syntax; 64-bit ABI for x86_64; <a href="http://www.debian.org">Debian</a> builds libnco_c++</li>
-<li><b>NCO 2.9.5</b>: <tt>ncflint</tt> handles <tt>missing_value</tt> data better, is commutative when weights are equal</li>
-<li><b>NCO 2.9.4</b>: <tt>ncecat</tt> works on pure scalar files; change to <tt>cvs.sf.net</tt>; AIX GCC builds</li>
-<li><b>NCO 2.9.3</b>: <tt>ncra</tt> and <tt>nces</tt> now <a name="bug_mss_val_zro_ncra">work correctly</a> when <tt>missing_value</tt> equals zero or any intermediate sums</li>
-<li><b>NCO 2.9.2</b>: <tt>ncap</tt> <tt>S/V</tt>, <tt>S%V</tt>, and <tt>S^V</tt> <a href="#bug_ncap_cmt">operations fixed</a> (<tt>S</tt> = scalar, <tt>V</tt> = variable)</li>
-<li><b>NCO 2.9.1</b>: <tt>ncwa</tt> works again on packed <tt>NC_FLOAT</tt> data (<a href="#bug_pck_ncwa">broke when?</a>)</li>
-<li><b>NCO 2.9.0</b>: Complete <tt>ncap</tt> modulo operator (<tt>V%S</tt>) and generic exponentiation (<tt>V^S</tt>), scalar divided by variable (<tt>S/V</tt>); workaround stack memory problem with GCC extensions; fix <tt>make check</tt></li>
-<li><b>NCO 2.8.8</b>: <tt>--enable-[optimize/debug]-custom</tt> options for GCC work again (broke in 2.8.6)</li>
-<li><b>NCO 2.8.7</b>: <tt>ncap</tt> packing works again (<a href="#bug_pck">broke in 2.8.4</a>); Cygwin builds work again</li>
-<li><b>NCO 2.8.6</b>: AIX and IRIX builds work again; custom GCC builds with <tt>-Werror</tt></li>
-<li><b>NCO 2.8.5</b>: Solaris <tt>make install</tt> works; <tt>ncap</tt> changes attribute values correctly; <a href="#bld_DODS">Support DODS 3.4+, deprecate 3.3-</a>; add <tt>--enable-[optimize/debug]-custom</tt> options to <tt>./configure</tt></li>
-<li><b>NCO 2.8.4</b>: Index-based hyperslabs work again (<a href="#bug_idx_hyp">broke in 2.7.3</a>, <i>upgrade highly recommended</i>); <tt>ncap</tt> peak memory usage reduced still more; support for AMD Opteron x86_64 architecture</li>
-<li><b>NCO 2.8.3</b>: Fix big <tt>ncap</tt> memory leak; fix regressions; remove scary packing warnings</li>
-<li><b>NCO 2.8.2</b>: <tt>ncbo</tt> handles distinct <tt>missing_value</tt>s correctly; improve error diagnostics</li>
-<li><b>NCO 2.8.1</b>: <a href="./nco.html#rx">“Variable wildcarding”</a>—extended regular expressions in <tt>-v var,...</tt> lists—support in all operators</li>
-<li><b>NCO 2.8.0</b>: New “binary” operator <a href="./nco.html#ncbo"><tt>ncbo</tt></a>, obsoletes <tt>ncdiff</tt>; <a href="http://www.debian.org">Debian</a> integration</li>
-<li><b>NCO 2.7.4</b>: Autotools build support for AIX; fix UDUnits confusion with floating point hyperslab specifications</li>
-<li><b>NCO 2.7.3</b>: Support <a href="http://www.unidata.ucar.edu/packages/udunits">UDUnits</a> (and some <a href="http://www.cgd.ucar.edu/cms/eaton/cf-metadata/CF-working.html">CF</a>) conventions, e.g., <tt>ncks -d wvl "1 picometer","1 furlong" -d time,"2001-03-19 06:00:0.0","2001-03-19 18:00:0.0"</tt></li>
-<li><b>NCO 2.7.2</b>: Printing (<tt>ncks -H</tt>) plays well with multi-slabbing</li>
-<li><b>NCO 2.7.1</b>: (Packaged) Fallback to B. Sittler's <tt>getopt()</tt> for long option support; store fixed, packed variables correctly with <tt>ncap</tt>.</li>
-<li><b>NCO 2.7.0</b>: Support for GNU/POSIX long options; <tt>ncks</tt> introduces <i>multi-slabbing</i> (= multiple hyperslabs) capability</li>
-<li><b>NCO 2.6.6</b>: Fix and document <tt>ncrename</tt> attribute renaming; add type conversion functions to <tt>ncap</tt></li>
-<li><b>NCO 2.6.5</b>: Cray, Sun build improvements</li>
-<li><b>NCO 2.6.4</b>: Mac OS X, NEC, SGI build improvements</li>
-<li><b>NCO 2.6.3</b>: Mac OS X builds work seamlessly; documentation fixed</li>
-<li><b>NCO 2.6.2</b>: Major improvements in autotools support; <tt>ncap</tt> supports user-defined dimensions</li>
-<li><b>NCO 2.6.1</b>: Minor fix to unpacking support</li>
-<li><b>NCO 2.6.0</b>: All arithmetic operators (<tt>ncap</tt>, <tt>ncdiff</tt>, <tt>nces</tt>, <tt>ncflint</tt>, <tt>ncra</tt>) support unpacking</li>
-<li><b>NCO 2.5.6</b>: Handle <tt>missing_value</tt> correctly for integer variables in <tt>ncra</tt>, merge <tt>autoconf</tt> build</li>
-<li><b>NCO 2.5.5</b>: Handle files without existing global “<tt>History</tt>” attribute correctly</li>
-<li><b>NCO 2.5.4</b>: Add support NEC-SX support; update Cray support; small build changes</li>
-<li><b>NCO 2.5.3</b>: Fix native builds under MS Windows with Cygwin <tt>ncap</tt>; hint to <tt>ncwa</tt></li>
-<li><b>NCO 2.5.2</b>: Add math functions to <tt>ncap</tt>; hint to <tt>ncwa</tt></li>
-<li><b>NCO 2.5.1</b>: <tt>ncatted</tt> deletes all attributes of <tt>att_var</tt> when <tt>att_nm</tt> not specified</li>
-<li><b>NCO 2.5.0</b>: man(1) pages from <a href="http://www.debian.org">Debian</a> distribution</li>
-<li><b>NCO 2.4.6</b>: Free (speech) sort routines</li>
-<li><b>NCO 2.4.5</b>: Arithmetic speedups</li>
-<li><b>NCO 2.4.4</b>: 64-bit AIX builds</li>
-<li><b>NCO 2.4.3</b>: Handle non-standard “History” attributes</li>
-<li><b>NCO 2.4.2</b>: <tt>ncap</tt> supports nesting files with <tt>#include</tt></li>
-<li><b>NCO 2.4.0</b>: <tt>ncks</tt> supports writing native binary output with <tt>-b</tt> switch</li>
-<li><b>NCO 2.3.1</b>: <tt>ncap</tt> builds on all Unices</li>
-<li><b>NCO 2.3.0</b>: Library redesign</li>
-<li><b>NCO 2.2.4</b>: <tt>ncap</tt> fully supports packing and unpacking variables</li>
-<li><b>NCO 2.2.3</b>: <tt>ncap</tt> supports manually unpacking variables stored with <tt>scale_factor</tt> and <tt>add_offset</tt></li>
-<li><b>NCO 2.2.2</b>: fix rare <tt>ncwa</tt> crash with weights</li>
-<li><b>NCO 2.2.1</b>: fix <tt>ncap</tt> divide and <tt>fmodf</tt> bugs</li>
-<li><b>NCO 2.2.0</b>: (RPM available) <a href="./nco_news.shtml#20020203">20020203</a>: <tt>ncap</tt> public debut (has division error, please upgrade)</li>
-<li><b>NCO 2.1.3</b>: <tt>ncap</tt> implements LHS casting</li>
-<li><b>NCO 2.1.2</b>: C++ API to netcdf; libnco_c++ open for business</li>
-<li><b>NCO 2.1.0</b>: <tt>ncap</tt> full lexer/parser operational</li>
-<li><b>NCO 2.0.3</b>: small fixes to 2.0.0 (e.g., <tt>ncks</tt> printing)</li>
-<li><b>NCO 2.0.2</b>: Add packing/unpacking capabilities based on <tt>scale_factor</tt> and <tt>add_offset</tt> convention</li>
-<li><b>NCO 2.0.1</b>: Add user-configurable multi-threaded capability to arithmetic-intensive operators <tt>ncwa</tt>, <tt>nces</tt>, and <tt>ncra</tt></li>
-<li><b>NCO 2.0.0</b>: (RPM available) <a href="./nco_news.shtml#20010507">20010507</a>: Switched all internal calls to netCDF 3.x API</li>
-<li><b>NCO 1.2.2</b>: <a href="./nco_news.shtml#20010211">20010211</a>: Allow weights with
-<tt>ncwa</tt> in min/max/ttl operations; easier building with HDF4.
-<tt>ncrename</tt> can now work on specific variables rather than whole file.
-<tt>ncks</tt> has <tt>-q</tt> option for cleaner printing</li>
-<li><b>NCO 1.2.1</b>: <a href="./nco_news.shtml#20000828">20000828</a>: Added type-conversion of integers to floating point before arithmetic; fixed broken <tt>-v</tt> option</li>
-<li><b>NCO 1.2</b>: <a href="./nco_news.shtml#20000730">20000730</a>: Added non-linear operations to <tt>ncra/nces</tt> and <tt>ncwa</tt>: min,max,total,rms,rmssdn,sqrt. Added <a href="http://opendap.org">DODS</a> compliance.</li>
-<li><b>NCO 1.1.48</b>: <a href="./nco_news.shtml#20000515">20000515</a>: Potentially serious bugfix to <tt>ncdiff</tt>, recommend upgrade</li>
-<li><b>NCO 1.1.47</b>: <a href="./nco_news.shtml#20000510">20000510</a>: Improved <tt>ncra</tt> and <tt>ncrcat</tt> to allow lazier specifications of input files</li>
+<li><a href="./highlights_old.shtml">Release Highlights from 2000–2012 (versions 1.1.47–4.2.3)</a></li>
</ul>
<hr></p>
-<!-- End http://nco.sf.net#vrs -->
+<!-- End http://nco.sf.net#hgh -->
<!-- http://nco.sf.net#bnr -->
<!-- http://nco.sf.net#binaries -->
@@ -935,17 +746,13 @@ Improve IRIX 6.5 support</li>
<p>NCO developers are too short-handed to provide pre-built binary
executables for all platforms.
Our source tarballs are always up-to-date, and work on our
-development systems
-(<a href="http://www.ubuntu.com">Ubuntu</a>-flavored <a
-href="http://www.debian.org">Debian</a> GNU/Linux for x86_64)
-and in our high-end scientific computing environments
-(<a href="http://www.ibm.com/servers/aix">AIX 5</a> for Power4/5/6/7).
+development systems (Fedora, Ubuntu, and Mac OS X).
We also attempt to provide (theoretically) platform-independent sources
-in the most common UNIX packaging formats (Debian and RPM).
-Below are links to these and to packages created by volunteers who
-port NCO to other platforms.
-Volunteers willing to perform regular regression testing and porting
-of NCO to other platforms are welcome.
+in the most common Linux package formats (Debian and RPM).
+Below are links to these and to packages for other platforms created
+by volunteers.
+Anyone willing to perform regular regression testing and porting
+of NCO to other platforms is welcome.
Previous versions of these binaries are still available by searching
the directory index <a href="src">here</a>.
@@ -962,7 +769,7 @@ Thanks to NSF for supporting AIX machines at NCAR over the years.
<h3><a href="http://www.debian.org">Debian</a> and <a href="http://www.ubuntu.com">Ubuntu</a> GNU/Linux</a></h3>
<ul>
<!--
-<li><a href="http://www.debian.org">Debian</a> and <a href="http://www.ubuntu.com">Ubuntu</a> GNU/Linux-compatible Intel systems, prebuilt binary executable <a href="http://www.debian.org">deb</a>: <a href="http://packages.debian.org/testing/math/nco.html">nco-4.4.4</a></li>
+<li><a href="http://www.debian.org">Debian</a> and <a href="http://www.ubuntu.com">Ubuntu</a> GNU/Linux-compatible Intel systems, prebuilt binary executable <a href="http://www.debian.org">deb</a>: <a href="http://packages.debian.org/testing/math/nco.html">nco-4.4.5</a></li>
-->
<a href="http://packages.debian.org/unstable/science/nco">Debian NCO</a> and
<a href="http://packages.ubuntu.com/natty/nco">Ubuntu NCO</a> homepages.
@@ -970,12 +777,12 @@ Thanks to NSF for supporting AIX machines at NCAR over the years.
NCO packages in the Debian/Ubuntu repositories (i.e., Sid and Raring) generally lag the packages distributed here by 6–12 months.
<a name="beta"></a><a name="prerelease"> <!-- http://nco.sf.net#beta -->
Newer (beta- or pre-release) packages are often available for intrepid Debian/Ubuntu users as described <a href="http://nco.cvs.sf.net/nco/nco/doc/beta.txt">here</a>.
-<dt>Debian package for most recent NCO release (install with, e.g., ‘<tt>dpkg --install nco_4.4.4-1_i386.deb</tt>’):</dt>
-<li><a href="src/nco_4.4.4-1_amd64.deb">nco_4.4.4-1_amd64.deb</a> (<!--#fsize file="src/nco_4.4.4-1_amd64.deb"-->): Executables AMD64-compatible (last updated <!--#flastmod file="src/nco_4.4.4-1_amd64.deb"-->)</li>
-<li><a href="src/nco_4.4.4-1.dsc">nco_4.4.4-1.dsc</a> (<!--#fsize file="src/nco_4.4.4-1.dsc"-->): Description (last updated <!--#flastmod file="src/nco_4.4.4-1.dsc"-->)</li>
-<li><a href="src/nco_4.4.4-1_amd64.changes">nco_4.4.4-1_amd64.changes</a> (<!--#fsize file="src/nco_4.4.4-1_amd64.changes"-->): Changes since last deb package (last updated <!--#flastmod file="src/nco_4.4.4-1_amd64.changes"-->)</li>
-<li><a href="src/nco_4.4.4.orig.tar.gz">nco_4.4.4.orig.tar.gz</a> (<!--#fsize file="src/nco_4.4.4.orig.tar.gz"-->): Upstream Source (last updated <!--#flastmod file="src/nco_4.4.4.orig.tar.gz"-->)</li>
-<li><a href="src/nco_4.4.4-1.diff.gz">nco_4.4.4-1.diff.gz</a> (<!--#fsize file="src/nco_4.4.4-1_amd64.changes"-->): Debian patch to upstream source (last updated <!--#flastmod file="src/nco_4.4.4-1_amd64.changes"-->)</li>
+<dt>Debian package for most recent NCO release (install with, e.g., ‘<tt>dpkg --install nco_4.4.5-1_i386.deb</tt>’):</dt>
+<li><a href="src/nco_4.4.5-1_amd64.deb">nco_4.4.5-1_amd64.deb</a> (<!--#fsize file="src/nco_4.4.5-1_amd64.deb"-->): Executables AMD64-compatible (last updated <!--#flastmod file="src/nco_4.4.5-1_amd64.deb"-->)</li>
+<li><a href="src/nco_4.4.5-1.dsc">nco_4.4.5-1.dsc</a> (<!--#fsize file="src/nco_4.4.5-1.dsc"-->): Description (last updated <!--#flastmod file="src/nco_4.4.5-1.dsc"-->)</li>
+<li><a href="src/nco_4.4.5-1_amd64.changes">nco_4.4.5-1_amd64.changes</a> (<!--#fsize file="src/nco_4.4.5-1_amd64.changes"-->): Changes since last deb package (last updated <!--#flastmod file="src/nco_4.4.5-1_amd64.changes"-->)</li>
+<li><a href="src/nco_4.4.5.orig.tar.gz">nco_4.4.5.orig.tar.gz</a> (<!--#fsize file="src/nco_4.4.5.orig.tar.gz"-->): Upstream Source (last updated <!--#flastmod file="src/nco_4.4.5.orig.tar.gz"-->)</li>
+<li><a href="src/nco_4.4.5-1.diff.gz">nco_4.4.5-1.diff.gz</a> (<!--#fsize file="src/nco_4.4.5-1_amd64.changes"-->): Debian patch to upstream source (last updated <!--#flastmod file="src/nco_4.4.5-1_amd64.changes"-->)</li>
Thanks to Daniel Baumann, Barry deFreese, Francesco Lovergine,
Brian Mays, Rorik Peterson, and Matej Vela for their help packaging
NCO for Debian over the years.
@@ -986,7 +793,7 @@ NCO for Debian over the years.
<a name="centos"></a><a name="cnt"></a><a name="rhel"></a> <!-- http://nco.sf.net#centos --> <!-- http://nco.sf.net#cnt --> <!-- http://nco.sf.net#rhel -->
<h3><a href="http://fedora.redhat.com">Fedora</a>, RedHat Enterprise Linux (<a href="http://www.redhat.com/rhel">RHEL</a>), and Community ENTerprise Operating System (<a href="http://www.centos.org">CentOS</a>) GNU/Linux</h3>
<ul>
-<dt>The <a href="https://admin.fedoraproject.org/pkgdb/packages/name/nco">Fedora NCO</a> RPMs are usually up-to-date so that ‘<tt>yum install nco</tt>’ will install a recent version.
+<dt>The <a href="https://admin.fedoraproject.org/pkgdb/package/nco">Fedora NCO</a> RPMs are usually up-to-date so that ‘<tt>yum install nco</tt>’ will install a recent version.
A comprehensive list of pre-built RPMs for many OS's is <a href="http://rpmfind.net/linux/rpm2html/search.php?query=nco">here</a>.
<li><a href="ftp://rpmfind.net/linux/fedora/linux/development/rawhide/x86_64/os/Packages/n/nco-4.3.2-1.fc20.x86_64.rpm">nco-4.3.2-1.fc20.x86_64.rpm</a>: Executables for x86_64/Fedora Core 20-compatible environments</li></dt>
<dt>If not, try our own most recent (we stopped building RPMs many years ago and are looking for a volunteer to do this instead) self-built NCO RPMs (install with, e.g., ‘<tt>yum install nco-3.9.5-1.fc7.i386.rpm</tt>’):
@@ -1019,23 +826,21 @@ Thanks to Gavin Burris and Kyle Wilcox for documenting build procedures for RHEL
<h3><a href="http://www.apple.com/macosx/">Mac OS X/Darwin</a></h3>
<ul>
<!--
-/usr/bin/scp /home/pvicente/nco/doc/index.shtml pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.4.macosx.10.9.tar.gz pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
+# Mac OS X 10.9 (Mavericks) systems (aerosol):
+/usr/bin/scp ~/nco/doc/index.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+cd ~/bin/MACOSX;tar cvzf ${DATA}/nco-4.4.5.macosx.10.9.tar.gz nc*;scp ${DATA}/nco-4.4.5.macosx.10.9.tar.gz zender,nco at web.sf.net:/home/project-web/nco/htdocs/src
-->
The most up-to-date binaries are probably those in the tarball below. Those unfamiliar with installing executables from tarballs may try the (older) <a href="http://en.wikipedia.org/wiki/Apple_Disk_Image">DMG</a> files (you may need to add <tt>/opt/local/bin</tt> to your executable path to access those operators).
-<li><a href="src/nco-4.4.2.macosx.10.9.tar.gz">nco-4.4.2.macosx.10.9.tar.gz</a> (<!--#fsize file="src/nco-4.4.2.macosx.10.9.tar.gz"-->): Executables MacOSX 10.9-compatible (last updated <!--#flastmod file="src/nco-4.4.2.macosx.10.9.tar.gz"-->).
-(NB: These executables require the <a href="http://trac.macosforge.org/projects/macports/wiki">MacPorts</a> dependencies for <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">NCO</a>). Maintained by NCO Project.</li>
+<li><a href="src/nco-4.4.5.macosx.10.9.tar.gz">nco-4.4.5.macosx.10.9.tar.gz</a> (<!--#fsize file="src/nco-4.4.5.macosx.10.9.tar.gz"-->): Executables MacOSX 10.9-compatible (last updated <!--#flastmod file="src/nco-4.4.5.macosx.10.9.tar.gz"-->).
+(NB: These executables require
+ the <a href="http://trac.macosforge.org/projects/macports/wiki">MacPorts</a>
+ <a href="#bld_macports">dependencies</a> for <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">NCO</a>). Maintained by NCO Project.</li>
<li><a href="src/nco-4.0.3_x86_10.6.dmg">nco-4.0.3_x86_10.6.dmg</a> (<!--#fsize file="src/nco-4.0.3_x86_10.6.dmg"-->): For Mac OS 10.6 (last updated <!--#flastmod file="src/nco-4.0.3_x86_10.6.dmg"-->). Maintained by Chad Cantwell.</li>
<li><a href="src/nco-4.0.7_x86_10.6.dmg">nco-4.0.7_x86_10.6.dmg</a> (<!--#fsize file="src/nco-4.0.7_x86_10.6.dmg"-->): For Mac OS 10.6 (last updated <!--#flastmod file="src/nco-4.0.7_x86_10.6.dmg"-->). Maintained by Chad Cantwell.</li>
<li><a href="http://fink.sf.net">Fink</a> packages for <a href="http://fink.sf.net/pdb/package.php/nco">NCO</a>: Currently NCO 3.9.5. Maintained by Alexander Hansen.</li>
-<li><a href="http://trac.macosforge.org/projects/macports/wiki">MacPorts</a> infrastructure for <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">NCO</a>: <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">Portfile</a> for NCO 3.9.9. Maintained by Takeshi Enomoto.</li>
+<li><a href="http://trac.macosforge.org/projects/macports/wiki">MacPorts</a> infrastructure for <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">NCO</a>: <a href="http://svn.macports.org/repository/macports/trunk/dports/science/nco">Portfile</a> for NCO 4.4.4. Maintained by Takeshi Enomoto.</li>
</ul>
-<a name="python"></a> <!-- http://nco.sf.net#python -->
-<a name="NCOpy"></a> <!-- http://nco.sf.net#NCOpy -->
-<a name="pyt"></a> <!-- http://nco.sf.net#pyt -->
-<h3>Python Bindings <a href="https://github.com/jhamman/nco-bindings">Source</a> and <a href="http://www.hydro.washington.edu/~jhamman/hydro-logic/blog/2014/01/29/NCOpy">Documentation</a>
-
<a name="visual"></a> <!-- http://nco.sf.net#visual -->
<a name="mvs"></a> <!-- http://nco.sf.net#mvs -->
<a name="windows"></a> <!-- http://nco.sf.net#windows -->
@@ -1048,24 +853,25 @@ To build NCO from source yourself using MSVC or Qt, please see the <a href="nco_
<ul>
<!-- Copy files from http://glace.ess.uci.edu
/usr/bin/scp /home/pvicente/nco/doc/index.shtml pvicente,nco at web.sf.net:/home/project-web/nco/htdocs
-/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.4.windows.mvs.exe pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
-/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.4.win32.cygwin.tar.gz pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
-/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.4.macosx.10.9.tar.gz pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
+/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.5.windows.mvs.exe pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
+/usr/bin/scp /home/pvicente/windows_setup/nco-4.4.5.win32.cygwin.tar.gz pvicente,nco at web.sf.net:/home/project-web/nco/htdocs/src
-->
-<li><a href="src/nco-4.4.2.windows.mvs.exe">nco-4.4.2.windows.mvs.exe</a> (<!--#fsize file="src/nco-4.4.2.windows.mvs.exe"-->) : Windows Self-Extracting Installer (last updated <!--#flastmod file="src/nco-4.4.2.windows.mvs.exe"-->). Maintained by NCO Project.</li>
+<li><a href="src/nco-4.4.4.windows.mvs.exe">nco-4.4.4.windows.mvs.exe</a> (<!--#fsize file="src/nco-4.4.4.windows.mvs.exe"-->) : Windows Self-Extracting Installer (last updated <!--#flastmod file="src/nco-4.4.4.windows.mvs.exe"-->). Maintained by Pedro Vicente.</li>
</ul>
<a name="cygwin"></a> <!-- http://nco.sf.net#cygwin -->
<h3><a href="http://www.microsoft.com">Microsoft</a> Windows</a> (running <a href="http://www.cygwin.org">Cygwin</a> environment, compiled with GNU-toolchain)</h3>
<ul>
-<li><a href="src/nco-4.4.2.win32.cygwin.tar.gz">nco-4.4.2.win32.cygwin.tar.gz</a> (<!--#fsize file="src/nco-4.4.2.win32.cygwin.tar.gz"-->): Executables Cygwin-compatible (last updated <!--#flastmod file="src/nco-4.4.2.win32.cygwin.tar.gz"-->). Maintained by NCO Project.</li>
-First install <tt>curl</tt> (in the "Web" category of Cygwin setup),
-and point the environment variable <tt>UDUNITS2_XML_PATH</tt> to the
-<tt>udunits2.xml</tt> file, e.g., with
-<tt>export UDUNITS2_XML_PATH='/usr/local/share/udunits/udunits2.xml'</tt>.
-Thanks to Mark Hadfield for creating Cygwin tarballs.
-Thanks to Cygnus Solutions and RedHat Inc. for developing and supporting Cygwin over the years.
+<li><a href="src/nco-4.4.4.win32.cygwin.tar.gz">nco-4.4.4.win32.cygwin.tar.gz</a> (<!--#fsize file="src/nco-4.4.4.win32.cygwin.tar.gz"-->): Executables Cygwin-compatible (last updated <!--#flastmod file="src/nco-4.4.4.win32.cygwin.tar.gz"-->). Maintained by NCO Project.</li>
</ul>
+First install <tt>curl</tt> (in the "Web" category of Cygwin setup), and point the environment variable <tt>UDUNITS2_XML_PATH</tt> to the <tt>udunits2.xml</tt> file, e.g., with <tt>export UDUNITS2_XML_PATH='/usr/local/share/udunits/udunits2.xml'</tt>.
+Thanks to Mark Hadfield and Pedro Vicente for creating Cygwin tarballs.
+Thanks to Cygnus Solutions and RedHat Inc. for developing and supporting Cygwin over the years.
+
+<a name="python"></a> <!-- http://nco.sf.net#python -->
+<a name="NCOpy"></a> <!-- http://nco.sf.net#NCOpy -->
+<a name="pyt"></a> <!-- http://nco.sf.net#pyt -->
+<h3><a href="http://www.python.org">Python</a> Bindings <a href="https://github.com/jhamman/nco-bindings">Source</a> and <a href="http://www.hydro.washington.edu/~jhamman/hydro-logic/blog/2014/01/29/NCOpy">Documentation</a>
<hr></p>
<!-- End http://nco.sf.net#bnr -->
@@ -1143,15 +949,13 @@ Otherwise, you may be on your own.</li>
<a name="NCAR"></a> <!-- http://nco.sf.net#NCAR -->
<a name="ncar"></a> <!-- http://nco.sf.net#ncar -->
<li><i>Does NCAR support NCO?</i>
-The NCAR CISL Technical Consulting Group (TCG) supports NCO like other
-community software packages such as <tt>lapack</tt>.
-No other NCAR division has coordinated NCO support.
+The NCAR CISL Consulting Service Group (CSG) supports NCO like other
+software packages.
The NCAR CISL-suported executables are made available through
-“modules” so try <tt>module add nco</tt>.
-If you notice problems with the NCO installation on CISL machines,
-or if you would benefit from a more recent release or patch, then
-inform the relevant system administrators, e.g.,
-<a href="mailto:consult1 at ncar.ucar.edu">NCAR User Support</a>.
+“modules” so try <tt>module load nco</tt>.
+If you notice problems with the NCO installation on CISL machines, or
+if you would benefit from a more recent release or patch, then ask
+<a href="http://www2.cisl.ucar.edu/docs/help">cislhelp</a>.
If you have a comment, suggestion, or bug report, then contact the
developers as described below.
</li>
@@ -1168,11 +972,11 @@ This list is for NCO-related announcements, not for questions.
<!-- http://nco.sf.net#README -->
<dt><a name="README/ChangeLog/TODO"></a></dt>
<h2>README/ChangeLog/TODO</h2>
-<p>Files containing useful information about the current NCO distribution:
+<p>Files containing useful information about the current distribution:
<ul>
-<li><a href="./README"><tt>README</tt></a> Platforms and software required by NCO</li>
-<li><a href="./ChangeLog"><tt>ChangeLog</tt></a> History of NCO changes</li>
-<li><a href="./TODO"><tt>TODO</tt></a> An unordered list of features and fixes we plan for NCO</li>
+<li><a href="./README"><tt>README</tt></a> Platforms and software required</li>
+<li><a href="./ChangeLog"><tt>ChangeLog</tt></a> Change History since 1997 (version 0.9)</li>
+<li><a href="./TODO"><tt>TODO</tt></a> An unordered list of features and fixes we plan</li>
</ul>
<hr></p>
<!-- End http://nco.sf.net#README -->
@@ -1181,14 +985,14 @@ This list is for NCO-related announcements, not for questions.
<dt><a name="Source"></a><a name="src"></a></dt>
<h2>Get NCO Source Code</h2>
-The best way to acquire NCO sources is with <a href="http://www.cvshome.org">CVS</a>.
+The best way to acquire the source is with <a href="http://www.cvshome.org">CVS</a>.
The second best way is to download the source as a compressed tarfile:
<ul>
<li>
-<a href="src/nco-4.4.4.tar.gz">nco-4.4.4.tar.gz</a>
-(<!--#fsize file="src/nco-4.4.4.tar.gz"--> compressed tar-file)<br>
-<!--#exec cmd="openssl dgst -md5 src/nco-4.4.4.tar.gz"--><br>
-<!--#exec cmd="openssl dgst -sha1 src/nco-4.4.4.tar.gz"-->
+<a href="src/nco-4.4.5.tar.gz">nco-4.4.5.tar.gz</a>
+(<!--#fsize file="src/nco-4.4.5.tar.gz"--> compressed tar-file)<br>
+<!--#exec cmd="openssl dgst -md5 src/nco-4.4.5.tar.gz"--><br>
+<!--#exec cmd="openssl dgst -sha1 src/nco-4.4.5.tar.gz"-->
</li>
</ul>
@@ -1211,19 +1015,19 @@ Hit <tt>return</tt> when asked for the CVS password.
This login procedure is only required the first time you access the CVS server.
Then you may retrieve any NCO distribution you wish.
Usually you wish to retrieve a recent tagged (i.e., released) version.
-This command retrieves and places NCO version <tt>4.4.4</tt> (which is
-tagged as <tt>nco-4_4_4</tt> due to CVS rules) into local directory
-<tt>nco-4.4.4</tt>:
-<p><tt>cvs -z3 -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco co -r nco-4_4_4 -d nco-4.4.4 nco</tt></p>
+This command retrieves and places NCO version <tt>4.4.5</tt> (which is
+tagged as <tt>nco-4_4_5</tt> due to CVS rules) into local directory
+<tt>nco-4.4.5</tt>:
+<p><tt>cvs -z3 -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco co -r nco-4_4_5 -d nco-4.4.5 nco</tt></p>
This command retrieves the current (“bleeding edge”)
development version of NCO into a local directory named <tt>nco</tt>:
<p><tt>cvs -z3 -d:pserver:anonymous at nco.cvs.sf.net:/cvsroot/nco co -kk nco</tt></p>
Track changes to the development version using
<p><tt>cd nco;cvs update -kk</tt></p>
One difference between running a "tagged" release
-(e.g., <tt>nco-4_4_4</tt>) and the development version is that the
+(e.g., <tt>nco-4_4_5</tt>) and the development version is that the
tagged release operators will print a valid version number (e.g.,
-<tt>4.4.4</tt>) when asked to do so with the <tt>-r</tt> flag
+<tt>4.4.5</tt>) when asked to do so with the <tt>-r</tt> flag
(e.g., <tt>ncks -r</tt>).
The development version simply places today's date in place of the
version.
@@ -1237,13 +1041,10 @@ over versions should largely disappear.
Some developers find this documentation helpful, as it can clarify code and data
relationships in the code.</p>
<ul>
-<li><a href="http://sand.ess.uci.edu/nco/doxygen/main/files.html">
-Source documentation for NCO and NetCDF4(alpha13)</a></li>
+<li><a href="http://dust.ess.uci.edu/nco/doxygen/main/files.html">
+Source documentation for NCO and netCDF4(alpha13)</a></li>
</ul>
-<p>Please be aware that the documentation may be slightly inaccurate and
-infrequently updated. Comments and suggestions are certainly welcomed on the
- <a href="http://sf.net/projects/nco/forums/forum/9829">forums</a>.
-</p>
+<p>The Doxygen documentation is infrequently (i.e., never since Daniel left) updated.</p>
</ul>
<hr></p>
<!-- End http://nco.sf.net#src -->
@@ -1262,22 +1063,22 @@ we recommend that you first try the pre-built binaries for your
system, e.g.,
<tt>
<dt>sudo aptitude install nco # Debian-based systems like Debian, Mint, Ubuntu</dt>
-<dt>sudo yum-install nco # RPM-based systems like CentOS, Fedora, RHEL</dt>
+<dt>sudo yum-install nco # RPM-based systems like CentOS, Fedora, openSUSE, RHEL</dt>
+<dt>sudo port install nco # MacPorts (after installing MacPorts on Mac OS X)</dt>
</tt>
-If the pre-built executables do not satisfy you, or are out-of-date
-and you want the latest, greatest NCO features, then the recommended
-first steps to build (i.e., compile, for the most part) NCO from
-source code are to install
+If pre-built executables do not satisfy you (e.g., are out-of-date)
+and you want the latest, greatest features, then the first steps to
+build (i.e., compile, for the most part) NCO from source code are to
+install the prerequisites:
<a href="http://www.antlr.org">ANTLR 2.7.x</a> (not version 3.x or 4.x!) (required for <tt>ncap2</tt>),
<a href="http://www.gnu.org/software/gsl">GSL</a> (desirable for <tt>ncap2</tt>),
<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a> (absolutely required),
<a href="http://opendap.org">OPeNDAP</a> (enables network transparency), and
-<a href="http://www.unidata.ucar.edu/packages/udunits">UDUnits</a> (allows dimensional unit transformations)
-before building NCO.
+<a href="http://www.unidata.ucar.edu/packages/udunits">UDUnits</a> (allows dimensional unit transformations).
If possible, install this software stack from pre-built binaries
(commands to do so on Debian and RPM systems are given just below).
-Failing that (e.g., you lack root access or are on a non-package
-system such as AIX), build these all with the same compiler (and switches).
+Failing that (e.g., lack of root access, or systems without packages
+such as AIX), build these all with the same compiler and switches.
Recent versions of netCDF automatically build OPeNDAP and UDUnits.
NCO is mostly written in C99, and although you <i>may</i> mix and
match compilers, this is often difficult in practice and is not recommended.
@@ -1336,7 +1137,7 @@ For Mac OS X with MacPorts:
<tt>
<dt>wget http://dust.ess.uci.edu/nco/nco.tar.gz</dt>
<dt>tar xvzf nco.tar.gz</dt>
-<dt>cd nco-4.4.4</dt>
+<dt>cd nco-4.4.5</dt>
<dt>./configure --prefix=/usr/local</dt>
<dt>make</dt>
<dt>sudo make install</dt>
@@ -1358,287 +1159,8 @@ For more sophisticated build/install options, see the next section.
<dt><a name="Makefile"></a></dt> <!-- http://nco.sf.net#Makefile -->
<dt><a name="hnt"></a></dt> <!-- http://nco.sf.net#hnt -->
<dt><a name="bld_hnt"></a></dt> <!-- http://nco.sf.net#bld_hnt -->
-<h2>Hints to Build-from-Source:</h2>
-
-<ul><b>Generic Build Hints:</b>
-
-<a name="bld_cnf"></a> <!-- http://nco.sf.net#bld_cnf -->
-<li><i>The two NCO build mechanisms:</i>
-NCO has two build mechanisms: (1) GNU configure and
-(2) a custom Makefile (<tt>nco/bld/Makefile</tt>)
-designed for hand-editing.
-Try the traditional GNU <tt>configure</tt> method first, i.e.,
-<tt>./configure;make;make check;make install</tt>.
-This method involves no hand-editing of makefiles, but trouble-free
-builds with it are less common than we would like.
-The file <tt>nco/configure.eg</tt> contains a table which describes the
-success you can expect building NCO with the <tt>configure</tt>
-mechanism.
-If the simple <tt>configure</tt> recipe above does not work, savvy
-users may find it straightforward to modify and use the following, more
-advanced <tt>configure</tt> recipe:
-<tt>
-<pre class="example">
-# gcc/g++ Sysadmins use/modify this to install/update NCO in /usr/local, based on netCDF4 also in /usr/local (works on givre 20100727):
-export GNU_TRP=`~/nco/autobld/config.guess`
-cd ~/nco;/bin/rm -f *.${GNU_TRP}.foo;make distclean
-CPPFLAGS='-DHAVE_NETCDF4_H -I/usr/local/include' LDFLAGS='-L/usr/local/lib' ./configure --prefix='/usr/local' --enable-ncap2 --enable-netcdf4 > nco.configure.${GNU_TRP}.foo 2>&1
-/bin/cp -f config.log nco.config.log.${GNU_TRP}.foo
-/bin/cp -f libtool nco.libtool.${GNU_TRP}.foo
-make clean;make > nco.make.${GNU_TRP}.foo 2>&1
-make check >> nco.make.${GNU_TRP}.foo 2>&1
-sudo make install >> nco.make.${GNU_TRP}.foo 2>&1
-</pre>
-</tt>
-This is the recipe that the developers use to test <tt>configure</tt>
-on their machines.
-Please contribute patches required to get the <tt>configure</tt>
-mechanism working properly for NCO on your platform.
-The <a href="http://dust.ess.uci.edu/nco/rgr">regressions archive</a>
-contains gory details of successful (and failed) builds for many platforms.
-Plaform-specific build hints (CentOS, Mac OS X, RHEL, Solaris)
-are listed <a href="#bld_plt_spc">below</a>.
-<br>
-
-All platforms continue to work fine with the <tt>nco/bld/Makefile</tt>
-method:
-<tt>
-<pre class="example">
-export MY_BIN_DIR='/home/username/bin' # Executables installed here
-export MY_OBJ_DIR='/home/username/obj' # Object files placed here
-export MY_LIB_DIR='/home/username/lib' # Libraries built here
-mkdir -p ${MY_BIN_DIR} ${MY_OBJ_DIR} ${MY_LIB_DIR}
-cd ~/nco/bld
-make dir
-make all
-make ncap2
-make test
-</pre>
-</tt>
-Disadvantages are that <tt>nco/bld/Makefile</tt> (1) Usually requires
-editing to fix your platforms paths; (2) Does not support shared
-libraries; and (3) Requires a degree from Hogwarts to understand.
-</li>
-
-<!-- http://nco.sf.net#dpl_sym -->
-<a name="dpl_sym"></a>
-<li><i>Duplicate symbols errors:</i>
-When building NCO with the netCDF4 library and headers, some compilers
-emit errors due to duplicate symbol definitions.
-This arises because of the complexity of the build system.
-Essentially, NCO has to define some netCDF API prototypes itself
-to handle the corner case where the netCDF4 distribution is used
-to build netCDF3 libraries.
-We have tried to address this issue using <tt>autoconf/configure</tt>
-but it is beyond our abilities.
-The fix is to manually tell NCO that the netCDF4 header
-file <tt>netcdf.h</tt> is in fact being used so that NCO should
-not attempt to define these prototypes.
-Do this, e.g., with <tt>CPPFLAGS='-DHAVE_NETCDF4_H'</tt> or
-<tt>USR_TKN='-DHAVE_NETCDF4_H'</tt> if you use <tt>configure</tt>.
-</li>
-
-<!-- http://nco.sf.net#bld_chn -->
-<a name="bld_chn"></a>
-<li><i>Build Chain Version Incompatibilities:</i>
-NCO requires GNU <tt>make</tt> version ≥ 3.78.1 to support target-specific variable values in <tt>bld/Makefile</tt>.
-NCO most often fails to build because <tt>ncap</tt> fails to build.
-Two of the most common reasons that <tt>ncap</tt> fails to build are
-(1) GNU <tt>bison</tt> is out-of-date (upgrade <tt>bison</tt>)
-and (2) <tt>--enable-optimize-*</tt> is specified to
-<tt>configure</tt> (do not specify it).<br>
-</li>
-
-<!-- http://nco.sf.net#bld_c99 -->
-<a name="bld_c99"></a>
-<li><i>C99-compliance & old compilers:</i>
-NCO versions ≥ 2.9.8 require the compiler to
-support the 1999 ISO C-Standard called C99.
-NCO takes advantage of two C99 features, restricted pointers and
-designated initializers.
-To build NCO versions ≥ 2.9.8 without a C99-compliant
-compiler, simply undefine the <tt>restrict</tt> type qualifier
-before compiling NCO.
-Do this, e.g., with <tt>CPPFLAGS='-Drestrict='</tt>.
-More details on C99 compatibility are in the header file
-<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco.h"><tt>nco/src/nco/nco.h</tt></a>.<br>
-</li>
-
-<!-- http://nco.sf.net#bld_netcdf -->
-<a name="bld_netcdf"></a>
-<li><i>Old netCDF libraries:</i>
-NCO versions ≥ 3.0.0 require netCDF versions
-≥ 3.6 to take advantage of the new 64-bit offset file type.
-The library <i>and</i> include directories (e.g., <tt>/usr/lib</tt> and
-<tt>/usr/include</tt>, respectively) for netCDF version ≥ 3.6
-must be on the path searched by the compiler, and must precede the
-locations of any older netCDF installations.
-To build NCO versions ≥ 3.0.0 with older netCDF versions
-< 3.6, simply define the pre-processor token
-<tt>NC_64BIT_OFFSET</tt> to <tt>0</tt> before compiling NCO.
-Do this, e.g., with <tt>CPPFLAGS='-DNC_64BIT_OFFSET=0'</tt> or
-<tt>USR_TKN='-DNC_64BIT_OFFSET=0'</tt> if you use <tt>configure</tt>
-or <tt>bld/Makefile</tt>, respectively.
-Users attempting to build NCO with OPeNDAP versions ≤ 3.6.x may
-need this workaround because OPeNDAP did not fully support netCDF
-version 3.6.x functionality until OPeNDAP versions ≥ 3.7.0.
-(The indicator for this problem is a build error like
-<tt>"nco_fl_utl.c", line 30.20: 1506-045 (S) Undeclared identifier
-NC_64BIT_OFFSET</tt>.)
-All modern NCO versions require netCDF versions ≥ 3.5.0 to
-support <tt>nc_type NC_NAT</tt> in NCO source code.
-NCO versions 3.9.0 and greater (May, 2007) require netCDF versions
-≥ 3.6.0 to resolve the <tt>nc_inq_format()</tt> function.
-</li>
-
-<!-- http://nco.sf.net#bld_ncap -->
-<a name="bld_ncap"></a>
-<li><i><tt>ncap</tt> build hints:</i>
-<tt>ncap</tt> is a sophisticated and somewhat fragile program.
-<tt>ncap</tt> requires <tt>flex</tt> to build correctly.
-AT&T <tt>lex</tt> will not work because it does not understand
-<tt>EOF</tt> rules used in <tt>ncap_lex.l</tt>.
-<tt>bison</tt> version 1.29 (the default version on early
-Mac OS X) is buggy and does not parse <tt>ncap_yacc.y</tt>
-correctly; previous and later <tt>bison</tt>'s work
-correctly.
-<tt>bison</tt> version 1.25 will not build <tt>ncap</tt> on Solaris.
-Please upgrade <tt>bison</tt> to the latest version (e.g., 1.875+)
-before reporting <tt>ncap</tt> build problems.
-If <tt>ncap</tt> keeps you from building NCO, and you do not need
-<tt>ncap</tt>, configure with <tt>--disable-ncap</tt> (and know that
-<tt>ncwa</tt> will fail to build as a result).
-</li>
-
-<!-- http://nco.sf.net#bld_GSL -->
-<a name="bld_gsl"></a><a name="bld_GSL"></a>
-<li><i>Build Hints with GSL:</i><br>
-NCO versions 3.9.6— support automatic building and linking
-for <a href="http://www.gnu.org/software/gsl">GSL</a>
-versions 1.4—.
-Earlier GSL versions are not supported.<br>
-</li>
-
-<!-- http://nco.sf.net#bld_DAP -->
-<a name="bld_dap"></a><a name="bld_DAP"></a><a name="bld_DODS"></a><a name="bld_OPeNDAP"></a>
-<li><i>Build Hints with DAP:</i><br>
-NCO versions 3.9.9— support automatic building and linking
-for DAP supplied from <a href="http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/DAP-Support.html">libnetcdf</a> versions 4.1-beta1 and beyond<br>
-NCO versions 3.1.3— support automatic building and linking
-for <a href="http://opendap.org">OPeNDAP</a> versions 3.6.x and
-GCC versions 4.0+.<br>
-NCO versions 3.0.1—3.1.2 support automatic building and linking
-for <a href="http://opendap.org">OPeNDAP</a> versions 3.5.x and
-GCC versions 3.4+.<br>
-NCO versions 2.8.5—3.0.0 support automatic building and linking
-for <a href="http://opendap.org">OPeNDAP</a> versions 3.4.x and
-GCC versions 3.3+.<br>
-NCO versions ?.?.?—2.8.4 support automatic building and linking
-for <a href="http://opendap.org">DODS</a> versions 3.2.x and
-GCC versions 3.2+.<br>
-No other version combinations are supported.
-</li>
-
-<!-- http://nco.sf.net#bld_nco_c++ -->
-<a name="bld_nco_c++"></a>
-<li><i><tt>libnco_c++</tt> build hints:</i>
-<tt>libnco_c++</tt> requires a good C++ compiler to build correctly.
-Few people need <tt>libnco_c++</tt>, so the workaround is not to build it.
-This is done by configuring with <tt>--disable-nco_cplusplus</tt>.
-</li>
-
-</ul>
-
-<!-- http://nco.sf.net#bld_plt_spc -->
-<a name="bld_plt_spc"></a>
-<ul><b>Platform-Specific Build Hints:</b>
-<!-- http://nco.sf.net#bld_aix -->
-<a name="bld_aix"></a>
-<li><i>AIX build hints:</i>
-NCO versions 2.8.7+ do not build with autotools under AIX when
-<tt>--enable-optimize-*</tt> is selected.
-The workaround is to not use <tt>--enable-optimize-*</tt>.
-NCO versions 2.9.7+ do not build shared libraries with AIX xlc
-compilers because of silly AIX library dependencies activated
-by OpenMP directives.
-The workaround is to configure with <tt>--disable-shared</tt>.
-</li>
-
-<!-- http://nco.sf.net#bld_irix -->
-<a name="bld_irix"></a>
-<li><i>IRIX build hints:</i>
-The most common problem with building on SGI IRIX is an out-of-date toolchain.
-</li>
-
-<!-- http://nco.sf.net#bld_osx -->
-<a name="bld_osx"></a>
-<li><i>Mac OS X build hints:</i>
-Mac OS X users report success building NCO without patches so
-long as they (1) Install the latest version of <tt>bison</tt>,
-(2) Disable shared libraries and (3) Disable extended regular
-expressions. This is done with
-<tt>./configure --disable-regex --disable-shared</tt>
-
-Building NCO with shared libraries on Mac OS X on may be possible.
-To try, first re-build and re-install the netCDF library using
-<tt>CFLAGS=-fno-common</tt>.
-Apparently netCDF, unlike most codes, does not set this automatically.
-Then build NCO normally.
-
-Mac OS X ships with a broken version of the POSIX <tt>cut</tt>
-utility which causes many NCO regression tests to appear to fail.
-In fact the NCO commands succeed, but the <tt>cut</tt> output fails.
-The workaround is not to heed the regression tests, or to install a
-working <tt>cut</tt>, e.g., from the GNU <tt>coreutils</tt> package.
-</li>
-
-<!-- http://nco.sf.net#bld_rhel -->
-<a name="bld_rhel"></a>
-<a name="bld_centos"></a> <!-- http://nco.sf.net#bld_centos -->
-<li><i>RHEL build hints:</i>
-Scripts for generating executables for recent (4.0.x, ~2011) versions of NCO for RedHat Enterprise Linux 5 (RHEL5) and CentOS5 platforms are described <a href="http://sf.net/projects/nco/forums/forum/9830/topic/4089501">here</a>.
-Older information on building x86_64 RPMs is available <a href="http://dust.ess.uci.edu/wangd/s9y">here</a>.
-</li>
-
-<!-- http://nco.sf.net#bld_slr -->
-<a name="bld_slr"></a>
-<li><i>Solaris build hints:</i>
-All recent NCO versions build with autotools on Solaris 2.7—2.9.
-The most common problem with building on Solaris with
-<tt>cc</tt>/<tt>CC</tt> is that <tt>bison</tt> may be out-of-date.
-Install an up-to-date <tt>bison</tt> (e.g., 1.875+).
-Solaris 2.10, i.e., Solaris10, had the audacity to change the
-prototype of the <tt>ctime_r()</tt> function and so does not build
-NCO 3.0.1.
-The fix is to upgrade to the current NCO version.
-</li>
-
-<!-- http://nco.sf.net#bld_sx -->
-<a name="bld_sx"></a>
-<li><i>SX build hints:</i>
-NEC SX does not understand the <tt>S_ISLNK</tt> macro,
-preferring instead the (non-POSIX) <tt>S_IFLNK</tt> macro.
-This macro appears in the file
-<a href="http://nco.cvs.sf.net/nco/nco/src/nco/nco_fl_utl.c"><tt>nco_fl_utl.c</tt></a>.
-The patch I wrote for this may be broken.
-Will someone with NEC SX please send us a working patch?
-</li>
-
-<!-- http://nco.sf.net#bld_wnd -->
-<a name="bld_wnd"></a>
-<li><i>Windows build hints:</i>
-Building on Microsoft Windows is possible with Cygwin.
-The resulting executables will behave normally on local files,
-but will not have some (most?) of NCO's network functionality
-(e.g., <tt>scp</tt>, <a href="http://opendap.org">OPeNDAP</a>).
-See the <a href="http://nco.sf.net/nco.html#wnd">User's Guide</a>
-for more details.
-</li>
-
-<!--Qt/MSVC -->
-<li><i>Windows build with Qt/MSVC:</i>
-As of NCO 4.2.0, you may build NCO from source using MSVC and Qt, please see the <a href="nco_qt_msvc.shtml">NCO Qt/MSVC build</a> page.
-</li>
+Still having trouble building NCO from source? Read these
+<a href="./build_hints.shtml">Build Hints</a>
</ul>
<hr></p>
@@ -1656,15 +1178,17 @@ The unsatisfied or adventurous may try my personal executables which
are built from the “main trunk” of NCO, not a tagged
version, and therefore may behave slightly differently.
<ul>
-<li>UCI ESS <tt>greenplanet.ps.uci.edu</tt> (Linux 2.6.x): <tt>~zender/bin/LINUX</tt></li>
-<li>UCI ESS <tt>dust.ess.uci.edu</tt> (Linux 3.2.x): <tt>~zender/bin/LINUXAMD64</tt></li>
<li>NCAR CISL <tt>yellowstone.ucar.edu</tt> (Linux 2.6.x): <tt>~zender/bin/LINUXAMD64</tt></li>
<li>NCAR CISL <tt>mirage0.ucar.edu</tt> (Linux 2.6.x): <tt>~zender/bin/LINUXAMD64</tt></li>
+<li>ORNL Rhea <tt></tt> (Linux 2.6.x): <tt>~zender/bin/LINUXAMD64</tt></li>
+<li>UCI ESS <tt>greenplanet.ps.uci.edu</tt> (Linux 2.6.x): <tt>~zender/bin/LINUX</tt></li>
+<li>UCI ESS <tt>dust.ess.uci.edu</tt> (Linux 3.2.x): <tt>~zender/bin/LINUXAMD64</tt></li>
</ul>
<hr></p>
<!-- End http://nco.sf.net#NCAR -->
<!-- http://nco.sf.net#BM -->
+<!-- 20140615: out-of-date
<dt><a name="BM"></dt>
<h2>Benchmarks</h2>
<p>
@@ -1695,68 +1219,27 @@ The MPI operators will run with most MPI implementations, including LAM, MPICH,
LAM installs easily with our own testing environment (latest Ubuntu).
</p>
<hr>
+--> <!-- Out of date -->
<!-- End http://nco.sf.net#BM -->
<!-- http://nco.sf.net#bug -->
<dt><a name="bug"></a></dt> <!-- http://nco.sf.net#bug -->
<dt><a name="prb"></a></dt> <!-- http://nco.sf.net#prb -->
-<h2>Known Problems</h2>
-
-Problems with recent releases:
+<h2>Known Problems from 2013 (version 4.2.4) Onwards</h2>
<ul><b>Recent Generic Run-time Problems:</b>
-<!-- http://nco.sf.net#bug_mm3 -->
-<a name="bug_mm3"></a>
-<li><i><tt>MM3</tt> slowdown:</i>
-A longstanding “feature” of netCDF3 was identified in
-March, 2012, and is now known by the tag MM3.
-The MM3 issue can lead to unusually slow performance.
-The problem is triggered by an aggregate pattern of file access so the
-workaround must be implemented in the application software (e.g., NCO)
-rather than in the netCDF library itself.
-The name MM3 fits because the problem is normally encountered on
-Multi-record Multi-variable netCDF3 files.
-And we call our “solution” the MM3-workaround.
-If you encounter unusually slow NCO performance while using NCO to
-analyze MM3 files on a large blocksize filesystem,
-chances are you are encountering an MM3-induced slowdown.
-NCO release 4.1.0 implements the MM3-workaround for <tt>ncks</tt>.
-It speeds-up common ncks sub-setting on NCAR's GLADE by 10-50x.
-MM3-induced slowdowns are present in other NCO operators and we are
-prioritizing our MM3-patches to those encountered most often.
-Thanks to Gary Strand for reporting this problem, and to Russ Rew for
-creating the workaround algorithm, which is also now in <tt>nccopy</tt>.
-</li>
-
-<!-- http://nco.sf.net#bug_nofill -->
-<a name="bug_nofill"></a>
-<li><i><tt>NOFILL</tt> bug:</i>
-All netCDF versions prior to 4.1.3 may create corrupt netCDF3 files
-when linked to any version of NCO except 4.0.8.
-The solution is to install netCDF version 4.1.3 or later.
-The corruption occurs silently (without warning or error messages).
-The problem has been seen "in the wild" only on filesystems with
-large block sizes (e.g., Lustre), although it may be more widespread.
-It is caused by a netCDF bug that NCO triggers by invoking
-NOFILL mode for faster writes. Hence it is called the NOFILL bug.
-The bug is hard to trigger, it depends on a rare interaction of
-filesystem block-size, hyperslab size, and order-of-variable writing.
-The bug exists in all versions of netCDF through 4.1.2.
-
-If you have a large block filesystem and cannot upgrade your netCDF
-library, then use NCO version 4.0.8, which disables NOFILL mode (and
-thus writes files more slowly).
-NCO 4.0.8 and will workaround the NOFILL bug on all versions of netCDF
-(i.e., 4.1.2 and earlier).
-Hence NCO 4.0.8 will always correctly write netCDF3 files.
-Other temporary workarounds include creating only netCDF4 files
-(e.g., <tt>ncks -4 ...</tt>) instead of netCDF3 files.
-The NOFILL patch included in NCO 4.0.8 was subsequently removed
-in NCO 4.0.9, which assumes that netCDF 4.1.3 or later is installed.
-</li>
+No known generic run-time problems with recent releases.
</ul>
<ul><b>Recent Operator-specific Run-time Problems:</b>
+<!-- http://nco.sf.net#bug_cnk_hyp -->
+<a name="bug_cnk_hyp"></a>
+<li><i>Chunking while hyperslabbing bug:</i>
+Versions 4.3.X—4.4.4 of most operators could send incorrect
+chunking requests to the netCDF library, resulting in failures.
+This occurred only while simultaneously hyperslabbing.
+The solution is to upgrade to NCO 4.4.5.
+</li>
<!-- http://nco.sf.net#bug_ncwa_mask_condition -->
<a name="bug_ncwa_mask_condition"></a>
@@ -1773,7 +1256,7 @@ should upgrade. NB: The <tt>-m -M -T</tt> form of <tt>ncwa</tt>
masking is/was not buggy.
Thus the workaround is to use the <tt>-m -M -T</tt> form
of <tt>ncwa</tt> masking, while the long-term solution is to upgrade
-to NCO 4.4.4.
+to NCO 4.4.4+.
</li>
<!-- http://nco.sf.net#bug_ncra_no_fl_close -->
@@ -1791,7 +1274,7 @@ This is embarassing because NCO has always been designed to work with
arbitrary numbers of input files and we want power users to be
comfortable running it on hundreds of thousands of input files.
The workaround is to avoid versions 4.3.9—4.4.0, while the
-long-term solution is to upgrade to NCO 4.4.1.
+long-term solution is to upgrade to NCO 4.4.1+.
</li>
<!-- http://nco.sf.net#bug_ncra_mro_mss_val -->
@@ -1806,7 +1289,7 @@ and the symptoms should be noticeable.
The workaround is to run the affected versions of ncra using the
<tt>--flt</tt> switch, so that single-precision floating point numbers
are not promoted prior to arithmetic.
-The solution is to upgrade to NCO 4.4.0.
+The solution is to upgrade to NCO 4.4.0+.
</li>
<!-- http://nco.sf.net#bug_ncwa_lmt -->
@@ -1819,7 +1302,7 @@ This could produce incorrect answers that look correct.
This bug only affected hyperslabbed statistics (those produced
by simultaneously invoking <tt>-a</tt> and <tt>-d</tt> switches);
“global averages” were unaffected.
-We urge all <tt>ncwa</tt> users to upgrade to NCO 4.3.6.
+We urge all <tt>ncwa</tt> users to upgrade to NCO 4.3.6+.
</li>
<!-- http://nco.sf.net#bug_ncpdq_upk -->
@@ -1844,368 +1327,7 @@ unpack data prior to arithmetic.
No known platform-specific problems with recent releases.
</ul>
-</ul>
-
-Problems with older releases:
-
-<ul><b>Older Generic Run-time Problems:</b>
-
-<!-- http://nco.sf.net#bug_hyp_dgn -->
-<a name="bug_hyp_dgn"></a>
-<li><i>Degenerate hyperslabbing bug:</i>
-Versions ???—4.0.6 could return incorrect hyperslabs when
-user-specified hyperslabs did not include at least one point.
-In such cases, instead of returning no data, hyperslabs could return all data.
-To determine whether your NCO is affected by this bug, run these commands:
-<tt>ncks -O -v lat -d lat,20.,20.001 ~/nco/data/in.nc ~/foo.nc;ncks -H ~/foo.nc</tt>
-If the returned hyperslab contains any data, then your NCO is buggy
-(because that hyperslab should be empty).
-This can lead to incorrect answers for hyperslabs that should be empty.
-Analogous problems would occur with empty auxiliary coordinate bounding boxes.
-Although most users do not specify empty hyperslabs, we urge all users
-to upgrade to NCO 4.0.7+ just to be safe.
-</li>
-
-<!-- http://nco.sf.net#bug_thr_msa -->
-<a name="bug_thr_msa"></a>
-<li><i>Threading problems with MSA:</i>
-NCO version 3.9.5 has a nasty bug that causes threaded arithmetic
-operators, e.g., <tt>nces</tt> to produce incorrect results under some
-conditions.
-The problem may occur whenever OpenMP is enabled and the operators
-run on a multi-core CPU with more than one thread.
-These incorrect answers, if generated, are relatively easy to notice.
-The number of threads used to generate a file is, by default, recorded
-in the global attribute <tt>nco_openmp_thread_number</tt> which may
-be examined with <tt>ncks -M foo.nc | grep nco_openmp_thread_number</tt>.
-The only action that will correct a file that you think (or know)
-contains corrupted data because of this NCO bug is to re-process the
-file with a non-buggy NCO version.
-<i>Version 3.9.5 is buggy and should be upgraded ASAP</i>.
-Be careful with data processed using this NCO version on multi-core CPUs.
-The (one-line!) patch to fix this bug in 3.9.5 is
-<a href="http://sf.net/forum/message.php?msg_id=6217274">here</a>.
-</li>
-
-<!-- http://nco.sf.net#bug_idx_hyp -->
-<a name="bug_idx_hyp"></a>
-<li><i>Index-based hyperslab problems:</i>
-NCO versions 2.7.3—2.8.3 have a nasty bug that causes
-index-based hyperslabs, e.g., <tt>-d lat,1,</tt> to
-behave like value-based hyperslabs, e.g., <tt>-d lat,1.0</tt> under
-some conditions.
-Unfortunately, the incorrect answers generated may be hard to notice!
-This problem was most often enountered by users trying to assemble
-monthly averages using the stride feature of <tt>ncrcat</tt>.
-One common symptom is that the time-offset of the output file is
-incorrect.
-<i>Versions 2.7.3—2.8.3 are buggy and should be upgraded ASAP</i>.
-Re-do any data-processing that used index-based hyperslabbing with
-these versions of NCO.
-</li>
-</ul>
-
-<ul><b>Older Operator-specific Run-time Problems:</b>
-
-<!-- http://nco.sf.net#bug_ncks_aux -->
-<a name="bug_ncks_aux"></a>
-<li><i><tt>ncks</tt> bug with auxiliary coordinates:</i>
-Versions 4.2.x–4.3.1 of <tt>ncks</tt> did not correctly
-support auxiliary coordinates (specified with <tt>-X</tt>).
-Auxiliary coordinates continued to work with the other hyperslabbing
-NCO operators. Auxiliary coordinates once again work in all
-hyperslabbing operators, including on netCDF4 group files in operators
-that support them.
-Fixed in version 4.3.2.
-</li>
-
-<!-- http://nco.sf.net#bug_ncatted_strcmp -->
-<a name="bug_ncatted_strcmp"></a>
-<li><i><tt>ncatted</tt> bug on implicit attribute names:</i>
-Versions 4.2.x–4.3.0 of <tt>ncatted</tt> could segfault when
-processing attributes specified implicitly (i.e., by leaving the
-attribute field blank in the <tt>-a</tt> specification.
-Fixed in version 4.3.1.
-</li>
-
-<!-- http://nco.sf.net#bug_ncbo_ccm_ccsm_cf -->
-<a name="bug_ncbo_ccm_ccsm_cf"></a>
-<li><i><tt>ncbo</tt> bug handling certain special variables:</i>
-Version 4.3.0 of <tt>ncbo</tt> inadvertently always turns off
-certain <a href="http://nco.sf.net/nco.html#prc_xcp">exceptions</a>
-to variable list processing.
-This may cause some grid-related variables (e.g., <tt>ntrm</tt> and <tt>nbdate</tt>)
-and some non-grid variables (e.g., <tt>ORO</tt> and <tt>gw</tt>) to be
-arithmetically processed (e.g., subtracted) even when that makes no
-sense in most climate model datasets.
-Fixed in version 4.3.1.
-</li>
-
-<!-- http://nco.sf.net#bug_ncks_mtd -->
-<a name="bug_ncks_mtd"></a>
-<li><i><tt>ncks</tt> bug copying metadata:</i>
-Version 4.2.6 of <tt>ncks</tt> does not copy variable metadata by default.
-Thus output files appear stripped of metadata.
-One can work around this problem in 4.2.6 by specifying the <tt>-m</tt> option.
-Otherwise an upgrade is recommended.
-Fixed in version 4.3.0.
-</li>
-
-<!-- http://nco.sf.net#bug_ncks_sbs -->
-<a name="bug_ncks_sbs"></a>
-<li><i><tt>ncks</tt> bug subsetting variables:</i>
-Version 4.2.4 of <tt>ncks</tt> sometimes dumps core
-when subsetting variables with <tt>-v var</tt>.
-Fixed in version 4.2.5.
-</li>
-
-<!-- http://nco.sf.net#bug_ncks_mk_rec_dmn -->
-<a name="bug_ncks_mk_rec_dmn"></a>
-<li><i><tt>ncks</tt> bug with altering record dimensions:</i>
-Version 4.2.4 of <tt>ncks</tt> ignored both the
-<tt>--mk_rec_dmn</tt> and the <tt>--fix_rec_dmn</tt> switches.
-It exited successfully without altering the record variable.
-Fixed in version 4.2.5.
-</li>
-
-<!-- http://nco.sf.net#bug_nces_rec_var -->
-<a name="bug_nces_rec_var"></a>
-<li><i><tt>nces</tt> bug with non-record files:</i>
-Versions 4.2.1—4.2.3 of <tt>nces</tt> incorrectly referenced
-the record variable on files which do not contain it.
-This caused a segmentation violation and core dump.
-</li>
-
-<!-- http://nco.sf.net#bug_ncra_flg_bfr_nrm -->
-<a name="bug_ncra_flg_bfr_nrm"></a>
-<li><i><tt>ncra</tt> bug when last file(s) is/are superfluous:</i>
-Versions 4.2.1—4.2.3 of <tt>ncra</tt> incorrectly skipped
-writing the results of the final normalization when trailing files
-were superfluous (not used).
-In the most common case, all values are zeros in the output file.
-Upgrade if you call <tt>ncra</tt> with trailing superfluous files.
-</li>
-
-<!-- http://nco.sf.net#bug_ncecat_nintap -->
-<a name="bug_ncecat_nintap"></a>
-<li><i><tt>ncecat</tt> bug when files generated with <tt>-n</tt>:</i>
-Version 4.2.2 of <tt>ncecat</tt> could incorrectly skip the first
-input file in the default mode (RECORD_AGGREGATE) when
-the <tt>-n NINTAP</tt> switch is used to automate filename generation.
-Upgrade if you use <tt>ncecat -n</tt>.
-</li>
-
-<!-- http://nco.sf.net#bug_ncra_cf_crd_rec_crd -->
-<a name="bug_ncra_cf_crd_rec_crd"></a>
-<li><i><tt>ncra</tt> bug handling CF <tt>coordinates</tt> attributes
-that contain the name of the record coordinate:</i>
-Versions 4.0.3—4.0.4 of <tt>ncra</tt> incorrectly treat the
-record variable (usually <tt>time</tt>) as a fixed variable if it
-is specified in the <tt>coordinates</tt> attribute of any variable in
-a file processed with CCM/CCSM/CF metadata conventions.
-This bug caused core dumps, and even weirder behavior like
-creating imaginary time slices in the ouput.
-Upgrade recommended if you work with NCAR CCSM/CESM model output.
-
-One workaround that does not require NCO upgrades is to remove the
-record coordinate name (usually <tt>time</tt>) from
-the <tt>coordinates</tt> attribute of all variables in CF-compliant
-files before processing the file with <tt>ncra</tt>.
-</li>
-
-<!-- http://nco.sf.net#bug_ncra_cf_YYYYMMDD_date -->
-<a name="bug_ncra_cf_YYYYMMDD_date"></a>
-<li><i><tt>ncra</tt> bug averaging YYYYMMDD-format <tt>date</tt>
-variables in CCSM/CF-compliant files:</i>
-Versions ???—4.0.5 of <tt>ncra</tt> contain a bug which
-produces an incorrect average (usually zero) of the <tt>date</tt>
-variable which many CCSM/CF-compliant files use to track model dates
-in the human-readable YYYYMMDD-format.
-Averaging YYYYMMDD-format integers is intrinsically difficult, since
-such dates have calendar assumptions built-in.
-NCO attempts this in CCSM/CF-compliant files by using the
-<tt>nbdate</tt> (beginning date) and <tt>time</tt> (days
-since <tt>nbdate</tt>) variables to find the average date,
-converting that to YYYYMMDD, and writing that as the average value
-of <tt>date</tt>.
-</li>
-
-<!-- http://nco.sf.net#bug_ncks_nc4_nc4_hyp_fix -->
-<a name="bug_ncks_nc4_nc4_hyp_fix"></a>
-<li><i><tt>ncks</tt> bug hyperslabbinging fixed netCDF4 dimensions:</i>
-Versions 4.0.3—4.0.4 of <tt>ncks</tt> contain a bug which
-triggers a core-dump when hyperslabbing (along a non-record
-dimension) a netCDF4-format input file into a netCDF4-format output
-file, e.g., <tt>ncks -d 0,1,lat in4.nc out4.nc</tt>.
-Three workarounds that do not require NCO upgrades (or downgrades) are
-to explicitly specify chunking with, e.g.,
-<tt>ncks --cnk_plc=all -d 0,1,lat in4.nc out4.nc</tt>, or, to use
-<tt>nces</tt> instead of <tt>ncks</tt> for hyperslabbing, e.g.,
-<tt>nces -d 0,1,lat in4.nc out4.nc</tt> (<tt>nces</tt> does a no-op
-when there is only one input file), or to write to a netCDF3 file,
-<tt>ncks -3 -d 0,1,lat in4.nc out3.nc</tt>.
-</li>
-
-<!-- http://nco.sf.net#bug_ncks_m -->
-<a name="bug_ncks_m"></a>
-<li><i>Core dump with <tt>ncks</tt>:</i>
-Printing variables to screen with <tt>ncks</tt> can trigger a segfault
-in NCO 3.9.9—4.0.3.
-Users may upgrade, downgrade, or apply this one-line patch to 3.9.9 sources:
-Remove this line
-“<tt>*cnk_sz=(size_t)NULL;</tt>”
-—near line 751 of <tt>nco/src/nco/nco_netcdf.c</tt>—
-should fix the problem.
-The problem in later NCO versions is due to a different bug and this
-patch will not work.
-</li>
-
-<!-- http://nco.sf.net#bug_ncrename_dot -->
-<a name="bug_ncrename_dot"></a>
-<li><i><tt>ncrename</tt> erroneous error exit:</i>
-Versions 4.0.1—4.0.3 of <tt>ncrename</tt> contain a bug where
-commands like <tt>ncrename -a .old_nm,new_nm in.nc out.nc</tt>
-would, if <tt>old_nm</tt> did not exist, write the correct file and
-then exit with an error message although no error had occurred.
-The files written were fine, and the error message can be safely
-ignored. This was due to not clearing an extraneous return code.
-
-<!-- http://nco.sf.net#bug_ncbo_rfr -->
-<a name="bug_ncbo_rfr"></a>
-<li><i><tt>ncbo</tt> segmentation fault:</i>
-<tt>ncbo</tt> versions 4.0.0—4.0.2 incorrectly refreshed
-internal metadata, leading to segmentation faults and core dumps with
-some exacting compilers, notably xlC on AIX.
-
-<!-- http://nco.sf.net#bug_ncra_date -->
-<a name="bug_ncra_date"></a>
-<li><i><tt>ncra</tt> segmentation fault:</i>
-<tt>ncra</tt> versions 4.0.0—4.0.1 mishandled some CF-compliant
-dates, leading to segmentation faults and core dumps.
-
-<!-- http://nco.sf.net#bug_ncap_cmt -->
-<a name="bug_ncap_cmt"></a>
-<li><i>Arithmetic problems with <tt>ncap</tt> division, modulo, and exponentiation:</i>
-<tt>ncap</tt> versions < 3.0.1 incorrectly exponentiate
-variables to variable powers (<tt>V^V</tt>).
-We recommend that all <tt>ncap</tt> users upgrade.<br>
-
-<tt>ncap</tt> versions up to 2.9.1 incorrectly handle division,
-modulo, and exponentiation operations of the form <tt>S/V</tt>,
-<tt>S%V</tt>, and <tt>S^V</tt> where first operand (<tt>S</tt>) is
-scalar (i.e., either typed directly in the <tt>ncap</tt> script or
-converted from an attribute) and the second operand (<tt>V</tt>) is
-a full variable (i.e., stored in a file or computed by <tt>ncap</tt>).
-Instead of the requested quantity, <tt>ncap</tt> returned
-<tt>V/S</tt>, <tt>V%S</tt>, and <tt>V^S</tt>.
-In other words <tt>ncap</tt> treated some non-commutative operations
-as commutative. This is now fixed.
-The
-<tt>V/V</tt>, <tt>V%V</tt>, <tt>V^V</tt>,
-<tt>V/S</tt>, <tt>V%S</tt>, <tt>V^S</tt>,
-<tt>S/S</tt>, <tt>S%S</tt>, and <tt>S^S</tt> operations were never
-affected.
-We recommend that all <tt>ncap</tt> users upgrade.
-</li>
-
-<!-- http://nco.sf.net#bug_ncbo_pck -->
-<a name="bug_ncbo_pck"></a>
-<li><i>Incorrect <tt>ncbo</tt> output for packed input:</i>
-<tt>ncbo</tt> versions ???—3.2.0 incorrectly write differences
-of packed input. This only affects packed variables.
-
-<!-- http://nco.sf.net#bug_ncflint_mss_val -->
-<a name="bug_ncflint_mss_val"></a>
-<li><i>Problems with <tt>ncflint</tt> and <tt>missing_value</tt>s:</i>
-The algorithm <tt>ncflint</tt> used to perform interpolation in
-versions up to 2.9.4 was not commutative.
-It returned the weighted valid datum when the other datum was
-<tt>missing_value</tt>, or it returned <tt>missing_value</tt>,
-depending on the order the input files were specified.
-As of version 2.9.5, <tt>ncflint</tt> always returns
-<tt>missing_value</tt> when either input datum is
-<tt>missing_value</tt>.
-Possible future implementations are discussed
-<a href="http://nco.sf.net/nco.html#ncflint">here</a>.
-
-<!-- http://nco.sf.net#bug_mss_val_zro_ncra -->
-<a name="bug_mss_val_zro_ncra"></a>
-<li><i>Problems with <tt>ncra</tt> and <tt>nces</tt> when <tt>missing_value</tt> = 0.0:</i>
-The algorithm <tt>ncra</tt> and <tt>nces</tt> used to perform
-arithmetic in versions up to 2.9.2 breaks if <tt>missing_value</tt>
-is 0.0.
-Why, you ask?
-Running average (or total, etc.) algorithms must initialize the answer
-to 0.0.
-This is done since the sum accumulates in place as <tt>ncra</tt> and
-<tt>nces</tt> proceeds across records and files.
-(Normalizing this accumulation by the total number of records is the
-last step).
-The old algorithm compared both the current running average and the
-new record to the <tt>missing_value</tt>.
-If either comparison matched, then nothing accumulated for that
-record.
-This zero-initialization led to a state where it was impossible
-to ever recognize valid data.
-As a result nothing accumulated and the answer was always zero.
-The record and ensemble averages would also fail (in a non-obvious)
-way whenever an intermediate sum equalled <tt>missing_value</tt>.
-The chances of the latter event ever happening are exceedingly
-remote.
-The new algorithm compares only the new record to the
-<tt>missing_value</tt>.
-This fixes both problems and is faster, too.
-
-<!-- http://nco.sf.net#bug_pck_ncwa -->
-<a name="bug_pck_ncwa"></a>
-<li><i>Packing problems with <tt>ncwa</tt>:</i>
-NCO versions ???—2.9.0 have a bug that causes <tt>ncwa</tt>
-to fail (produce garbage answers) when processing packed
-<tt>NC_FLOAT</tt> data. Version 2.9.1 fixes this problem.
-This problem may have been noticed most by
-<a href="http://opendap.org">OPeNDAP</a> users since many
-netCDF climate datasets served by
-<a href="http://opendap.org">OPeNDAP</a> are packed
-<tt>NC_FLOAT</tt>s.
-Upgrade to 2.9.1 if you use <tt>ncwa</tt> on packed data.
-</li>
-
-<!-- http://nco.sf.net#bug_pck -->
-<a name="bug_pck"></a>
-<li><i>Packing problems with <tt>ncap</tt>:</i>
-NCO versions 2.8.4—2.8.6 have a bug that causes the <tt>ncap</tt>
-intrinsic packing function <tt>pack()</tt> to fail.
-Version 2.8.7 fixes this problem.
-</li>
-</ul>
-
-<ul><b>Older Platform-specific Run-time Problems:</b>
-<a name="bug_ncap_flt_fnc_aix"></a>
-<li><i>Float-valued intrinsic arithmetic functions in <tt>ncap</tt> on AIX:</i>
-<tt>ncap</tt> versions through 4.0.4 have a bug that causes all float-valued
-intrinsic math functions to fail under AIX.
-Float-valued math functions are the ISO C99 functions, e.g.,
-<tt>cosf()</tt>, <tt>fabsf()</tt>, <tt>logf()</tt>.
-The user does not invoke these functions directly—
-the user always specifies the <i>generic function name</i>, e.g.,
-<tt>cos()</tt>, <tt>abs()</tt>, <tt>log()</tt>.
-NCO automatically calls the native single precision (i.e.,
-float-valued) math functions when the generic function argument
-is a native float (e.g., naked constants like <tt>1.0f</tt> or
-variables stored as <tt>NC_FLOAT</tt>).
-Double precision arguments cause NCO to invoke the standard
-(double-valued) form of the generic function, e.g., <tt>cos()</tt>,
-<tt>fabs()</tt>, <tt>log()</tt>.
-<!-- Whevnever this bug is fixed, here is some text
-Version info:
-<tt>ncap</tt> float functions work in AIX (<a href="#bug_ncap_flt_fnc_aix">long-time bug</a>, upgrade will be required for AIX ncap users)
-ANNOUNCE info:
-First, AIX NCO installations should upgrade to this version to get the
-AIX-specific ncap bug-fix.
-Bug-fixes:
-1. fxm: AIX uses NCO-supplied float-valued functions (e.g., cosf())
--->
-</li>
+<li><a href="./problems_old.shtml">Known Problems through 2012 (version 4.2.3)</a></li>
</ul>
<p><hr></p>
@@ -2216,7 +1338,7 @@ Bug-fixes:
<a name="people"></a> <!-- http://nco.sf.net#people -->
<dt><a name="People"></a></dt> <!-- http://nco.sf.net#People -->
<h2>People:</h2>
-<p>Current Developers (please <a href="#Contact">communicate</a> with us using the project forums rather than contacting us individually):
+<p>Current Developers (please <a href="#Contact">contact</a> us via the project forums not via email):
<ul>
<li>
@@ -2227,12 +1349,15 @@ Professor of Earth System Science
Computer Science
(<a href="http://www.ics.uci.edu">CS</a>).
<i>Role</i>: Project PI.
-<i>Contributions</i>: NCO core library, porting, release manager
+<i>Contributions</i>: Core library, porting, release manager
<i>Related Research</i>:
-1. Extend empirically verified analytic model for terascale data
-reduction of gridded datasets to account for cluster- and network-
-effects.
-2. Enable and optimize NCO for intra-file-level parallelism using
+1. Group-Oriented Data Analysis and Distribution
+(<a href="http://nco.sf.net/nco.html#godad">GODAD</a>).
+2. Extend empirically verified analytic model
+(described <a href="http://www.ess.uci.edu/~zender#ZeM07">here</a>)
+for terascale data reduction of gridded datasets to account for
+cluster- and network-effects.
+3. Enable and optimize NCO for intra-file-level parallelism using
netCDF4/HDF5 parallel filesystem features.
<i>Other Interests</i>: Atmospheric Physics, Climate Change.
</li>
@@ -2249,25 +1374,13 @@ software engineer.
</li>
<li><dt>
-<a name="vicente"></a><a name="Vicente"></a> <!-- http://nco.sf.net#vicente -->
-<a href="http://dust.ess.uci.edu/pvicente">Pedro Vicente</a>,
-software engineer.
-<i>Roles</i>: Scientific programmer
-<i>Current Research</i>:
-1. Support for hierarchical datasets.
-2. Optimization of hierarchical access.
-<i>Other Interests</i>: HDF and netCDF data visualization.
-</li>
-
-<li><dt>
<a name="wenshan"></a><a name="Wenshan"></a> <!-- http://nco.sf.net#wenshan -->
<a href="http://dust.ess.uci.edu/wenshanw">Wenshan Wang</a>,
-software engineer.
-<i>Roles</i>: Graduate Student
+<i>Roles</i>: PhD Candidate
<i>Current Research</i>:
-1. Causes and implications of snowpack darkening.
+1. Causes and implications of Greenland snowmelt.
2. Rapid evaluation and exploitation of multi-model datasets.
-<i>Other Interests</i>: Passing Comps.
+<i>Other Interests</i>: Advancing to candidacy.
</li>
</ul>
@@ -2276,6 +1389,21 @@ software engineer.
<ul>
<li>
+<a name="capps"></a><a name="Capps"></a> <!-- http://nco.sf.net#capps -->
+<a href="http://dust.ess.uci.edu/scapps/web">Dr. Scott Capps</a>,
+earned Earth System Science Ph.D. (2009) with Zender at UCI, then
+postdoc at UCLA, now at Vertum Partners.
+<!--
+<i>Related Research</i>:
+1. Test NCO on real tera-scale geoscience analysis problems and
+identify necessary improvements in <tt>ncap2</tt> and in SWAMP.
+2. Role of satellite-observed sub-gridscale wind variability
+on air-surface exchange.
+<i>Other Interests</i>: Weather, climate
+-->
+</li>
+
+<li>
<a name="jenks"></a><a name="Jenks"></a> <!-- http://nco.sf.net#jenks -->
<a href="http://spds.ece.uci.edu/~sjenks">Stephen Jenks</a>,
former Assistant Professor of Electrical Engineering and Computer Science
@@ -2289,16 +1417,15 @@ former Assistant Professor of Electrical Engineering and Computer Science
</li>
<li>
-<a name="capps"></a><a name="Capps"></a> <!-- http://nco.sf.net#capps -->
-<a href="http://dust.ess.uci.edu/scapps/web">Dr. Scott Capps</a>,
-earned Earth System Science Ph.D. (2009) with Zender at UCI, now at UCLA.
+<a name="vicente"></a><a name="Vicente"></a> <!-- http://nco.sf.net#vicente -->
+<a href="http://dust.ess.uci.edu/pvicente">Pedro Vicente</a>,
+software engineer, 201206—201405.
<!--
-<i>Related Research</i>:
-1. Test NCO on real tera-scale geoscience analysis problems and
-identify necessary improvements in <tt>ncap2</tt> and in SWAMP.
-2. Role of satellite-observed sub-gridscale wind variability
-on air-surface exchange.
-<i>Other Interests</i>: Weather, climate
+<i>Roles</i>: Scientific programmer
+<i>Current Research</i>:
+1. Support for hierarchical datasets.
+2. Optimization of hierarchical access.
+<i>Other Interests</i>: HDF and netCDF data visualization.
-->
</li>
@@ -2336,7 +1463,7 @@ community.
<a name="contact"></a> <!-- http://nco.sf.net#contact -->
<dt><a name="Contact"></a></dt> <!-- http://nco.sf.net#Contact -->
<h2>Contacting the Project:</h2>
-<p>Contact us through the Project Forums (rather than personal e-mail)
+<p>Contact us via the Project Forums (rather than personal e-mail)
so other users can benefit from and contribute to our exchange.
Let us know how NCO is working for you—we'd like to hear.
Have you read the <a href="#RTFM">documentation</a> and browsed the
@@ -2364,15 +1491,15 @@ site.</li>
<a href="http://sf.net/projects/nco/forums/forum/9831">Developer</a> /
<a href="http://sf.net/projects/nco/forums/forum/9829">Discussion</a> /
<a href="http://sf.net/projects/nco/forums/forum/9830">Help</a> /
-<a href="http://nco.sf.net">Homepage</a> /
<a href="#RTFM">Manual</a> /
<a href="http://sf.net/projects/nco">Project</a> /
<a href="http://nco.cvs.sf.net/nco/nco/src/nco/">Source</a> /
</td>
<td align="right" valign="top">
+[<a href="https://acme-climate.atlassian.net/wiki/display/ACME/ACME+Home">ACME</a>]
[<a href="http://www.antlr.org">ANTLR</a>]
-[<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/latest-cf-conventions-document-1">CF</a>]
+[<a href="http://cfconventions.org/1.6.html">CF</a>]
[<a href="https://wiki.earthdata.nasa.gov/display/ESDSWG/Dataset+Interoperability+Working+Group">DIWG</a>]
[<a href="http://www.gnu.org/software/gsl">GSL</a>]
[<a href="http://www.unidata.ucar.edu/packages/netcdf">netCDF</a>]
diff --git a/doc/milestones_old.shtml b/doc/milestones_old.shtml
new file mode 100644
index 0000000..fed824d
--- /dev/null
+++ b/doc/milestones_old.shtml
@@ -0,0 +1,96 @@
+<!-- $Header: /cvsroot/nco/nco/doc/milestones_old.shtml,v 1.1 2014/06/13 19:43:50 zender Exp $
+
+Purpose: Milestones archive
+
+URL:
+http://nco.sf.net/milestones_old.shtml
+http://dust.ess.uci.edu/nco/milestones_old.shtml
+file:///home/zender/nco/doc/milestones_old.shtml
+
+Usage:
+/usr/bin/scp ~/nco/doc/milestones_old.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+scp -p ~/nco/doc/milestones_old.shtml dust.ess.uci.edu:/var/www/html/nco
+-->
+
+<!doctype html public "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+ <title>NCO Homepage</title>
+ <meta name="GENERATOR" content="Mozilla/3.04Gold (X11; I; Linux 2.0.0 i686) [Netscape]">
+ <meta name="Author" content="Charles S. Zender">
+ <meta name="Keywords" content="NCO Homepage, netCDF, netCDF operator, GCM, HDF, scientific data">
+</head>
+<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
+
+<dt><a name="News"></a></dt>
+<h2>Releases & Milestones from 2003–2012 (versions 2.8.4–4.2.3)</h2>
+
+<ul>
+<li>2012 Dec 05: NCO <a href="http://dust.ess.uci.edu/smn/smn_nco_agu_201212.pdf">Talk</a> at Fall AGU, San Francisco, California</li>
+<li>2012 Nov 28: NCO <a href="http://dust.ess.uci.edu/smn/pst_nco_esds_201211.pdf">Poster</a> at NASA ESDSWG, Annapolis, Maryland</li>
+<li>2012 Nov 13: NCO 4.2.3 (GPE)</li>
+<li>2012 Oct 29: NCO 4.2.2 (<tt>ncks, ncecat</tt> Groups)</li>
+<li>2012 Aug 02: NCO 4.2.1 (RAM disks)</li>
+<li>2012 Jun 12: NCO 4.2.0 (Windows support)</li>
+<li>2012 Apr 23: Received funding for NASA ACCESS 2011 <a href="#prp_access">project</a></li>
+<li>2012 Mar 29: NCO 4.1.0 (MD5 support, MM3)</li>
+<li>2012 Feb 13: NCO 4.0.9</li>
+<li>2011 Jun 03: Submitted NASA ACCESS 2011 <a href="http://dust.ess.uci.edu/prp/prp_access/prp_access.pdf">proposal</a></li>
+<li>2011 Apr 28: NCO 4.0.8 (HPSS support, NOFILL workaround, <i>upgrade recommended</i>)</li>
+<li>2011 Feb 21: NCO 4.0.7 (<i>upgrade recommended</i>)</li>
+<li>2011 Jan 15: NCO 4.0.6</li>
+<li>2010 Oct 13: NCO 4.0.5</li>
+<li>2010 Sep 24: NCO 4.0.4 (chunking everywhere)</li>
+<li>2010 Sep 02: NCO 4.0.3</li>
+<li>2010 Jun 27: NCO 4.0.2</li>
+<li>2010 Apr 05: NCO 4.0.1</li>
+<li>2010 Jan 05: NCO 4.0.0 (bilinear interpolation, calendar attributes)</li>
+<li>2009 Jul 15: NCO 3.9.9 (chunking, re-basing, GSL stats/interp)</li>
+<li>2009 Apr 29: NCO 3.9.8 (GSL RNG/PDF functions)</li>
+<li>2009 Mar 18: NCO 3.9.7</li>
+<li>2009 Jan 22: NCO 3.9.6 (GSL special functions) (<i>upgrade highly recommended</i>)</li>
+<li>2008 Sep 24: <tt>ncap2</tt> <a href="http://nco.sf.net/nco.html#ncap2">documentation</a></li>
+<li>2008 Aug 31: <a href="http://www.nsf.gov">NSF</a> funding ends</a></li>
+<li>2008 Aug 08: NCO <a href="http://nco.wiki.sf.net">Wiki</a>!</li>
+<li>2008 May 22: SWAMP <a href="http://dust.ess.uci.edu/ppr/smn_WZJ08_ccgrid_200805.pdf">Talk</a> at CCGRID08 in Lyon, France</li>
+<li>2008 May 11: NCO 3.9.5</li>
+<li>2008 Apr 28: NCO <a href="http://dust.ess.uci.edu/ppr/ppr_Zen08.pdf">overview</a> paper in EMS</li>
+<li>2008 Mar 04: NCO 3.9.4</li>
+<li>2007 Dec 10: SWAMP <a href="http://dust.ess.uci.edu/ppr/pst_WZJ074.pdf">Poster</a> at Fall AGU, San Francisco, California</li>
+<li>2007 Dec 07: NCO 3.9.3 (SWAMP!)</li>
+<li>2007 Dec 04: NCO <a href="http://dust.ess.uci.edu/ppr/ppr_ZeM07.pdf">scaling paper</a> in IJHPCA</li>
+<li>2007 Aug 29: NCO 3.9.2 (<tt>_FillValue</tt>s)</li>
+<li>2007 Aug 27: <a href="http://swamp.googlecode.com">SWAMP site</a> spins-off from NCO</li>
+<li>2007 Jun 29: NCO 3.9.1 (netCDF4 deflation)</li>
+<li>2007 May 26: NCO 3.9.0 (netCDF4 atomic types)</li>
+<li>2007 May 02: SWAMP <a href="http://dust.ess.uci.edu/smn/smn_WZJ07_gpc_200705.pdf">Talk</a> at GPC, Paris, France</li>
+<li>2007 Apr 20: NCO 3.2.0</li>
+<li>2007 Mar 29: NCO 3.1.9 x86_64 RPMs</li>
+<li>2007 Mar 10: NCO 3.1.9 (i386/x86_64 debs and i386 RPMs)</li>
+<li>2007 Feb 22: SWAMP <a href="http://dust.ess.uci.edu/smn/smn_WZJ07_opendap_200702.pdf">Talk</a> at OPeNDAP Developer's Workshop, Boulder, Colorado</li>
+<li>2007 Jan 15: <a href="http://dust.ess.uci.edu/smn/smn_nco_ams_200701.pdf">Talk</a> and <a href="http://dust.ess.uci.edu/ppr/abs_xtn_ZeW07.pdf">Extended Abstract</a> on NCO Scaling at AMS IIPS, San Antonio, Texas</li>
+<li>2007 Jan 09: <a href="http://dust.ess.uci.edu/ppr/pst_ZMW06.pdf">Poster</a> on NCO Scaling at Fall AGU, San Francisco, California</li>
+<li>2006 Dec 09: <a href="http://dust.ess.uci.edu/ppr/pst_WZJ06.pdf">Poster</a> on SWAMP at Fall AGU, San Francisco, California</li>
+<li>2006 Dec 06: NCO 3.1.8</li>
+<li>2006 Nov 11: NCO 3.1.7</li>
+<li>2006 Sep 18: NCO 3.1.6</li>
+<li>2006 Aug 29: NCO 3.1.5</li>
+<li>2006 Jun 07: NCO 3.1.4</li>
+<li>2006 May 30: NCO 3.1.3</li>
+<li>2006 Apr 21: NCO 3.1.2</li>
+<li>2006 Jan 30: NCO 3.1.1</li>
+<li>2005 Dec 02: NCO 3.1.0 (MPI!)</li>
+<li>2005 Oct 28: NCO 3.0.3</li>
+<li>2005 Oct 17: <a href="#BM">NCO parallel benchmarks</a></li>
+<li>2005 Aug 22: NCO 3.0.2</li>
+<li>2005 Jun 10: NCO 3.0.1</li>
+<li>2005 Mar 24: NCO 3.0.0</li>
+<li>2004 Sep 07: NCO 2.9.9 (<tt>ncpdq</tt> packs data quietly)</li>
+<li>2004 Sep 01: Funding for NSF <a href="#prp_sei">SEI Project</a> begins</li>
+<li>2004 Aug 07: NCO 2.9.8 (<a href="./nco.html#ncpdq"><tt>ncpdq</tt></a> re-orders dimensions)</li>
+<li>2004 Mar 04: Submit NSF <a href="http://dust.ess.uci.edu/prp/prp_sei/prp_sei.pdf">SEI proposal</a></li>
+</ul>
+<hr></p>
+
+</body>
+</html>
diff --git a/doc/nco.dvi b/doc/nco.dvi
index b7d0e91..2572796 100644
Binary files a/doc/nco.dvi and b/doc/nco.dvi differ
diff --git a/doc/nco.html b/doc/nco.html
index a06f505..96501fc 100644
--- a/doc/nco.html
+++ b/doc/nco.html
@@ -2,10 +2,10 @@
<html>
<!-- Created by GNU Texinfo 5.1, http://www.gnu.org/software/texinfo/ -->
<head>
-<title>NCO 4.4.4 User Guide</title>
+<title>NCO 4.4.5 User Guide</title>
-<meta name="description" content="NCO 4.4.4 User Guide">
-<meta name="keywords" content="NCO 4.4.4 User Guide">
+<meta name="description" content="NCO 4.4.5 User Guide">
+<meta name="keywords" content="NCO 4.4.5 User Guide">
<meta name="resource-type" content="document">
<meta name="distribution" content="global">
<meta name="Generator" content="makeinfo">
@@ -47,7 +47,7 @@ ul.no-bullet {list-style: none}
</head>
<body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000">
-<h1 class="settitle" align="center"><acronym>NCO</acronym> 4.4.4 User Guide</h1>
+<h1 class="settitle" align="center"><acronym>NCO</acronym> 4.4.5 User Guide</h1>
@@ -196,7 +196,13 @@ Irvine, CA 92697-3100<br>
<li><a name="toc-Large-File-Support-1" href="#Large-File-Support">3.10 Large File Support</a></li>
<li><a name="toc-Subsetting-Files-1" href="#Subsetting-Files">3.11 Subsetting Files</a></li>
<li><a name="toc-Subsetting-Coordinate-Variables-1" href="#Subsetting-Coordinate-Variables">3.12 Subsetting Coordinate Variables</a></li>
- <li><a name="toc-Group-Path-Editing-1" href="#Group-Path-Editing">3.13 Group Path Editing</a></li>
+ <li><a name="toc-Group-Path-Editing-1" href="#Group-Path-Editing">3.13 Group Path Editing</a>
+ <ul class="no-bullet">
+ <li><a name="toc-Deletion_002c-Truncation_002c-and-Flattening-of-Groups" href="#Flattening-Groups">3.13.1 Deletion, Truncation, and Flattening of Groups</a></li>
+ <li><a name="toc-Moving-Groups-1" href="#Moving-Groups">3.13.2 Moving Groups</a></li>
+ <li><a name="toc-Dismembering-Files-1" href="#Dismembering-Files">3.13.3 Dismembering Files</a></li>
+ <li><a name="toc-Checking-CF_002dcompliance-1" href="#Checking-CF_002dcompliance">3.13.4 Checking CF-compliance</a></li>
+ </ul></li>
<li><a name="toc-C-and-Fortran-Index-conventions" href="#C-and-Fortran-Index-Conventions">3.14 C and Fortran Index conventions</a></li>
<li><a name="toc-Hyperslabs-1" href="#Hyperslabs">3.15 Hyperslabs</a></li>
<li><a name="toc-Stride-1" href="#Stride">3.16 Stride</a></li>
@@ -294,7 +300,8 @@ Irvine, CA 92697-3100<br>
<li><a name="toc-Contributing-1" href="#Contributing">5 Contributing</a>
<ul class="no-bullet">
<li><a name="toc-Contributors-1" href="#Contributors">5.1 Contributors</a></li>
- <li><a name="toc-Proposals-for-Institutional-Funding-1" href="#Proposals-for-Institutional-Funding">5.2 Proposals for Institutional Funding</a></li>
+ <li><a name="toc-Citation-1" href="#Citation">5.2 Citation</a></li>
+ <li><a name="toc-Proposals-for-Institutional-Funding-1" href="#Proposals-for-Institutional-Funding">5.3 Proposals for Institutional Funding</a></li>
</ul></li>
<li><a name="toc-Quick-Start-1" href="#Quick-Start">6 Quick Start</a>
<ul class="no-bullet">
@@ -355,8 +362,8 @@ examples from the field of climate modeling and analysis.
The <acronym>NCO</acronym> homepage is <a href="http://nco.sf.net">http://nco.sf.net</a>, and
there is a mirror at <a href="http://dust.ess.uci.edu/nco">http://dust.ess.uci.edu/nco</a>.
</p>
-<p>This documentation is for <acronym>NCO</acronym> version 4.4.4.
-It was last updated 20 May 2014.
+<p>This documentation is for <acronym>NCO</acronym> version 4.4.5.
+It was last updated 8 July 2014.
Corrections, additions, and rewrites of this documentation are very
welcome.
</p>
@@ -469,23 +476,24 @@ Grenoble, France<br>
</p>
<br>
<br>
-<p>The end of the <acronym>NSF</acronym> SEI grant in August, 2008 curtailed <acronym>NCO</acronym>
-development.
-Fortunately we could justify supporting Henry Butowsky on other research
+<p>The end of the <acronym>NSF</acronym> <acronym>SEI</acronym> grant in August, 2008 curtailed
+<acronym>NCO</acronym> development.
+Fortunately we could justify supporting Henry Butowsky on other research
grants until May, 2010 while he developed the key <code>ncap2</code>
features used in our climate research.
-And recentely the NASA ACCESS program commenced funding NCO support for
-netCDF4 group functionality.<br>
-Thus <acronym>NCO</acronym> will grow and evade bit-rot for the foreseeable future.
-</p>
-<p>On a personal level, I continue to receive with gratitude the thanks of
-<acronym>NCO</acronym> users at nearly every scientific meeting I attend.
-People introduce themselves, shake my hand and extol, sometimes rather
-effusively, these time-saving tools.
+And recently the <acronym>NASA</acronym> <acronym>ACCESS</acronym> program commenced
+funding us to support netCDF4 group functionality.
+Thus <acronym>NCO</acronym> will grow and evade bit-rot for the foreseeable
+future.
+</p>
+<p>I continue to receive with gratitude the thanks of <acronym>NCO</acronym> users
+at nearly every scientific meeting I attend.
+People introduce themselves, shake my hand and extol <acronym>NCO</acronym>,
+often effusively, while I grin in stupid embarassment.
These exchanges lighten me like anti-gravity.
Sometimes I daydream how many hours <acronym>NCO</acronym> has turned from grunt
work to productive research for researchers world-wide, or from research
-into early happy hours.
+into early happy-hours.
It’s a cool feeling.
</p>
<br>
@@ -493,6 +501,7 @@ It’s a cool feeling.
April, 2012<br>
Irvine, California<br>
</p>
+
<a name="smr"></a> <!-- http://nco.sf.net/nco.html#smr --><hr>
<a name="Summary"></a>
<div class="header">
@@ -636,7 +645,7 @@ descriptions of <a href="http://nco.sf.net/#bug">Known Problems</a> etc.
are on our homepage
(<a href="http://nco.sf.net/">http://nco.sf.net/</a>).
</p>
-<p>There are twelve operators in the current version (4.4.4).
+<p>There are twelve operators in the current version (4.4.5).
The function of each is explained in <a href="#Operator-Reference-Manual">Operator Reference Manual</a>.
Many of the tasks that <acronym>NCO</acronym> can accomplish are described during
the explanation of common <acronym>NCO</acronym> Features (see <a href="#Common-features">Common features</a>).
@@ -978,7 +987,7 @@ following <acronym>UNIX</acronym> commands in the directory where the
<acronym>NCO</acronym> executables are installed.
</p><div class="example">
<pre class="example">ln -s -f ncbo ncdiff # ncbo --op_typ='+'
-ln -s -f ncra ncecat # ncra --pseudonym='ncecat'
+ln -s -f ncra nces # ncra --pseudonym='nces'
ln -s -f ncra ncrcat # ncra --pseudonym='ncrcat'
ln -s -f ncbo ncadd # ncbo --op_typ='+'
ln -s -f ncbo ncsubtract # ncbo --op_typ='-'
@@ -986,7 +995,7 @@ ln -s -f ncbo ncmultiply # ncbo --op_typ='*'
ln -s -f ncbo ncdivide # ncbo --op_typ='/'
ln -s -f ncpdq ncpack # ncpdq
ln -s -f ncpdq ncunpack # ncpdq --unpack
-# NB: Cygwin executable (and link) names have an '.exe' suffix, e.g.,
+# NB: Windows/Cygwin executable/link names have '.exe' suffix, e.g.,
ln -s -f ncbo.exe ncdiff.exe
...
</pre></div>
@@ -1841,8 +1850,8 @@ Initially the record dimension is <code>time</code>.
Our goal is to create a single file that contains joins all the
spatially adjacent regions into one single time-evolving dataset.
</p><div class="example">
-<pre class="example">for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
- ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
+<pre class="verbatim">for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
+ ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
done
ncrcat foo_??.nc out.nc # Concatenate along x
ncpdq -a time,x out.nc out.nc # Revert to time as record dimension
@@ -1952,7 +1961,7 @@ more, typically) of input filenames to the multi-file operators is
to pass the filenames with the <acronym>UNIX</acronym> <em>standard input</em>
feature, aka <code>stdin</code>:
</p><div class="example">
-<pre class="example"># Pipe large numbers of filenames to stdin
+<pre class="verbatim"># Pipe large numbers of filenames to stdin
/bin/ls | grep ${CASEID}_'......'.nc | ncecat -o foo.nc
</pre></div>
<p>This method avoids all constraints on command line size imposed by
@@ -1995,7 +2004,7 @@ and to pipe the results to <code>xargs</code> which, in turn, passes the
matching filenames to an <acronym>NCO</acronym> multi-file operator, e.g.,
<code>ncecat</code>.
</p><div class="example">
-<pre class="example"># Use xargs to transfer filenames on the command line
+<pre class="verbatim"># Use xargs to transfer filenames on the command line
/bin/ls | grep ${CASEID}_'......'.nc | xargs -x ncecat -o foo.nc
</pre></div>
<a name="index-pipes"></a>
@@ -2034,7 +2043,7 @@ directory. If there are 999,999 netCDF files present, the links are
named <samp>000001.nc</samp> to <samp>999999.nc</samp>:
<a name="index-_002dn-loop-1"></a>
</p><div class="example">
-<pre class="example"># Create enumerated symbolic links
+<pre class="verbatim"># Create enumerated symbolic links
/bin/ls | grep \.nc | perl -e \
'$idx=1;while(<STDIN>){chop;symlink $_,sprintf("%06d.nc",$idx++);}'
ncecat -n 999999,6,1 000001.nc foo.nc
@@ -2503,7 +2512,11 @@ Next: <a href="#Metadata-Optimization" accesskey="n" rel="next">Metadata Optimiz
<a name="index-L10N"></a>
<p><acronym>NCO</acronym> support for <em>internationalization</em> of textual input
and output (e.g., Warning messages) is nascent.
-We hope to produce foreign language string catalogues in 2004.
+We introduced the first foreign language string catalogues (French and
+Spanish) in 2004, yet did not activate these in distributions because
+the catalogues were nearly empty.
+We seek volunteers to populate our templates with translations for their
+favorite languages.
</p>
<a name="hdr"></a> <!-- http://nco.sf.net/nco.html#hdr -->
<a name="hdr_pad"></a> <!-- http://nco.sf.net/nco.html#hdr_pad --><hr>
@@ -2817,12 +2830,15 @@ ncra -n 5,2,1 85.nc 8589.nc
force.
The second method relies on the operating system shell to <em>glob</em>
(expand) the <em>regular expression</em> <code>8[56789].nc</code>.
-The shell passes valid filenames which match the expansion to
-<code>ncra</code>.
-The third method uses the ‘<samp>-p <var>input-path</var></samp>’ argument to specify
+The shell then passes the valid filenames (those which match the
+regular expansion) to <code>ncra</code>.
+In this case <code>ncra</code> never knows that a regular expression was
+used, because the shell intercepts and expands and matches the regular
+expression before <code>ncra</code> is actually invoked.
+The third method uses the ‘<samp>-p <var>input-path</var></samp>’ argument to specify
the directory where all the input files reside.
<acronym>NCO</acronym> prepends <var>input-path</var> (e.g.,
-<samp>/data/usrname/model</samp>) to all <var>input-files</var> (though not to
+<samp>/data/username/model</samp>) to all <var>input-files</var> (though not to
<var>output-file</var>).
Thus, using ‘<samp>-p</samp>’, the path to any number of input files need only
be specified once.
@@ -2831,7 +2847,7 @@ automatically generated if necessary.
</p>
<p>The last method passes (with ‘<samp>-n</samp>’) syntax concisely describing
the entire set of filenames
-<a name="DOCF19" href="#FOOT19"><sup>19</sup></a>.
+<a name="DOCF19" href="#FOOT19"><sup>19</sup></a>.
<a name="index-multi_002dfile-operators-1"></a>
<a name="index-files_002c-multiple"></a>
This option is only available with the <em>multi-file operators</em>:
@@ -2848,8 +2864,8 @@ For example, in the file <samp>ccm3_h0001.nc</samp>, we have
<var>alphanumeric_prefix</var> = <samp>ccm3_h</samp>, <var>numeric_suffix</var> =
<samp>0001</samp>, and <var>filetype</var> = <samp>nc</samp>.
</p>
-<p><acronym>NCO</acronym> is able to decode lists of such filenames encoded using the
-‘<samp>-n</samp>’ option.
+<p><acronym>NCO</acronym> decodes lists of such filenames encoded using the
+‘<samp>-n</samp>’ syntax.
The simpler (3-argument) ‘<samp>-n</samp>’ usage takes the form
<code>-n <var>file_number</var>,<var>digit_number</var>,<var>numeric_increment</var></code>
where <var>file_number</var> is the number of files, <var>digit_number</var> is
@@ -2898,12 +2914,12 @@ ncra -n 3,2,1,12,1 85_12.nc 85_1202.nc
suffice to specify consecutive months (<code>06, 07, 08</code>) which do not
“wrap” back to a minimum value.
The second example shows how to use the optional fourth and fifth
-elements of the ‘<samp>-n</samp>’ option to specify a wrap value to <acronym>NCO</acronym>.
-The fourth argument to ‘<samp>-n</samp>’, if present, specifies the maximum
+elements of the ‘<samp>-n</samp>’ option to specify a wrap value.
+The fourth argument to ‘<samp>-n</samp>’, when present, specifies the maximum
integer value of <var>numeric_suffix</var>.
-In this case the maximum value is 12,<!-- /@w --> and will be formatted as
+In the example the maximum value is 12,<!-- /@w --> and will be formatted as
<samp>12</samp> in the filename string.
-The fifth argument to ‘<samp>-n</samp>’, if present, specifies the minimum
+The fifth argument to ‘<samp>-n</samp>’, when present, specifies the minimum
integer value of <var>numeric_suffix</var>.
The default minimum filename suffix is 1,<!-- /@w --> which is formatted as
<samp>01</samp> in this case.
@@ -3011,16 +3027,18 @@ an <acronym>OPeNDAP</acronym> server.
Examples of each are given below, following a brief description of the
particular access protocol.
</p>
-<a name="ftp"></a> <!-- http://nco.sf.net/nco.html#ftp --><p>To access a file via an anonymous <acronym>FTP</acronym> server, supply the
-remote file’s <acronym>URL</acronym>.
+<a name="ftp"></a> <!-- http://nco.sf.net/nco.html#ftp --><p>To access a file via an anonymous <acronym>FTP</acronym> server, simply supply
+the remote file’s <acronym>URL</acronym>.
+Anonymous <acronym>FTP</acronym> usually requires no further credentials,
+e.g., no <samp>.netrc</samp> file is necessary.
<acronym>FTP</acronym> is an intrinsically insecure protocol because it transfers
-passwords in plain text format.
+passwords in plain text format.
Users should access sites using anonymous <acronym>FTP</acronym>, or better yet,
-secure <acronym>FTP</acronym> when possible.
+secure <acronym>FTP</acronym> (<acronym>SFTP</acronym>, see below) when possible.
Some <acronym>FTP</acronym> servers require a login/password combination for a
valid user account.
-<acronym>NCO</acronym> allows these transactions so long as the required
-information is stored in the <samp>.netrc</samp> file.
+<acronym>NCO</acronym> allows transactions that require additional credentials
+so long as the required information is stored in the <samp>.netrc</samp> file.
Usually this information is the remote machine name, login, and
password, in plain text, separated by those very keywords, e.g.,
</p><div class="example">
@@ -3040,7 +3058,7 @@ specified with a homebrew syntax of the form
<pre class="example">sftp://machine.domain.tld:/path/to/filename
</pre></div>
<p>Note the second colon following the top-level-domain, <code>tld</code>.
-This syntax is a hybrid between an <acronym>FTP URL</acronym> and a standard
+This syntax is a hybrid between an <acronym>FTP URL</acronym> and standard
remote file syntax.
</p>
<a name="rcp"></a> <!-- http://nco.sf.net/nco.html#rcp -->
@@ -3238,7 +3256,7 @@ input and output file format:
one = 1
</pre></div>
<p>And, of course, <acronym>OPeNDAP</acronym>-enabled <acronym>NCO</acronym> clients continue
-to support other, orthogonal features such as UDUnits
+to support orthogonal features such as UDUnits
(see <a href="#UDUnits-Support">UDUnits Support</a>):
</p><div class="example">
<pre class="example">% ncks -u -C -H -v wvl -d wvl,'0.4 micron','0.7 micron' \
@@ -3262,9 +3280,9 @@ http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/su
<a name="index-unpacking"></a>
<p>All with one command!
The data in this particular input file also happen to be packed
-(see <a href="#Methods-and-functions">Methods and functions</a>), although this is completely transparent
-to the user since <acronym>NCO</acronym> automatically unpacks data before
-attempting arithmetic.
+(see <a href="#Methods-and-functions">Methods and functions</a>), although this complication is
+transparent to the user since <acronym>NCO</acronym> automatically unpacks data
+before attempting arithmetic.
</p>
<p><acronym>NCO</acronym> obtains remote files from the <acronym>OPeNDAP</acronym> server
(e.g., <samp>www.cdc.noaa.gov</samp>) rather than the local machine.
@@ -3827,14 +3845,10 @@ Next: <a href="#Subsetting-Coordinate-Variables" accesskey="n" rel="next">Subset
<a name="index-_002d_002dxcl"></a>
<a name="index-_002d_002dunn"></a>
<a name="index-_002d_002dunion"></a>
+<a name="index-_002d_002dgxvx"></a>
+<a name="index-_002d_002dgrp_005fxtr_005fvar_005fxcl"></a>
<table class="cartouche" border="1"><tr><td>
-<p>Options <code>--unn</code><br>
-Availability: <code>ncbo</code>, <code>nces</code>,
-<code>ncecat</code>, <code>ncflint</code>, <code>ncks</code>, <code>ncpdq</code>,
-<code>ncra</code>, <code>ncrcat</code>, <code>ncwa</code><br>
-Short options: <br>
-Long options: ‘<samp>--unn</samp>’ and ‘<samp>--union</samp>’<br>
-Options <code>-g <var>grp</var></code><br>
+<p>Options <code>-g <var>grp</var></code><br>
Availability: <code>ncbo</code>, <code>nces</code>,
<code>ncecat</code>, <code>ncflint</code>, <code>ncks</code>, <code>ncpdq</code>,
<code>ncra</code>, <code>ncrcat</code>, <code>ncwa</code><br>
@@ -3846,6 +3860,16 @@ Availability: (<code>ncap2</code>), <code>ncbo</code>, <code>nces</code>,
<code>ncra</code>, <code>ncrcat</code>, <code>ncwa</code><br>
Short options: ‘<samp>-v</samp>’, ‘<samp>-x</samp>’<br>
Long options: ‘<samp>--variable</samp>’, ‘<samp>--exclude</samp>’ or ‘<samp>--xcl</samp>’<br>
+Options <code>--unn</code><br>
+Availability: <code>ncbo</code>, <code>nces</code>,
+<code>ncecat</code>, <code>ncflint</code>, <code>ncks</code>, <code>ncpdq</code>,
+<code>ncra</code>, <code>ncrcat</code>, <code>ncwa</code><br>
+Short options: <br>
+Long options: ‘<samp>--unn</samp>’ and ‘<samp>--union</samp>’<br>
+Options <code>--grp_xtr_var_xcl</code><br>
+Availability: <code>ncks</code><br>
+Short options: <br>
+Long options: ‘<samp>--gxvx</samp>’ and ‘<samp>--grp_xtr_var_xcl</samp>’<br>
</p></td></tr></table>
<p>Subsetting variables refers to explicitly specifying variables and
groups to be included or excluded from operator actions.
@@ -3882,6 +3906,22 @@ distinctions.
When learning this syntax it is helpful to keep in mind the similarity
between group hierarchies and directory structures.
</p>
+<a name="gxvx"></a> <!-- http://nco.sf.net/nco.html#gxvx -->
+<a name="grp_xtr_var_xcl"></a> <!-- http://nco.sf.net/nco.html#grp_xtr_var_xcl --><p>As of <acronym>NCO</acronym> 4.4.4 (June, 2014), <code>ncks</code> (alone) supports
+an option to include specified groups yet exclude specified variables.
+The ‘<samp>--grp_xtr_var_xcl</samp>’ switch (with long option equivalent
+‘<samp>--gxvx</samp>’) extracts all contents of groups given as arguments to
+‘<samp>-g <var>grp</var>[,…]</samp>’, except for variables given as arguments
+to ‘<samp>-v <var>var</var>[,…]</samp>’.
+Use this when one or a few variables in hierarchical files are not to be
+extracted, and all other variables are.
+This is useful when coercing netCDF4 files into netCDF3 files such as
+with converting, flattening, or dismembering files
+(see <a href="#Flattening-Groups">Flattening Groups</a>).
+</p><div class="example">
+<pre class="example">ncks --grp_xtr_var_xcl -g g1 -v v1 # Extract all of group g1 except v1
+</pre></div>
+
<a name="index-mv"></a>
<a name="index-cp"></a>
<a name="index-recursion"></a>
@@ -4118,7 +4158,7 @@ those groups, and file <samp>in.nc</samp> with variables <code>Q</code>,
<code>Q01</code>–<code>Q99</code>, <code>Q100</code>, <code>QAA</code>–<code>QZZ</code>,
<code>Q_H2O</code>, <code>X_H2O</code>, <code>Q_CO2</code>, <code>X_CO2</code>.
</p><div class="example">
-<pre class="example">ncks -v '.+' in.nc # All variables (default)
+<pre class="verbatim">ncks -v '.+' in.nc # All variables (default)
ncks -v 'Q.?' in.nc # Variables that contain Q
ncks -v '^Q.?' in.nc # Variables that start with Q
ncks -v '^Q+.?.' in.nc # Q, Q0--Q9, Q01--Q99, QAA--QZZ, etc.
@@ -4215,12 +4255,15 @@ automatically specifying that <em>all</em> coordinate variables in the
Thus ‘<samp>-c</samp>’ allows the user to select all the coordinate variables
without having to know their names.
<a name="index-CF-conventions"></a>
-As of <acronym>NCO</acronym> version 3.9.6 (January, 2009)
-both ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’ honor the <acronym>CF</acronym> <code>coordinates</code>
-convention described in <a href="#CF-Conventions">CF Conventions</a>.
+As of <acronym>NCO</acronym> version 4.4.5 (July, 2014)
+both ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’ honor the <acronym>CF</acronym> <code>ancillary_variables</code>
+convention described in <a href="#CF-Conventions">CF Conventions</a>.
As of <acronym>NCO</acronym> version 4.0.8 (April, 2011)
both ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’ honor the <acronym>CF</acronym> <code>bounds</code>
convention described in <a href="#CF-Conventions">CF Conventions</a>.
+As of <acronym>NCO</acronym> version 3.9.6 (January, 2009)
+both ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’ honor the <acronym>CF</acronym> <code>coordinates</code>
+convention described in <a href="#CF-Conventions">CF Conventions</a>.
</p>
<a name="gpe"></a> <!-- http://nco.sf.net/nco.html#gpe --><hr>
<a name="Group-Path-Editing"></a>
@@ -4283,6 +4326,24 @@ Hence, ‘<samp>-G :-1</samp>’ is the same as ‘<samp>-G @1</samp
This is simply a way of making the <var>lvl_nbr</var> argument
positive-definite.
</p>
+<table class="menu" border="0" cellspacing="0">
+<tr><td align="left" valign="top">• <a href="#Flattening-Groups" accesskey="1">Flattening Groups</a>:</td><td> </td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">• <a href="#Moving-Groups" accesskey="2">Moving Groups</a>:</td><td> </td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">• <a href="#Dismembering-Files" accesskey="3">Dismembering Files</a>:</td><td> </td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">• <a href="#Checking-CF_002dcompliance" accesskey="4">Checking CF-compliance</a>:</td><td> </td><td align="left" valign="top">
+</td></tr>
+</table>
+<hr>
+<a name="Flattening-Groups"></a>
+<div class="header">
+<p>
+Next: <a href="#Moving-Groups" accesskey="n" rel="next">Moving Groups</a>, Previous: <a href="#Group-Path-Editing" accesskey="p" rel="previous">Group Path Editing</a>, Up: <a href="#Group-Path-Editing" accesskey="u" rel="up">Group Path Editing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+</div>
+<a name="Deletion_002c-Truncation_002c-and-Flattening-of-Groups"></a>
+<h4 class="subsection">3.13.1 Deletion, Truncation, and Flattening of Groups</h4>
<a name="flatten"></a> <!-- http://nco.sf.net/nco.html#flatten -->
<a name="delete"></a> <!-- http://nco.sf.net/nco.html#delete -->
<a name="truncate"></a> <!-- http://nco.sf.net/nco.html#truncate --><a name="index-_0040-_0028separator-character_0029"></a>
@@ -4350,7 +4411,7 @@ groups and their placement in the output file as shown by the following
commands.
All commands below may be assumed to end with ‘<samp>in.nc out.nc</samp>’.
</p><div class="example">
-<pre class="example"># Prepending paths without editing:
+<pre class="verbatim"># Prepending paths without editing:
ncks # /g?/v? -> /g?/v?
ncks -v v1 # /g?/v1 -> /g?/v1
ncks -g g1 # /g1/v? -> /g1/v?
@@ -4393,7 +4454,15 @@ ncks -G g1:-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/g1/v1
</pre></div>
<a name="mv"></a> <!-- http://nco.sf.net/nco.html#mv -->
-<a name="move"></a> <!-- http://nco.sf.net/nco.html#move --><a name="index-move-groups"></a>
+<a name="move"></a> <!-- http://nco.sf.net/nco.html#move --><hr>
+<a name="Moving-Groups"></a>
+<div class="header">
+<p>
+Next: <a href="#Dismembering-Files" accesskey="n" rel="next">Dismembering Files</a>, Previous: <a href="#Flattening-Groups" accesskey="p" rel="previous">Flattening Groups</a>, Up: <a href="#Group-Path-Editing" accesskey="u" rel="up">Group Path Editing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+</div>
+<a name="Moving-Groups-1"></a>
+<h4 class="subsection">3.13.2 Moving Groups</h4>
+<a name="index-move-groups"></a>
<a name="index-groups_002c-moving"></a>
<a name="index-rename-groups"></a>
<a name="index-groups_002c-renaming"></a>
@@ -4441,7 +4510,15 @@ all other groups (e.g., <code>ecmwf</code>, <code>giss</code>).
</p>
<a name="dismember"></a> <!-- http://nco.sf.net/nco.html#dismember -->
<a name="disaggregate"></a> <!-- http://nco.sf.net/nco.html#disaggregate -->
-<a name="ncdismember"></a> <!-- http://nco.sf.net/nco.html#ncdismember --><a name="index-disaggregate"></a>
+<a name="ncdismember"></a> <!-- http://nco.sf.net/nco.html#ncdismember --><hr>
+<a name="Dismembering-Files"></a>
+<div class="header">
+<p>
+Next: <a href="#Checking-CF_002dcompliance" accesskey="n" rel="next">Checking CF-compliance</a>, Previous: <a href="#Moving-Groups" accesskey="p" rel="previous">Moving Groups</a>, Up: <a href="#Group-Path-Editing" accesskey="u" rel="up">Group Path Editing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+</div>
+<a name="Dismembering-Files-1"></a>
+<h4 class="subsection">3.13.3 Dismembering Files</h4>
+<a name="index-disaggregate"></a>
<a name="index-dismember"></a>
<a name="index-ncdismember"></a>
<p>Let us show how to completely disaggregate (or, more memorably)
@@ -4513,7 +4590,8 @@ for grp_in in ${grp_lst} ; do
eval ${cmd}
if [ ${flg_cf} = 'cf' ]; then
# cfchecker needs Conventions <= 1.5
- ncatted -h -a Conventions,global,o,c,"CF-${cf_vrs}" ${drc_out}/${grp_out}.nc
+ no_bck_sls=`echo ${drc_out}/${grp_out} | sed 's/\\\ / /g'`
+ ncatted -h -a Conventions,global,o,c,CF-${cf_vrs} ${no_bck_sls}.nc
else # !flg_cf
echo ${drc_out}/${grp_out}.nc
fi # !flg_cf
@@ -4554,6 +4632,14 @@ as <code>NC_STRING</code> and <code>NC_UBYTE</code>) to corresponding netCDF3
atomic types (<code>NC_CHAR</code> and <code>NC_SHORT</code>) when the output format
is netCDF3.
</p>
+<hr>
+<a name="Checking-CF_002dcompliance"></a>
+<div class="header">
+<p>
+Previous: <a href="#Dismembering-Files" accesskey="p" rel="previous">Dismembering Files</a>, Up: <a href="#Group-Path-Editing" accesskey="u" rel="up">Group Path Editing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+</div>
+<a name="Checking-CF_002dcompliance-1"></a>
+<h4 class="subsection">3.13.4 Checking CF-compliance</h4>
<a name="index-CF-compliance-checker"></a>
<a name="index-cfchecker"></a>
<a name="index-ncdismember-1"></a>
@@ -4614,15 +4700,15 @@ of the procedure necessary to check <acronym>HDF</acronym> files for
<acronym>CF</acronym>-compliance:
</p><div class="example">
<pre class="verbatim">cat > ~/ncdismember.txt << 'EOF'
- Preparing an RPM-based OS to Test Hierarchical Files for CF-Compliance
+ Preparing an RPM-based OS to Test HDF & netCDF Files for CF-Compliance
By Charlie Zender, UCI & NASA Dataset Interoperability Working Group (DIWG)
Installation Summary:
-1. HDF4 [with netCDF support _disabled_]
+1. HDF4 [with internal netCDF support _disabled_]
2. HDF5
-3. netCDF version 4.3.1 (or later) [with HDF4 support _enabled_]
-4. NCO version 4.4.0 (or later)
+3. netCDF [with external HDF4 support _enabled_]
+4. NCO
5. numpy
6. netcdf4-python
7. python-lxml
@@ -4653,20 +4739,19 @@ cd hdf5-1.8.11
./configure --enable-shared --prefix=${H5DIR}
make && make check && make install
-# 3. netCDF version 4.3.1. Build in non-default manner with HDF4. No RPM.
+# 3. netCDF version 4.3.1 or later. Build in non-default manner with HDF4.
# Per http://www.unidata.ucar.edu/software/netcdf/docs/build_hdf4.html
# Earlier versions of netCDF may fail checking some HDF4 files
-wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.1.tar.gz
-tar xvzf netcdf-4.3.1.tar.gz
-cd netcdf-4.3.1
+wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz
+tar xvzf netcdf-4.3.2.tar.gz
+cd netcdf-4.3.2
CPPFLAGS="-I${H5DIR}/include -I${H4DIR}/include" \
LDFLAGS="-L${H5DIR}/lib -L${H4DIR}/lib" \
./configure --enable-hdf4 --enable-hdf4-file-tests
-make && make check && make installas
+make && make check && make install
-# 4. NCO version 4.4.4. No RPM for this version. Must install by hand.
-# Earlier versions of NCO are relatively useless for ncdismember
-cd ${DATA}/tmp
+# 4. NCO version 4.4.0 or later. Some RPMs available. Or install by hand.
+# Later versions of NCO have much better support for ncdismember
wget http://nco.sourceforge.net/src/nco-4.4.4.tar.gz .
tar xvzf nco-4.4.4.tar.gz
cd nco-4.4.4
@@ -4684,14 +4769,13 @@ sudo yum install python-lxml -y
# 8. CFunits-python. No RPM available. Must install by hand.
# http://code.google.com/p/cfunits-python/
-cd ${DATA}/tmp
wget http://cfunits-python.googlecode.com/files/cfunits-0.9.6.tar.gz .
+tar xvzf cfunits-0.9.6.tar.gz
cd cfunits-0.9.6
sudo python setup.py install
# 9. CFChecker. No RPM available. Must install by hand.
# https://bitbucket.org/mde_/cfchecker
-cd ${DATA}/tmp
wget https://bitbucket.org/mde_/cfchecker/downloads/CFchecker-1.5.15.tar.bz2 .
tar xvjf CFchecker-1.5.15.tar.bz2
cd CFchecker
@@ -4994,7 +5078,7 @@ concatenate the resulting files together:
<a name="index-Bourne-Shell"></a>
<a name="index-C-Shell"></a>
</p><div class="example">
-<pre class="example">for idx in 02 14 26 38 50; do # Bourne Shell
+<pre class="verbatim">for idx in 02 14 26 38 50; do # Bourne Shell
ncks -d time,${idx} 8501_8912.nc foo.${idx}
done
foreach idx (02 14 26 38 50) # C Shell
@@ -5152,7 +5236,7 @@ Traditionally, we would first compute the climatological monthly
mean for each month of summer.
Each of these is a 150-year mean, i.e.,
</p><div class="example">
-<pre class="example"># Step 1: Create climatological monthly files clm06.nc..clm08.nc
+<pre class="verbatim"># Step 1: Create climatological monthly files clm06.nc..clm08.nc
for mth in {6..8}; do
mm=`printf "%02d" $mth`
ncra -O -F -d time,${mm},,12 -n 150,4,1 1850.nc clm${mm}.nc
@@ -5505,7 +5589,7 @@ ranges.
This works on datasets that associate coordinate variables to
grid-mappings using the <acronym>CF</acronym>-convention (see <a href="#CF-Conventions">CF Conventions</a>)
<code>coordinates</code> and <code>standard_name</code> attributes described
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system">here</a>.
+<a href="http://cfconventions.org/1.6.html#coordinate-system">here</a>.
Currently, <acronym>NCO</acronym> understands auxiliary coordinate variables
pointed to by the <code>standard_name</code> attributes for <var>latitude</var> and
<var>longitude</var>.
@@ -6195,31 +6279,34 @@ performance.
<p>The user specifies the desired chunking policy with the ‘<samp>-P</samp>’ switch
(or its long option equivalents, ‘<samp>--cnk_plc</samp>’ and
‘<samp>--chunk_policy</samp>’) and its <var>cnk_plc</var> argument.
-Five chunking policies are currently implemented:<br>
+As of August, 2014, six chunking policies are currently implemented:<br>
<a name="index-all"></a>
<a name="index-g2d"></a>
<a name="index-g3d"></a>
+<a name="index-r1d"></a>
<a name="index-xpl"></a>
<a name="index-xst"></a>
<a name="index-cnk_005fall"></a>
<a name="index-cnk_005fg2d"></a>
<a name="index-cnk_005fg3d"></a>
+<a name="index-cnk_005fr1d"></a>
<a name="index-cnk_005fxpl"></a>
<a name="index-cnk_005fxst"></a>
<a name="index-plc_005fall"></a>
<a name="index-plc_005fg2d"></a>
<a name="index-plc_005fg3d"></a>
+<a name="index-plc_005fr1d"></a>
<a name="index-plc_005fxpl"></a>
<a name="index-plc_005fxst"></a>
</p><dl compact="compact">
-<dt><em>Chunk All Variables [<em>default</em>]</em></dt>
+<dt><em>Chunk All Variables</em></dt>
<dd><p>Definition: Chunk all variables possible.
For obvious reasons, scalar variables cannot be chunked.<br>
Alternate invocation: <code>ncchunk</code><br>
<var>cnk_plc</var> key values: ‘<samp>all</samp>’, ‘<samp>cnk_all</samp>’, ‘<samp>plc_all</samp>’<br>
Mnemonic: All<br>
</p></dd>
-<dt><em>Chunk Variables with at least Two Dimensions</em></dt>
+<dt><em>Chunk Variables with at least Two Dimensions [<em>default</em>]</em></dt>
<dd><p>Definition: Chunk all variables possible with at least two dimensions<br>
Alternate invocation: none<br>
<var>cnk_plc</var> key values: ‘<samp>g2d</samp>’, ‘<samp>cnk_g2d</samp>’, ‘<samp>plc_g2d</samp>’<br>
@@ -6231,6 +6318,16 @@ Alternate invocation: none<br>
<var>cnk_plc</var> key values: ‘<samp>g3d</samp>’, ‘<samp>cnk_g3d</samp>’, ‘<samp>plc_g3d</samp>’<br>
Mnemonic: <em>G</em>reater than or equal to <em>3</em> <em>D</em>imensions<br>
</p></dd>
+<dt><em>Chunk One-Dimensional Record Variables</em></dt>
+<dd><p>Definition: Chunk all 1-D record variables<br>
+Alternate invocation: none<br>
+Any specified (with ‘<samp>--cnk_dmn</samp>’) record dimension chunksizes will
+be applied to 1-D record variables (and to no other variables).
+Other dimensions may be chunked with their own ‘<samp>--cnk_dmn</samp>’ options
+that will apply to all variables.
+<var>cnk_plc</var> key values: ‘<samp>r1d</samp>’, ‘<samp>cnk_r1d</samp>’, ‘<samp>plc_r1d</samp>’<br>
+Mnemonic: <em>R</em>ecord <em>1</em>-<em>D</em> variables<br>
+</p></dd>
<dt><em>Chunk Variables Containing Explicitly Chunked Dimensions</em></dt>
<dd><p>Definition: Chunk all variables possible that contain at least one
dimension whose chunksize was explicitly set with the ‘<samp>--cnk_dmn</samp>’ option.
@@ -6409,6 +6506,21 @@ ncwa -O -4 -D 4 -a time --cnk_plc=g2d --cnk_map=rd1 --cnk_dmn lat,32 \
--cnk_dmn lon,128 dstmch90_clm_0112.nc ~/foo.nc
</pre></div>
+<a name="r1d"></a> <!-- http://nco.sf.net/nco.html#r1d --><p>Chunking policy ‘<samp>r1d</samp>’ changes the chunksize of 1-D record variables
+(and no other variables) to the specified (with ‘<samp>--cnk_dmn</samp>’)
+chunksize.
+Any specified record dimension chunksizes will be applied to 1-D
+record variables only.
+Other dimensions may be chunked with their own ‘<samp>--cnk_dmn</samp>’ options
+that will apply to all variables.
+For example,
+</p><div class="example">
+<pre class="example">ncks --cnk_plc=r1d --cnk_dmn=time,1000. in.nc out.nc
+</pre></div>
+<p>This sets <code>time</code> chunks to 1000 only in 1-D record variables.
+Without the ‘<samp>r1d</samp>’ policy, <code>time</code> chunks would change in all
+variables.
+</p>
<a name="index-record-dimension-2"></a>
<p>It is appropriate to conclude by informing users about an aspect of
chunking that may not be expected.
@@ -6745,7 +6857,7 @@ an arbitrary number (set to one hundred thousand) of files are all
symbolically linked to the same file.
Everything is on the local filesystem (not <acronym>DAP</acronym>).
</p><div class="example">
-<pre class="example"># Create symbolic links for benchmark
+<pre class="verbatim"># Create symbolic links for benchmark
cd ${DATA}/nco # Do all work here
for idx in {1..99999}; do
idx_fmt=`printf "%05d" ${idx}`
@@ -7278,7 +7390,7 @@ This is why type conversion is limited to the operators <code>ncap2</code>,
<code>ncwa</code>.
</li><li> The arithmetic operation could benefit from type conversion.
Operations that could benefit include averaging, summation, or any
-"hard" arithmetic that could overflow or underflow.
+“hard” arithmetic that could overflow or underflow.
Larger representable sums help avoid overflow, and more precision
helps to avoid underflow.
Type conversion does not benefit searching for minima and maxima
@@ -7345,8 +7457,8 @@ These functions round <var>x</var> to the nearest integer, halfway cases away
from zero.
The problem with <code>lround()</code> is that it always rounds real values
ending in <code>.5</code> away from zero.
-This rounds, for example, <code>1.5d</code> and <code>2.5d</code> to <code>1s</code>
-and <code>2s</code>, respectively.
+This rounds, for example, <code>1.5d</code> and <code>2.5d</code> to <code>2s</code>
+and <code>3s</code>, respectively.
</p>
<a name="index-lrint_0028_0029_002e"></a>
<a name="index-IEEE"></a>
@@ -7500,9 +7612,9 @@ seven significant figures for single precision floats (<code>tpt_flt</code>),
and sixteen significant figures for double precision (<code>tpt_dbl</code>).
The input precision determines the answer precision.
</p>
-<p>IEEE arithmetic guarantees that two methods will produce bit-for-bit
-identical answers only if they compute the same operations in the same
-order.
+<p><acronym>IEEE</acronym> arithmetic guarantees that two methods will produce
+bit-for-bit identical answers only if they compute the same operations
+in the same order.
Bit-for-bit identical answers may also occur by happenstance when
rounding errors exactly compensate one another.
This is demonstrated by repeating the example above with the
@@ -7969,8 +8081,8 @@ Nevertheless, we refer to all such metadata collectively as <acronym>CF</acronym
metadata.
Skip this section if you never work with <acronym>CF</acronym> metadata.
</p>
-<p>The <acronym>CF</acronym> netCDF conventions are described
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system">here</a>.
+<p>The latest <acronym>CF</acronym> netCDF conventions are described
+<a href="http://cfconventions.org/1.6.html">here</a>.
Most <acronym>CF</acronym> netCDF conventions are transparent to <acronym>NCO</acronym>
<a name="DOCF46" href="#FOOT46"><sup>46</sup></a>.
There are no known pitfalls associated with using any <acronym>NCO</acronym>
@@ -8041,7 +8153,7 @@ or alter the <code>Conventions</code> attribute.
<p>As of <acronym>NCO</acronym> version 4.0.8 (April, 2011), <acronym>NCO</acronym>
supports the <acronym>CF</acronym> <code>bounds</code> convention for cell boundaries
described
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#cell-boundaries">here</a>.
+<a href="http://cfconventions.org/1.6.html#cell-boundaries">here</a>.
This convention allows coordinate variables (including multidimensional
coordinates) to describe the boundaries of their cells.
This is done by naming the variable which contains the bounds in
@@ -8051,6 +8163,25 @@ NCO-generated subsets of <acronym>CF</acronym>-compliant files with <code>bounds
attributes will include the coordinates specified by the <code>bounds</code>
attribute, if any.
Hence the subsets will themselves be <acronym>CF</acronym>-compliant.
+Bounds are subject to the user-specified override switches
+(including ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’) described in
+<a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a>.
+</p>
+<a name="cnv_CF_ncl"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_ncl -->
+<a name="ncl"></a> <!-- http://nco.sf.net/nco.html#ncl --><a name="index-ancillary_005fvariables"></a>
+<a name="index-ancillary-variables-convention"></a>
+<p>As of <acronym>NCO</acronym> version 4.4.5 (July, 2014), <acronym>NCO</acronym>
+supports the <acronym>CF</acronym> <code>ancillary_variables</code> convention for
+described
+<a href="http://cfconventions.org/1.6.html#ancillary-data">here</a>.
+This convention allows ancillary variables to be associated with one or
+more primary variables.
+<acronym>NCO</acronym> attaches any such variables to the extraction list along
+with the primary variable and its usual (one-dimensional) coordinates,
+if any.
+Ancillary variables are subject to the user-specified override switches
+(including ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’) described in
+<a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a>.
</p>
<a name="cnv_CF_crd"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_crd --><a name="index-coordinates-1"></a>
<a name="index-coordinates-convention"></a>
@@ -8065,14 +8196,15 @@ Hence the subsets will themselves be <acronym>CF</acronym>-compliant.
<a name="index-_002d_002dcrd-1"></a>
<p>As of <acronym>NCO</acronym> version 3.9.6 (January, 2009), <acronym>NCO</acronym>
supports the <acronym>CF</acronym> <code>coordinates</code> convention described
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system">here</a>.
+<a href="http://cfconventions.org/1.6.html#coordinate-system">here</a>.
This convention allows variables to specify additional coordinates
(including multidimensional coordinates) in a space-separated string
attribute named <code>coordinates</code>.
-NCO attaches any such coordinates to the extraction list along with
-variable and its usual (one-dimensional) coordinates, if any.
-These auxiliary coordinates are subject to the user-specified overrides
-described in <a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a>.
+<acronym>NCO</acronym> attaches any such coordinates to the extraction list along
+with variable and its usual (one-dimensional) coordinates, if any.
+These auxiliary coordinates are subject to the user-specified override
+switches (including ‘<samp>-c</samp>’ and ‘<samp>-C</samp>’) described in
+<a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a>.
</p>
<a name="cnv_CF_cll_mth"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_cll_mth -->
<a name="cll_mth"></a> <!-- http://nco.sf.net/nco.html#cll_mth -->
@@ -8085,7 +8217,7 @@ described in <a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Va
<a name="index-cell-methods-convention"></a>
<p>As of <acronym>NCO</acronym> version 4.4.2 (February, 2014), <acronym>NCO</acronym>
supports some of the <acronym>CF</acronym> <code>cell_methods</code>
-<a href="http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.7-draft1/cf-conventions.html#cell-methods">convention</a>
+<a href="http://cfconventions.org/1.6.html#cell-methods">convention</a>
to describe the analysis procedures that have been applied to data.
The convention creates (or appends to an existing) <code>cell_methods</code>
attribute a space-separated list of couplets of the form <var>dmn: op</var>
@@ -8262,7 +8394,6 @@ Next: <a href="#ncatted-netCDF-Attribute-Editor" accesskey="n" rel="next">ncatte
<a name="index-arithmetic-processor"></a>
<a name="index-ncap"></a>
<a name="index-ncap2-5"></a>
-
<table class="cartouche" border="1"><tr><td>
<p><code>ncap2</code> understands a relatively full-featured
language of operations, including loops, conditionals, arrays,
@@ -8518,7 +8649,7 @@ to precision and rank.<br>
Examples:
</p>
<div class="example">
-<pre class="example">dimensions: time=10, lat=2, lon=4
+<pre class="verbatim">dimensions: time=10, lat=2, lon=4
Suppose we have the two variables:
double P(time,lat,lon);
@@ -8621,7 +8752,7 @@ returned else exp3 is returned.
</p>
<p>Example:
</p><div class="example">
-<pre class="example">weight_avg=weight.avg();
+<pre class="verbatim">weight_avg=weight.avg();
weight_avg at units= (weight_avg == 1 ? "kilo" : "kilos");
PS_nw=PS-(PS.min() > 100000 ? 100000 : 0);
</pre></div>
@@ -8869,7 +9000,7 @@ The number of hyperslab arguments MUST equal the variable’s rank.
</p>
<p>A simple 1D example:
</p><div class="example">
-<pre class="example">($time.size=10)
+<pre class="verbatim">($time.size=10)
od[$time]={20,22,24,26,28,30,32,34,36,38};
od(7); // 34
@@ -8882,7 +9013,7 @@ od(:) // 20,22,24,26,28,30,32,34,36,38
<p>A more complex three dimensional example:
</p><div class="example">
-<pre class="example">($lat.size=2,$lon.size=4)
+<pre class="verbatim">($lat.size=2,$lon.size=4)
th[$time,$lat,$lon]=
{1, 2, 3, 4, 5, 6, 7, 8,
9,10,11,12,13,14,15,16,
@@ -8956,7 +9087,7 @@ Use the <code>reverse()</code> method to reverse a dimension’s elements in
variable with at least one dimension.
This is equivalent to a negative stride, e.g.,
</p><div class="example">
-<pre class="example">th_rv=th(1 ,:,:).reverse($lon); // {12,11,10,9 }, {16,15,14,13}
+<pre class="verbatim">th_rv=th(1 ,:,:).reverse($lon); // {12,11,10,9 }, {16,15,14,13}
od_rv=od.reverse($time); // {38,36,34,32,30,28,26,24,22,20}
</pre></div>
@@ -8998,7 +9129,7 @@ Next: <a href="#Number-literals" accesskey="n" rel="next">Number literals</a>, P
<p>Attributes are referred to by <em>var_nm at att_nm</em> <br>
All the following are valid statements:
</p><div class="example">
-<pre class="example">global at text="Test Attributes"; /* Assign a global variable attribute */
+<pre class="verbatim">global at text="Test Attributes"; /* Assign a global variable attribute */
a1[$time]=time*20;
a1 at long_name="Kelvin";
a1 at min=a1.min();
@@ -9012,7 +9143,7 @@ a1($time.size-1)=a1 at max;
<p>A <em>value list</em> can be used on the RHS of an assign...
<a name="index-value-list"></a>
</p><div class="example">
-<pre class="example">a1 at trip1={1,2,3} ;
+<pre class="verbatim">a1 at trip1={1,2,3} ;
a1 at triplet={a1 at min,(a1 at min+a1@max)/2,a1 at max};
</pre></div>
<p>The netCDF specification allows all attribute types to have a size
@@ -9031,7 +9162,7 @@ The following is an <code>ncdump</code> of the metadata for variable <var>a1</va
<p>The <code>size()</code> method can be used with attributes.
For example, to save an attribute text string in a variable,
</p><div class="example">
-<pre class="example">defdim("sng_len", a1 at long_name.size());
+<pre class="verbatim">defdim("sng_len", a1 at long_name.size());
sng_arr[$sng_len]=a1 at long_name; // sng_arr now contains "Kelvin"
</pre></div>
<p>Attributes defined in a script are stored in memory and are written to Output after script completion.
@@ -9055,7 +9186,7 @@ th_min=1.0 + 2*three_dmn_var_dbl.min($time);
<p>If the attribute name contains non-regular characters use ID quoting. See see <a href="#ID-Quoting">ID Quoting</a>
</p><div class="example">
-<pre class="example">'b..m1 at c--lost'=23;
+<pre class="verbatim">'b..m1 at c--lost'=23;
</pre></div>
<a name="ncap_num"></a> <!-- http://nco.sf.net/nco.html#ncap_num --><hr>
@@ -9073,11 +9204,11 @@ To use the new netCDF4 types <acronym>NCO</acronym> must be compiled/linked to
the netCDF4 library and the output file must be <acronym>HDF5</acronym>.
</p>
<div class="example">
-<pre class="example">n1[$time]=1UL; // n1 will now by type <code>NC_UINT</code>
-n2[$lon]=4b; // n2 will be of type <code>NC_BYTE</code>
-n3[$lat]=5ull; // n3 will be of type <code>NC_UINT64</code>
-n3 at a1=6.0d; // attribute will be type <code>NC_DOUBLE</code>
-n3 at a2=-666L; // attribute will be type <code>NC_INT</code>
+<pre class="verbatim">n1[$time]=1UL; // n1 will now by type @code{NC_UINT}
+n2[$lon]=4b; // n2 will be of type @code{NC_BYTE}
+n3[$lat]=5ull; // n3 will be of type @code{NC_UINT64}
+n3 at a1=6.0d; // attribute will be type @code{NC_DOUBLE}
+n3 at a2=-666L; // attribute will be type @code{NC_INT}
</pre></div>
<p>A floating point number without a postfix will default to
@@ -9085,13 +9216,13 @@ n3 at a2=-666L; // attribute will be type <code>NC_INT</code>
An integer without a postfix will default to type <code>NC_INT</code>.
There is no postfix for characters, use a quoted string instead.
</p><div class="example">
-<pre class="example">n4[$rlev]=0.1 // n4 will be of type <code>NC_DOUBLE</code>
-n5[$lon_grd]=2.0 // n5 will be of type <code>NC_DOUBLE</code>
-n6[$gds_crd]=2e3; // n6 will be of type <code>NC_DOUBLE</code>
-n7[$gds_crd]=2e3f; // n7 will be of type <code>NC_FLOAT</code>
-n6 at a1=41; // attribute will be type <code>NC_INT</code>
-n6 at a2=-21; // attribute will be type <code>NC_INT</code>
-n6 at units="kelvin" // attribute will be type <code>NC_CHAR</code>
+<pre class="verbatim">n4[$rlev]=0.1 // n4 will be of type @code{NC_DOUBLE}
+n5[$lon_grd]=2.0 // n5 will be of type @code{NC_DOUBLE}
+n6[$gds_crd]=2e3; // n6 will be of type @code{NC_DOUBLE}
+n7[$gds_crd]=2e3f; // n7 will be of type @code{NC_FLOAT}
+n6 at a1=41; // attribute will be type @code{NC_INT}
+n6 at a2=-21; // attribute will be type @code{NC_INT}
+n6 at units="kelvin" // attribute will be type @code{NC_CHAR}
</pre></div>
<dl compact="compact">
@@ -9145,7 +9276,7 @@ Next: <a href="#print-statement" accesskey="n" rel="next">print statement</a>, P
The <em>Conditional Operator (ternary operator)</em> has also been
implemented.
</p><div class="example">
-<pre class="example">if(exp1)
+<pre class="verbatim">if(exp1)
stmt1;
else if(exp2)
stmt2;
@@ -9157,13 +9288,13 @@ if(exp1){
stmt1;
stmt1a;
stmt1b;
-} else if(exp2)
+}else if(exp2)
stmt2;
-else {
+else{
stmt3;
stmt3a;
stmt3b;
-}
+}
</pre></div>
<p>For a variable or attribute expression to be logically true
@@ -9175,7 +9306,7 @@ OR (<code>||</code>) and AND (<code>&&</code>) operators.
The whole expression is evaluated regardless if one of the AND/OR
operands are True/False.
</p><div class="example">
-<pre class="example"># Simple example
+<pre class="verbatim"># Simple example
if(time>0)
print("All values of time are greater than zero\n");
else if( time<0)
@@ -9236,7 +9367,7 @@ will be saved and can be printed), and then print the variable.
</p>
<p>examples
</p><div class="example">
-<pre class="example">print(lon);
+<pre class="verbatim">print(lon);
lon[0]=0
lon[1]=90
lon[2]=180
@@ -9330,16 +9461,16 @@ They only work on variables in Output.
</p></dd>
<dt><code>delete_miss()</code></dt>
<dd><a name="index-delete_005fmiss_0028_0029"></a>
-<p>Deletes the missing value associated with a variable.
+<p>Delete the missing value associated with a variable.
</p></dd>
<dt><code>number_miss()</code></dt>
<dd><a name="index-number_005fmiss_0028_0029"></a>
-<p>Counts the number of missing values a variable contains.
+<p>Count the number of missing values a variable contains.
</p></dd>
</dl>
<div class="example">
-<pre class="example">th=three_dmn_var_dbl;
+<pre class="verbatim">th=three_dmn_var_dbl;
th.change_miss(-1e10d);
/* Set values less than 0 or greater than 50 to missing value */
where(th < 0.0 || th > 50.0) th=th.get_miss();
@@ -9640,7 +9771,7 @@ Next: <a href="#Loops" accesskey="n" rel="next">Loops</a>, Previous: <a href="#R
The full syntax of a <code>where()</code> statement is as follows:
</p>
<div class="example">
-<pre class="example">// Single assign (the 'elsewhere' block is optional)
+<pre class="verbatim">// Single assign (the 'elsewhere' block is optional)
where(mask)
var1=expr1;
elsewhere
@@ -9696,15 +9827,25 @@ to set its values less than 8 or greater than 80 to 0<!-- /@w -->:
<pre class="example">where(RDM < 8 || RDM > 80) RDM=0;
</pre></div>
+<a name="WRF"></a> <!-- http://nco.sf.net/nco.html#WRF -->
+<a name="SLD"></a> <!-- http://nco.sf.net/nco.html#SLD -->
+<a name="wrf"></a> <!-- http://nco.sf.net/nco.html#wrf -->
+<a name="sld"></a> <!-- http://nco.sf.net/nco.html#sld --><a name="index-Weather-and-Research-Forecast-_0028WRF_0029-Model"></a>
+<a name="index-Swath_002dlike-Data-_0028SLD_0029"></a>
+<a name="index-WRF-_0028Weather-and-Research-Forecast-Model_0029"></a>
+<a name="index-SLD-_0028Swath_002dlike-Data_0029"></a>
<p>Consider irregularly gridded data, described using rank 2<!-- /@w --> coordinates:
<code>double lat(south_north,east_west)</code>,
<code>double lon(south_north,east_west)</code>,
<code>double temperature(south_north,east_west)</code>.
+This type of structure is often found in regional weather/climate model
+(such as <acronym>WRF</acronym>) output, and in satellite swath data.
+For this reason we call it “Swath-like Data”, or <acronym>SLD</acronym>.
To find the average temperature in a region bounded by
[<var>lat_min</var>,<var>lat_max</var>] and [<var>lon_min</var>,<var>lon_max</var>]:
</p><div class="example">
-<pre class="example">temperature_msk[$south_north,$east_west]=0.0;
-where(lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max)
+<pre class="verbatim">temperature_msk[$south_north,$east_west]=0.0;
+where((lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max))
temperature_msk=temperature;
elsewhere
temperature_msk=temperature at _FillValue;
@@ -9713,6 +9854,52 @@ temp_avg=temperature_msk.avg();
temp_max=temperature.max();
</pre></div>
+<a name="NARR"></a> <!-- http://nco.sf.net/nco.html#NARR -->
+<a name="narr"></a> <!-- http://nco.sf.net/nco.html#narr --><a name="index-NARR-_0028North-American-Regional-Reanalysis_0029a"></a>
+<a name="index-North-American-Regional-Reanalysis-_0028NARR_0029"></a>
+<p>For North American Regional Reanalysis (<acronym>NARR</acronym>) data
+(example
+<a href="http://dust.ess.uci.edu/diwg/narr_uwnd.199605.nc">dataset</a>)
+the procedure looks like this
+</p><div class="example">
+<pre class="verbatim">ncap2 -O -v -S ~/narr.nco ${DATA}/hdf/narr_uwnd.199605.nc ~/foo.nc
+</pre></div>
+<p>where <samp>narr.nco</samp> is an <code>ncap2</code> script like this:
+</p><div class="example">
+<pre class="verbatim">/* North American Regional Reanalysis (NARR) Statistics
+ NARR stores grids with 2-D latitude and longitude, aka Swath-like Data (SLD)
+ Here we work with three variables:
+ lat(y,x), lon(y,x), and uwnd(time,level,y,x);
+ To study sub-regions of SLD, we use masking techniques:
+ 1. Define mask as zero times variable to be masked
+ Then mask automatically inherits variable attributes
+ And average below will inherit mask attributes
+ 2. Optionally, create mask as RAM variable (as below with asterisk *)
+ NCO does not write RAM variable to output
+ Masks are often unwanted, and can be big, so this speeds execution
+ 3. Example could be extended to preserve mean lat and lon of sub-region
+ Follow uwnd example to do this: lat_msk=0.0*lat ... lat_avg=lat.avg($y,$x) */
+*uwnd_msk=0.0*uwnd;
+where((lat >= 35.6 && lat <= 37.0) && (lon >= -100.5 && lon <= -99.0))
+ uwnd_msk=uwnd;
+elsewhere
+ uwnd_msk=uwnd at _FillValue;
+
+// Average only over horizontal dimensions x and y (preserve level and time)
+uwnd_avg=uwnd_msk.avg($y,$x);
+</pre></div>
+<p>Stripped of comments and formatting, this example is a three-statement
+script executed by a one-line command.
+<acronym>NCO</acronym> needs only this meagre input to unpack and copy the input
+data and attributes, compute the statistics, and then define and write
+the output file.
+Unless the comments pointed out that wind variable (<code>uwnd</code>) was
+four-dimensional and the latitude/longitude grid variables were both
+two-dimensional, there would be no way to tell.
+This shows how <acronym>NCO</acronym> hides from the user the complexity of
+analyzing multi-dimensional <acronym>SLD</acronym>.
+We plan to extend such <acronym>SLD</acronym> features to more operators soon.
+</p>
<a name="ncap_lop"></a> <!-- http://nco.sf.net/nco.html#ncap_lop --><hr>
<a name="Loops"></a>
<div class="header">
@@ -9730,7 +9917,7 @@ To break out of a loop use the <code>break</code> command.
To iterate to the next cycle use the <code>continue</code> command.
</p>
<div class="example">
-<pre class="example">// Set elements in variable double temp(time,lat)
+<pre class="verbatim">// Set elements in variable double temp(time,lat)
// If element < 0 set to 0, if element > 100 set to 100
*sz_idx=$time.size;
*sz_jdx=$lat.size;
@@ -9844,7 +10031,7 @@ de-sorting map <var>dsr_map</var> which is inverse map of the input map
This gives the user access to both the forward and inverse sorting maps
which can be useful in special situations.
</p><div class="example">
-<pre class="example">a1[$time]={10,2,3,4,6,5,7,3,4,1};
+<pre class="verbatim">a1[$time]={10,2,3,4,6,5,7,3,4,1};
a1_sort=sort(a1);
print(a1_sort);
// 1, 2, 3, 3, 4, 4, 5, 6, 7, 10;
@@ -9864,7 +10051,7 @@ If the map variable already exists, then the only restriction is that it
be of at least the same size as the input variable.
To apply a map use <code>remap(var_in,srt_map)</code>.
</p><div class="example">
-<pre class="example">defdim("nlat",5);
+<pre class="verbatim">defdim("nlat",5);
a3[$lon]={2,5,3,7};
a4[$nlat,$lon]={
@@ -10185,14 +10372,13 @@ EOF
ncap2 -S ncap2.in in.nc out.nc
</pre></div>
-<a name="wrf"></a> <!-- http://nco.sf.net/nco.html#wrf -->
-<a name="WRF"></a> <!-- http://nco.sf.net/nco.html#WRF --><a name="index-WRF"></a>
+<a name="index-WRF"></a>
<p>Grids like those produced by the <acronym>WRF</acronym> model are complex because
one must use global metadata to determine the grid staggering and
offsets to translate <code>XLAT</code> and <code>XLONG</code> into real latitudes,
longitudes, and missing points.
The <acronym>WRF</acronym> grid documentation should describe this.
-For <acronym>WRF</acronym> files creating regional masks looks like
+For <acronym>WRF</acronym> files creating regional masks looks, in general, like
</p><div class="example">
<pre class="example">mask_var = (XLAT >= lat_min && XLAT <= lat_max) && (XLONG >= lon_min && XLONG <= lon_max);
</pre></div>
@@ -10263,7 +10449,7 @@ After calculations <code>var_out</code> is converted to the input type of
</p>
<p>Suppose the first part of an <code>ncap2</code> script is
</p><div class="example">
-<pre class="example">defdim("X",4);
+<pre class="verbatim">defdim("X",4);
defdim("Y",5);
// Temperature
@@ -10279,7 +10465,7 @@ y_in[$Y]={1.0,2.0,3.0,4.0,5};
</pre></div>
<p>Now we interpolate with the following variables:
</p><div class="example">
-<pre class="example">defdim("Xn",3);
+<pre class="verbatim">defdim("Xn",3);
defdim("Yn",4);
T_out[$Xn,$Yn]=0.0;
x_out[$Xn]={0.0,0.02,3.01};
@@ -10314,7 +10500,7 @@ typically these are in the range (-90,90).
This <code>ncap2</code> script illustrates both wrapping and extrapolation
of end points:
</p><div class="example">
-<pre class="example">defdim("lat_in",6);
+<pre class="verbatim">defdim("lat_in",6);
defdim("lon_in",5);
// Coordinate input vars
@@ -10384,7 +10570,7 @@ The <acronym>GSL</acronym> function prototype is <br>
<code>int gsl_sf_gamma_e(const double x, gsl_sf_result * result)</code>
The <code>ncap2</code> script would be:
</p><div class="example">
-<pre class="example">lon_in[lon]={-1,0.1,0,2,0.3};
+<pre class="verbatim">lon_in[lon]={-1,0.1,0,2,0.3};
lon_out=gsl_sf_gamma(lon_in);
lon_out= _, 9.5135, 4.5908, 2.9915
</pre></div>
@@ -10412,7 +10598,7 @@ lon_out=0.11490, 0.0012, 0.00498, 0.011165
The Bessel order argument, an integer, can also be a non-scalar
variable, i.e., an array.
</p><div class="example">
-<pre class="example">n_in[lon]={0,1,2,3};
+<pre class="verbatim">n_in[lon]={0,1,2,3};
lon_out=gsl_sf_bessel_Jn(n_in,0.5);
lon_out= 0.93846, 0.24226, 0.03060, 0.00256
</pre></div>
@@ -10791,7 +10977,7 @@ Next: <a href="#GSL-least_002dsquares-fitting" accesskey="n" rel="next">GSL leas
<p>A simple example
</p>
<div class="example">
-<pre class="example">x_in[$lon]={1.0,2.0,3.0,4.0};
+<pre class="verbatim">x_in[$lon]={1.0,2.0,3.0,4.0};
y_in[$lon]={1.1,1.2,1.5,1.8};
// Ram variable is declared and defined here
@@ -10886,7 +11072,7 @@ If data_x or data_y is less than type <code>double</code> then it is converted t
<p>The below example shows <strong>gsl_fit_linear()</strong> in action
</p>
<div class="example">
-<pre class="example">defdim("d1",10);
+<pre class="verbatim">defdim("d1",10);
xin[d1]={1,2,3,4,5,6,7,8,9,10.0};
yin[d1]={3.1,6.2,9.1,12.2,15.1,18.2,21.3,24.0,27.0,30.0};
gsl_fit_linear(xin,1,yin,1,$d1.size,&c0,&c1,&cov00,&cov01,&cov11,&sumsq);
@@ -10942,7 +11128,7 @@ double gsl_stats_quantile_from_sorted_data (var_sorted_data, data_stride, n, var
<p>Some examples
</p>
<div class="example">
-<pre class="example">a1[time]={1,2,3,4,5,6,7,8,9,10 };
+<pre class="verbatim">a1[time]={1,2,3,4,5,6,7,8,9,10};
a1_avg=gsl_stats_mean(a1,1,10);
print(a1_avg); // 5.5
@@ -10952,7 +11138,6 @@ print(a1_var); // 16.0
// bounding error, vector attempts to access element a1(10)
a1_sd=gsl_stats_sd(a1,5,3);
-
</pre></div>
<p>For functions with the signature
@@ -11128,7 +11313,7 @@ for more complete demonstrations of <code>ncap2</code> functionality
as twice the existing attribute <var>double_att</var> of variable
<var>att_var</var>:
</p><div class="example">
-<pre class="example">ncap2 -s 'one at new=2*att_var at double_att' in.nc out.nc
+<pre class="verbatim">ncap2 -s 'one at new=2*att_var at double_att' in.nc out.nc
</pre></div>
<p>Average variables of mixed types (result is of type <code>double</code>):
@@ -11279,6 +11464,7 @@ variables in <code>ncap2</code> command-line scripts
In such cases it may be necessary to use the shell backslash character
‘<samp>\</samp>’ to protect the <code>ncap2</code> meta-character.
</p>
+
<a name="index-appending-data"></a>
<a name="index-time_002daveraging"></a>
<a name="index-ncks-2"></a>
@@ -11553,7 +11739,8 @@ Example:
<dt><code>round(x)</code></dt>
<dd><p><em>Round</em>
Nearest integer to <var>x</var> is returned in floating point format.
-Round halfway cases away from zero, regardless of current IEEE rounding direction.
+Round halfway cases away from zero, regardless of current <acronym>IEEE</acronym>
+rounding direction.
Example:
<em>round(0.5) = 1.0</em>
</p></dd>
@@ -11591,7 +11778,8 @@ Example:
<dt><code>trunc(x)</code></dt>
<dd><p><em>Truncate</em>
Nearest integer to <var>x</var> is returned in floating point format.
-Round halfway cases toward zero, regardless of current IEEE rounding direction.
+Round halfway cases toward zero, regardless of current <acronym>IEEE</acronym>
+rounding direction.
Example:
<em>trunc(0.5) = 0.0</em>
</p></dd>
@@ -11709,7 +11897,7 @@ netcdf-3.6.0-p1 <br>
netcdf-3.6.1 <br>
netcdf-3.6.2 <br>
</p><div class="example">
-<pre class="example">/*
+<pre class="verbatim">/*
* ( [a-zA-Z]|[0-9]|'_'|'-'|'+'|'.'|'|':'|'@'|'('|')' )+
* Verify that name string is valid CDL syntax, i.e., all characters are
* alphanumeric, '-', '_', '+', or '.'.
@@ -11722,7 +11910,7 @@ netcdf-3.6.2 <br>
<p>netcdf-3.6.3<br>
netcdf-4.0 Final 2008/08/28<br>
</p><div class="example">
-<pre class="example">/*
+<pre class="verbatim">/*
* Verify that a name string is valid syntax. The allowed name
* syntax (in RE form) is:
*
@@ -12104,20 +12292,22 @@ from whatever it currently is to "temperature":
<a name="NaN"></a> <!-- http://nco.sf.net/nco.html#NaN --><a name="index-NaN"></a>
<a name="index-IEEE-NaN"></a>
<a name="index-Not_002da_002dNumber"></a>
-<p><acronym>NCO</acronym> arithmetic operators will not work as expected on IEEE
-NaN (short for Not-a-Number) and NaN-like numbers such as positive
-infinity and negative infinity.
-One way to work-around this problem is to change IEEE NaNs to normal
-missing values.
+<p><acronym>NCO</acronym> arithmetic operators may not work as expected on
+<acronym>IEEE</acronym> NaN (short for Not-a-Number) and NaN-like numbers such as
+positive infinity and negative infinity
+<a name="DOCF52" href="#FOOT52"><sup>52</sup></a>.
+One way to work-around this problem is to change <acronym>IEEE</acronym> NaNs to
+normal missing values.
As of <acronym>NCO</acronym> 4.1.0 (March, 2012), <code>ncatted</code> works with
NaNs.
First set the missing value (i.e., the value of the <code>_FillValue</code>
-attribute) for the variable(s) in question to the IEEE NaN value.
+attribute) for the variable(s) in question to the <acronym>IEEE</acronym> NaN value.
</p><div class="example">
<pre class="example">ncatted -a _FillValue,,o,f,NaN in.nc
</pre></div>
-<p>Then change the missing value from the IEEE NaN value to a normal IEEE
-number, like 1.0e36 (or to whatever the original missing value was).
+<p>Then change the missing value from the <acronym>IEEE</acronym> NaN value to a
+normal <acronym>IEEE</acronym> number, like 1.0e36 (or to whatever the original
+missing value was).
</p><div class="example">
<pre class="example">ncatted -a _FillValue,,m,f,1.0e36 in.nc
</pre></div>
@@ -12312,11 +12502,11 @@ Examples: ‘<samp>ncbo --op_typ=/ 1.nc 2.nc 3.nc</samp>’, ‘<sam
i.e., ‘<samp>+</samp>’, ‘<samp>-</samp>’, ‘<samp>*</samp>’, and ‘<samp>/</samp>’<!-- /@w -->.
Some of these single characters may have special meanings to the shell
<a name="index-naked-characters"></a>
-<a name="DOCF52" href="#FOOT52"><sup>52</sup></a>.
+<a name="DOCF53" href="#FOOT53"><sup>53</sup></a>.
<a name="index-Bash-shell"></a>
Place these characters inside quotes to keep them from being interpreted
(globbed) by the shell
-<a name="DOCF53" href="#FOOT53"><sup>53</sup></a>.
+<a name="DOCF54" href="#FOOT54"><sup>54</sup></a>.
<a name="index-globbing-4"></a>
<a name="index-shell-4"></a>
<a name="index-quotes-2"></a>
@@ -12361,12 +12551,12 @@ Should users or system adminitrators decide to activate them, the
procedure is simple.
For example, to use ‘<samp>ncadd</samp>’ instead of ‘<samp>ncbo --op_typ=add</samp>’,
simply create a symbolic link from <code>ncbo</code> to <code>ncadd</code>
-<a name="DOCF54" href="#FOOT54"><sup>54</sup></a>.
+<a name="DOCF55" href="#FOOT55"><sup>55</sup></a>.
The alternatate invocations supported for each operation type are listed
above.
Alternatively, users may always define ‘<samp>ncadd</samp>’ as an <em>alias</em> to
‘<samp>ncbo --op_typ=add</samp>’
-<a name="DOCF55" href="#FOOT55"><sup>55</sup></a>.
+<a name="DOCF56" href="#FOOT56"><sup>56</sup></a>.
</p>
<p>It is important to maintain portability in <acronym>NCO</acronym> scripts.
Therefore we recommend that site-specfic invocations (e.g.,
@@ -12384,7 +12574,7 @@ stores the results in <var>file_3</var>.
<a name="index-broadcasting-variables-2"></a>
Variables in <var>file_1</var> or <var>file_2</var> are <em>broadcast</em> to conform
to the corresponding variable in the other input file if
-necessary<a name="DOCF56" href="#FOOT56"><sup>56</sup></a>.
+necessary<a name="DOCF57" href="#FOOT57"><sup>57</sup></a>.
Now <code>ncbo</code> is completely symmetric with respect to <var>file_1</var>
and <var>file_2</var>, i.e.,
<em><var>file_1</var> - <var>file_2</var> = - (<var>file_2</var> - <var>file_1</var></em>.
@@ -12413,14 +12603,14 @@ In these cases, creating <var>file_2</var> with <code>ncra</code> rather than
<code>ncwa</code> will cause the <code>ncbo</code> operation to fail.
For concreteness say the record dimension in <code>file_1</code> is
<code>time</code>.
-If <var>file_2</var> were created by averaging <var>file_1</var> over the
-<code>time</code> dimension with the <code>ncra</code> operator rather than with
-the <code>ncwa</code> operator, then <var>file_2</var> will have a <code>time</code>
+If <var>file_2</var> was created by averaging <var>file_1</var> over the
+<code>time</code> dimension with the <code>ncra</code> operator (rather than with
+the <code>ncwa</code> operator), then <var>file_2</var> will have a <code>time</code>
dimension of size 1<!-- /@w --> rather than having no <code>time</code> dimension at
all
<a name="index-degenerate-dimension-3"></a>
<a name="index-_002db-1"></a>
-<a name="DOCF57" href="#FOOT57"><sup>57</sup></a>.
+<a name="DOCF58" href="#FOOT58"><sup>58</sup></a>.
In this case the input files to <code>ncbo</code>, <var>file_1</var> and
<var>file_2</var>, will have unequally sized <code>time</code> dimensions which
causes <code>ncbo</code> to fail.
@@ -12572,7 +12762,7 @@ twelve months:
<a name="index-Bourne-Shell-1"></a>
<a name="index-C-Shell-1"></a>
</p><div class="example">
-<pre class="example">for idx in {1..12}; do # Bash Shell (version 3.0+)
+<pre class="verbatim">for idx in {1..12}; do # Bash Shell (version 3.0+)
idx=`printf "%02d" ${idx}` # Zero-pad to preserve order
ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
ncra foo.${idx} t_anm_8589_${idx}.nc
@@ -12589,7 +12779,7 @@ end
<p>Note that <code>ncra</code> understands the <code>stride</code> argument so the
two commands inside the loop may be combined into the single command
</p><div class="example">
-<pre class="example">ncra -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+<pre class="verbatim">ncra -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
</pre></div>
<p>Finally, use <code>ncrcat</code> to concatenate the 12 average<!-- /@w --> monthly
anomaly files into one twelve-record file which contains the entire
@@ -12631,7 +12821,7 @@ input groups within each file.
Each file (or group) receives an equal weight.
<code>nces</code> was formerly (until <acronym>NCO</acronym> version 4.3.9,
released December, 2013) known as <code>ncea</code> (netCDF Ensemble
-Averager)<a name="DOCF58" href="#FOOT58"><sup>58</sup></a>.
+Averager)<a name="DOCF59" href="#FOOT59"><sup>59</sup></a>.
<a name="index-ensemble-1"></a>
For example, <code>nces</code> will average a set of files or groups,
weighting each file or group evenly.
@@ -12653,7 +12843,7 @@ is the operator to use.
<p>Variables in the <var>output-file</var> are the same size as the variable
hyperslab in each input file or group, and each input file or group
must be the same size after hyperslabbing
-<a name="DOCF59" href="#FOOT59"><sup>59</sup></a>
+<a name="DOCF60" href="#FOOT60"><sup>60</sup></a>
<a name="index-record-dimension-3"></a>
<a name="index-hyperslab-2"></a>
<code>nces</code> does allow files to differ in the record dimension size
@@ -13272,7 +13462,7 @@ Next: <a href="#ncpdq-netCDF-Permute-Dimensions-Quickly" accesskey="n" rel="next
<pre class="example">ncks [-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b <var>binary-file</var>] [-C] [-c] [--cdl]
[--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz]
[-D <var>dbg</var>] [-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]] [-F] [--fix_rec_dmn <var>dim</var>]
-[-G <var>gpe_dsc</var>] [-g <var>grp</var>[,…]] [-H] [-h] [--hdn] [--hdr_pad <var>nbr</var>]
+[-G <var>gpe_dsc</var>] [-g <var>grp</var>[,…]] [--grp_xtr_var_xcl] [-H] [-h] [--hdn] [--hdr_pad <var>nbr</var>]
[-L <var>dfl_lvl</var>] [-l <var>path</var>] [-M] [-m] [--mk_rec_dmn <var>dim</var>] [--md5_digest]
[--no_blank] [--no_tmp_fl] [-O] [-o <var>output-file</var>] [-P] [-p <var>path</var>]
[-Q] [-q] [-R] [-r] [--rad] [--ram_all] [-s <var>format</var>]
@@ -13368,7 +13558,7 @@ if any) must agree (conform) in both files.
Then the variable values (and any coordinate dimension values)
from <var>input-file</var> will overwrite the corresponding variable values
(and coordinate dimension values, if any) in <var>output-file</var>
-<a name="DOCF60" href="#FOOT60"><sup>60</sup></a>.
+<a name="DOCF61" href="#FOOT61"><sup>61</sup></a>.
</p>
<p>Since there can only be one record dimension in a file, the record
dimension must have the same name (though not necessarily the same size) in
@@ -13536,7 +13726,7 @@ valid <acronym>CDL</acronym> (network Common data form Description Language).
<code>ncgen</code> and excreted by <code>ncdump</code>.
Compare <code>ncks</code> “traditional” with <acronym>CDL</acronym> printing:
</p><div class="example">
-<pre class="example">zender at roulee:~$ ncks -v one ~/nco/data/in.nc
+<pre class="verbatim">zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
@@ -13844,7 +14034,7 @@ into <acronym>NcML</acronym>, including metadata and data, using all
<acronym>NCO</acronym>’s subsetting and hyperslabbing capabilities.
Compare <code>ncks</code> “traditional” with <acronym>XML</acronym> printing:
</p><div class="example">
-<pre class="verbatim">zender@@roulee:~$ ncks -v one ~/nco/data/in.nc
+<pre class="verbatim">zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
@@ -13889,19 +14079,19 @@ the strings used as <acronym>NcML</acronym> separators for attributes and
variables of character-type and numeric-type, respectively.
Their default separators are "*" and " ":
</p><div class="example">
-<pre class="verbatim">zender@@roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
+<pre class="verbatim">zender at roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
...
<values separator="*">abc*bcd*cde*def</values>
...
- zender@@roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
+ zender at roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
...
<values separator=", ">abc, bcd, cde, def, efg, fgh, ghi, hij, jkl, klm</values>
...
-zender@@roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
...
<values>1 2 3 4 5 6 7 8 9 10</values>
...
-zender@@roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
...
<values separator=", ">1, 2, 3, 4, 5, 6, 7, 8, 9, 10</values>
...
@@ -13993,7 +14183,7 @@ In this example, <code>ncks -m -v z</code> is too verbose so a robust
procedure could be implemented as a shell command or function called,
say, <code>ncattget</code>
</p><div class="example">
-<pre class="example">function ncattget { ncks -M -m ${3} | grep -E -i "^${2} attribute [0-9]+: ${1}" | cut -f 11- -d ' ' | sort ; }
+<pre class="verbatim">function ncattget { ncks -M -m ${3} | grep -E -i "^${2} attribute [0-9]+: ${1}" | cut -f 11- -d ' ' | sort ; }
</pre></div>
<p>The shell <code>ncattget</code> is invoked with three arugments that are,
in order, the names of the attribute, variable, and file to examine.
@@ -14218,19 +14408,21 @@ coordinates, except variable <code>time</code>, from netCDF <samp>in.nc</samp>:
<pre class="example">ncks -x -v time in.nc out.nc
</pre></div>
<p>As a special case of this, consider how to remove a
-<acronym>CF</acronym> Convention comliant <code>bounds</code> or <code>coordinates</code>
-variable (see <a href="#CF-Conventions">CF Conventions</a>) such as <code>time_bounds</code>.
-<acronym>NCO</acronym> subsetting assumes the user wants all coordinates
-and bounds and axes associated with all extracted variables
+<acronym>CF</acronym> Convention comliant <code>ancillary_variables</code>,
+<code>bounds</code>, or <code>coordinates</code> variable (see <a href="#CF-Conventions">CF Conventions</a>)
+such as <code>time_bounds</code>.
+<acronym>NCO</acronym> subsetting assumes the user wants all ancillary variables,
+axes, bounds and coordinates associated with all extracted variables
(see <a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a>).
-Hence to exclude a <code>bounds</code> or <code>coordinates</code> variable while
-retaining the “parent” variable (here <code>time</code>), one must use the
-‘<samp>-C</samp>’ switch:
+Hence to exclude a <code>ancillary_variables</code>, <code>bounds</code>, or
+<code>coordinates</code> variable while retaining the “parent” variable
+(here <code>time</code>), one must use the ‘<samp>-C</samp>’ switch:
</p><div class="example">
<pre class="example">ncks -C -x -v time_bounds in.nc out.nc
</pre></div>
<p>The ‘<samp>-C</samp>’ switch tells the operator <em>NOT</em> to necessarily
-include all the <acronym>CF</acronym> coordinates and bounds and axes.
+include all the <acronym>CF</acronym> ancillary variables, axes, bounds, and
+coordinates.
Hence the output file will contain <code>time</code> and not
<code>time_bounds</code>.
</p>
@@ -14552,7 +14744,7 @@ The record dimension is always the most slowly varying dimension in a
record variable (see <a href="#C-and-Fortran-Index-Conventions">C and Fortran Index Conventions</a>).
The specified re-ordering fails if it requires creating more than
one record dimension amongst all the output variables
-<a name="DOCF61" href="#FOOT61"><sup>61</sup></a>.
+<a name="DOCF62" href="#FOOT62"><sup>62</sup></a>.
</p>
<p>Two special cases of dimension re-ordering and reversal deserve special
mention.
@@ -14628,7 +14820,7 @@ ncl_convert2nc modis.hdf
ncpdq --hdf_upk -P xst_new modis.nc modis.nc
</pre></div>
<p><acronym>NCO</acronym> now
-<a name="DOCF62" href="#FOOT62"><sup>62</sup></a>
+<a name="DOCF63" href="#FOOT63"><sup>63</sup></a>
automatically detects <acronym>HDF4</acronym> files.
In this case it produces an output file <samp>modis.nc</samp> which preserves
the <acronym>HDF</acronym> packing used in the input file.
@@ -14639,7 +14831,7 @@ and then repacks those same variables using the netCDF algorithm
As described above the ‘<samp>--P xst_new</samp>’ packing policy only repacks
variables that are already packed.
Not-packed variables are copied directly without loss of precision
-<a name="DOCF63" href="#FOOT63"><sup>63</sup></a>.
+<a name="DOCF64" href="#FOOT64"><sup>64</sup></a>.
</p>
<p>Re-order file <samp>in.nc</samp> so that the dimension <code>lon</code> always
precedes the dimension <code>lat</code> and store the results in
@@ -15176,7 +15368,7 @@ In this case <code>p</code> must exist in the input file (or
<p>Rename the attribute <code>long_name</code> to <code>largo_nombre</code> in the
variable <code>u</code>, and no other variables in netCDF <samp>in.nc</samp>.
</p><div class="example">
-<pre class="example">ncrename -a u at long_name,largo_nombre in.nc
+<pre class="verbatim">ncrename -a u at long_name,largo_nombre in.nc
</pre></div>
<p>Rename the group <code>g8</code> to <code>g20</code> in netCDF4 file
@@ -15238,7 +15430,7 @@ those variables which possess it), the attribute <code>hieght</code> is
changed to <code>height</code> in the variable <code>tpt</code>, and in the
variable <code>prs_sfc</code>, if it exists.
</p><div class="example">
-<pre class="example">ncrename -a _FillValue,missing_value -a .units,CGS_units \
+<pre class="verbatim">ncrename -a _FillValue,missing_value -a .units,CGS_units \
-a tpt at hieght,height -a prs_sfc at .hieght,height in.nc out.nc
</pre></div>
<p>The presence and absence of the ‘<samp>.</samp>’ and ‘<samp>@</samp>’ features
@@ -15256,7 +15448,7 @@ The variable <code>prs_sfc</code> need not exist, and need not contain the
<p>Rename the global or group attribute <code>Convention</code> to
<code>Conventions</code>
</p><div class="example">
-<pre class="example">ncrename -a Convention,Conventions in.nc # Variable and global atts.
+<pre class="verbatim">ncrename -a Convention,Conventions in.nc # Variable and global atts.
ncrename -a .Convention,Conventions in.nc # Variable and global atts.
ncrename -a @Convention,Conventions in.nc # Global atts. only
ncrename -a @.Convention,Conventions in.nc # Global atts. only
@@ -15393,7 +15585,7 @@ of the hyperslab.
<a name="index-_002dI"></a>
Option ‘<samp>-I</samp>’ overrides this default behavior and causes
<code>ncwa</code> not to weight or mask coordinate variables
-<a name="DOCF64" href="#FOOT64"><sup>64</sup></a>.
+<a name="DOCF65" href="#FOOT65"><sup>65</sup></a>.
In the above case, this causes the value of <code>latitude</code> in the
<var>output-file</var> to be 45.0<!-- /@w -->, an appealing result.
Thus, ‘<samp>-I</samp>’ specifies simple arithmetic averages for the coordinate
@@ -15401,7 +15593,7 @@ variables.
In the case of latitude, ‘<samp>-I</samp>’ specifies that you prefer to archive
the arithmetic mean latitude of the averaged hyperslabs rather than the
area-weighted mean latitude.
-<a name="DOCF65" href="#FOOT65"><sup>65</sup></a>.
+<a name="DOCF66" href="#FOOT66"><sup>66</sup></a>.
</p>
<a name="index-average-1"></a>
<a name="index-operation-types-2"></a>
@@ -15445,7 +15637,7 @@ the ‘<samp>-B</samp>’ or ‘<samp>--mask_condition</samp>’
The older method is to use the three switches ‘<samp>-m</samp>’, ‘<samp>-T</samp>’, and
‘<samp>-M</samp>’ to specify the <var>mask_var</var>, <var>mask_comp</var>, and
<var>mask_val</var>, respectively.
-<a name="DOCF66" href="#FOOT66"><sup>66</sup></a>.
+<a name="DOCF67" href="#FOOT67"><sup>67</sup></a>.
The <var>mask_condition</var> string is automatically parsed into its three
constituents <var>mask_var</var>, <var>mask_comp</var>, and <var>mask_val</var>.
</p>
@@ -15525,7 +15717,7 @@ the integration command
</p>
<p>Given file <samp>85_0112.nc</samp>:
</p><div class="example">
-<pre class="example">netcdf 85_0112 {
+<pre class="verbatim">netcdf 85_0112 {
dimensions:
lat = 64 ;
lev = 18 ;
@@ -15575,7 +15767,7 @@ for the <samp>85_0112.nc</samp> file described by the sample header above.
<a name="index-climate-model-5"></a>
<p>Compute the meridional (latitudinal) mean, with values weighted by
the corresponding element of <var>gw</var>
-<a name="DOCF67" href="#FOOT67"><sup>67</sup></a>:
+<a name="DOCF68" href="#FOOT68"><sup>68</sup></a>:
</p><div class="example">
<pre class="example">ncwa -w gw -a lat in.nc out.nc
</pre></div>
@@ -15593,7 +15785,7 @@ The sum of the Gaussian weights is 2.0.<!-- /@w -->
<a name="index-climate-model-6"></a>
<p>Compute the area-mean over the globe using only points for which
<var>ORO</var> < 0.5
-<a name="DOCF68" href="#FOOT68"><sup>68</sup></a>:
+<a name="DOCF69" href="#FOOT69"><sup>69</sup></a>:
</p><div class="example">
<pre class="example">ncwa -B 'ORO < 0.5' -w gw -a lat,lon in.nc out.nc
ncwa -m ORO -M 0.5 -T lt -w gw -a lat,lon in.nc out.nc
@@ -15601,7 +15793,7 @@ ncwa -m ORO -M 0.5 -T lt -w gw -a lat,lon in.nc out.nc
<p>It is considerably simpler to specify the complete <var>mask_cond</var> with
the single string argument to ‘<samp>-B</samp>’ than with the three separate
switches ‘<samp>-m</samp>’, ‘<samp>-T</samp>’, and ‘<samp>-M</samp>’
-<a name="DOCF69" href="#FOOT69"><sup>69</sup></a>.
+<a name="DOCF70" href="#FOOT70"><sup>70</sup></a>.
If in doubt, enclose the <var>mask_cond</var> within quotes since some
of the comparators have special meanings to the shell.
</p>
@@ -15634,7 +15826,7 @@ correctly integrate the cell areas into a total regional area.
<p>Mask a file to contain <var>_FillValue</var> everywhere except where
<em><var>thr_min</var> <= <var>msk_var</var> <= <var>thr_max</var></em>:
</p><div class="example">
-<pre class="example"># Set masking variable and its scalar thresholds
+<pre class="verbatim"># Set masking variable and its scalar thresholds
export msk_var='three_dmn_var_dbl' # Masking variable
export thr_max='20' # Maximum allowed value
export thr_min='10' # Minimum allowed value
@@ -15668,7 +15860,7 @@ contains more information on how to contribute.
<a href="https://www.paypal.com/xclick/business=zender%40uci.edu&item_name=NCO+development&item_number=nco_dnt_dvl&no_note=1&tax=0¤cy_code=USD">PayPal</a>.
<acronym>NCO</acronym> has been shared for over 10 years<!-- /@w --> yet only two
users have contributed any money to the developers
-<a name="DOCF70" href="#FOOT70"><sup>70</sup></a>.
+<a name="DOCF71" href="#FOOT71"><sup>71</sup></a>.
So you could be the third!
</p>
<a name="dvl"></a> <!-- http://nco.sf.net/nco.html#dvl -->
@@ -15676,7 +15868,9 @@ So you could be the third!
<a name="ppl"></a> <!-- http://nco.sf.net/nco.html#ppl --><table class="menu" border="0" cellspacing="0">
<tr><td align="left" valign="top">• <a href="#Contributors" accesskey="1">Contributors</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
-<tr><td align="left" valign="top">• <a href="#Proposals-for-Institutional-Funding" accesskey="2">Proposals for Institutional Funding</a>:</td><td> </td><td align="left" valign="top">
+<tr><td align="left" valign="top">• <a href="#Citation" accesskey="2">Citation</a>:</td><td> </td><td align="left" valign="top">
+</td></tr>
+<tr><td align="left" valign="top">• <a href="#Proposals-for-Institutional-Funding" accesskey="3">Proposals for Institutional Funding</a>:</td><td> </td><td align="left" valign="top">
</td></tr>
</table>
@@ -15684,7 +15878,7 @@ So you could be the third!
<a name="Contributors"></a>
<div class="header">
<p>
-Next: <a href="#Proposals-for-Institutional-Funding" accesskey="n" rel="next">Proposals for Institutional Funding</a>, Previous: <a href="#Contributing" accesskey="p" rel="previous">Contributing</a>, Up: <a href="#Contributing" accesskey="u" rel="up">Contributing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+Next: <a href="#Citation" accesskey="n" rel="next">Citation</a>, Previous: <a href="#Contributing" accesskey="p" rel="previous">Contributing</a>, Up: <a href="#Contributing" accesskey="u" rel="up">Contributing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Contributors-1"></a>
<h3 class="section">5.1 Contributors</h3>
@@ -15731,7 +15925,7 @@ research, releases.
<dd><p>Non-linear operations and <code>min()</code>, <code>max()</code>, <code>total()</code>
support in <code>ncra</code> and <code>ncwa</code>.
Type conversion for arithmetic.
-Migration to netCDF3 API.
+Migration to netCDF3 <acronym>API</acronym>.
<code>ncap2</code> parser, lexer, <acronym>GSL</acronym>-support, and I/O<!-- /@w -->.
Multislabbing algorithm.
Variable wildcarding.
@@ -15740,7 +15934,7 @@ Numerous hacks.
<a name="index-Rorik-Peterson"></a>
</p></dd>
<dt>Rorik Peterson</dt>
-<dd><p>Original autotool build support.
+<dd><p>Original autotools build support.
Long command-line options.
Original UDUnits support.
Debianization.
@@ -15767,7 +15961,7 @@ netCDF4 groups.
<a name="index-Russ-Rew-1"></a>
</p></dd>
<dt>Russ Rew</dt>
-<dd><p>Advice on NCO structural algorithms
+<dd><p>Advice on <acronym>NCO</acronym> structural algorithms
<a name="index-Brian-Mays"></a>
</p></dd>
<dt>Brian Mays</dt>
@@ -15814,12 +16008,13 @@ netCDF4 groups.
<a name="index-Martin-Schmidt"></a>
<a name="index-Lori-Sentman"></a>
<a name="index-Michael-Schulz"></a>
+<a name="index-Rich-Signell"></a>
<a name="index-Gary-Strand"></a>
<a name="index-Andrew-Wittenberg"></a>
<a name="index-George-White"></a>
<a name="index-Remik-Ziemlinski"></a>
</p></dd>
-<dt>Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski</dt>
+<dt>Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Rich Signell, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski</dt>
<dd><p>Excellent bug reports and feature requests.
<a name="index-Daniel-Baumann"></a>
<a name="index-Nick-Bower"></a>
@@ -15877,6 +16072,34 @@ netCDF4 groups.
</dl>
<p>Please let me know if your name was omitted!
</p>
+<a name="ctt"></a> <!-- http://nco.sf.net/nco.html#ctt --><hr>
+<a name="Citation"></a>
+<div class="header">
+<p>
+Next: <a href="#Proposals-for-Institutional-Funding" accesskey="n" rel="next">Proposals for Institutional Funding</a>, Previous: <a href="#Contributors" accesskey="p" rel="previous">Contributors</a>, Up: <a href="#Contributing" accesskey="u" rel="up">Contributing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+</div>
+<a name="Citation-1"></a>
+<h3 class="section">5.2 Citation</h3>
+<a name="index-citation"></a>
+<p>The recommended citations for <acronym>NCO</acronym> software are
+</p><div class="example">
+<pre class="verbatim">Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience
+Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10),
+1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+
+Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.3,
+http://nco.sf.net/nco.pdf.
+</pre></div>
+<p>Use the former when referring to overall design, purpose, and
+optimization of <acronym>NCO</acronym>, and use the latter when referring to
+specific features and/or the User Guide itself.
+</p>
+<p>Additional information on citing <acronym>NCO</acronym> is in the User Guide at
+<a href="http://nco.sf.net#ctt">http://nco.sf.net#ctt</a>.
+A complete list of <acronym>NCO</acronym> publications and presentations is at
+<a href="http://nco.sf.net#pub">http://nco.sf.net#pub</a>.
+This list links to the full papers and seminars themselves.
+</p>
<a name="prp"></a> <!-- http://nco.sf.net/nco.html#prp -->
<a name="prp_sei"></a> <!-- http://nco.sf.net/nco.html#prp_sei -->
<a name="fnd"></a> <!-- http://nco.sf.net/nco.html#fnd --><table class="menu" border="0" cellspacing="0">
@@ -15888,10 +16111,10 @@ netCDF4 groups.
<a name="Proposals-for-Institutional-Funding"></a>
<div class="header">
<p>
-Previous: <a href="#Contributors" accesskey="p" rel="previous">Contributors</a>, Up: <a href="#Contributing" accesskey="u" rel="up">Contributing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
+Previous: <a href="#Citation" accesskey="p" rel="previous">Citation</a>, Up: <a href="#Contributing" accesskey="u" rel="up">Contributing</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#General-Index" title="Index" rel="index">Index</a>]</p>
</div>
<a name="Proposals-for-Institutional-Funding-1"></a>
-<h3 class="section">5.2 Proposals for Institutional Funding</h3>
+<h3 class="section">5.3 Proposals for Institutional Funding</h3>
<a name="index-funding"></a>
<a name="index-proposals"></a>
<a name="index-NSF"></a>
@@ -15977,7 +16200,7 @@ file of <samp>in.nc</samp> with the record dimension as <code>time</code>.
<a name="index-average-2"></a>
<a name="index-time_002daveraging-1"></a>
</p><div class="example">
-<pre class="example">for yyyy in {1990..2005}; do # Loop over years
+<pre class="verbatim">for yyyy in {1990..2005}; do # Loop over years
for moy in {1..12}; do # Loop over months
mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
@@ -15996,7 +16219,7 @@ ncrcat -O in_??????.nc out.nc
<a name="index-average-3"></a>
<a name="index-time_002daveraging-2"></a>
</p><div class="example">
-<pre class="example">for yyyy in {1990..2005}; do # Loop over years
+<pre class="verbatim">for yyyy in {1990..2005}; do # Loop over years
ncra -O -d time,"${yyyy}-01-01","${yyyy}-12-31" in.nc in_${yyyy}.nc
done
@@ -16074,7 +16297,7 @@ If you want to know the monthly average of Jan 1990, you can write like,
</pre></div>
<p>You might want to use loop if you need the average of each month.
</p><div class="example">
-<pre class="example">for moy in {1..12}; do # Loop over months
+<pre class="verbatim">for moy in {1..12}; do # Loop over months
mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
ncra -O snd_????${mm}??.nc out_${mm}.nc
@@ -16096,7 +16319,8 @@ Suppose you have daily data with one month of them in one data file.
The monthly average is simply to apply <code>ncra</code> on the specific data file.
And for seasonal averages, you can specify the three months by shell scripts.
</p>
-<a name="cmip5"></a> <!-- http://nco.sf.net/nco.html#cmip5 --><hr>
+<a name="cmip5"></a> <!-- http://nco.sf.net/nco.html#cmip5 -->
+<a name="godad"></a> <!-- http://nco.sf.net/nco.html#godad --><hr>
<a name="CMIP5-Example"></a>
<div class="header">
<p>
@@ -16105,6 +16329,7 @@ Next: <a href="#Parallel" accesskey="n" rel="next">Parallel</a>, Previous: <a hr
<a name="CMIP5-Example-1"></a>
<h2 class="chapter">7 <acronym>CMIP5</acronym> Example</h2>
<a name="index-CMIP5"></a>
+<a name="index-GODAD"></a>
<p>The fifth phase of the Coupled Model Intercomparison Project
(<a href="http://cmip-pcmdi.llnl.gov/cmip5/index.html?submenuheader=0"><acronym>CMIP5</acronym></a>)
@@ -16113,11 +16338,37 @@ responses of climate models from around the world.
However, it is a tremendous workload to retrieve a single climate
statistic from all these models, each of which includes several ensemble
members.
-Not only that, it is too often a repetitive process which impedes new
+Not only that, it is too often a tedious process that impedes new
research and hypothesis testing.
-Our <acronym>NASA</acronym> <acronym>ACCESS</acronym> project is designed to simplify and
-accelerate this process.
-To begin, we document below a prototypical example of <acronym>CMIP5</acronym>
+Our <acronym>NASA</acronym> <acronym>ACCESS</acronym> 2011 project simplified and
+accelerated this process.
+</p>
+<p>Traditional geoscience data analysis requires users to work with
+numerous flat (data in one level or namespace) files.
+In that paradigm instruments or models produce, and then repositories
+archive and distribute, and then researchers request and analyze,
+collections of flat files.
+<acronym>NCO</acronym> works well with that paradigm, yet it also embodies the
+necessary algorithms to transition geoscience data analysis from relying
+solely on traditional (or “flat”) datasets to allowing newer
+hierarchical (or “nested”) datasets.
+</p>
+<p>Hierarchical datasets support and enable combining all datastreams that
+meet user-specified criteria into a single or small number of files that
+hold <em>all</em> the science-relevant data.
+<acronym>NCO</acronym> (and no other software to our knowledge) exploits this
+capability now.
+Data and metadata may be aggregated into and analyzed in hierarchical
+structures.
+We call the resulting data storage, distribution, and analysis
+paradigm Group-Oriented Data Analysis and Distribution
+(<acronym>GODAD</acronym>).
+<acronym>GODAD</acronym> lets the scientific question organize the data, not the
+<em>ad hoc</em> granularity of all relevant datasets.
+This chapter illustrates <acronym>GODAD</acronym> techniques applied to
+analysis of the <acronym>CMIP5</acronym> dataset.
+</p>
+<p>To begin, we document below a prototypical example of <acronym>CMIP5</acronym>
analysis and evaluation using traditional <acronym>NCO</acronym> commands on
netCDF3-format model and <acronym>HDF-EOS</acronym> format observational
(<acronym>NASA</acronym> <acronym>MODIS</acronym> satellite instrument) datasets.
@@ -16159,8 +16410,8 @@ Next: <a href="#Global-Distribution-of-Long_002dterm-Average" accesskey="n" rel=
<a name="index-file-combination"></a>
<p>Sometimes, the data of one ensemble member will be stored in several
files to reduce single file size.
-But it is not convenient to process in a batch mode.
-The following script illustrates how to concatenate these files into one.
+It is more convenient to concatenate these files into a single
+timeseries, and the following script illustrates how.
Key steps include:
</p><ol>
<li> Obtain number and names (or partial names) of files in a directory
@@ -16258,20 +16509,20 @@ for var_id in {0..1}; do # Loop over two variables
done
</pre></div>
-<p>Right now, <acronym>CMIP5</acronym> model data downloaded from Earth System Grid
+<p><acronym>CMIP5</acronym> model data downloaded from the Earth System Grid
Federation (<a href="http://pcmdi9.llnl.gov/esgf-web-fe/"><acronym>ESGF</acronym></a>)
-will not contain <tt class="key">group</tt> features yet.
-Therefore users can aggregate the flat files into groups themselves.
-The following script shows how to aggregate models to one file.
+does not contain group features yet.
+Therefore users must aggregate flat files into hierarchical ones themselves.
+The following script shows how.
Each dataset becomes a group in the output file.
There can be several levels of groups.
-In this example, we employ two experiments as the top-level.
-The second-level comprises different models.
-Some models have more than one ensemble member.
-These ensemble members are on the third level.
-In each sub-group of ensemble members, we appended two variables,
-<var>snc</var> and <var>snd</var> (these stand for snow cover and snow depth, by
-the way).
+In this example, we employ two experiments (“scenarios”) as the top-level.
+The second-level comprises different models (e.g., CCSM4, CESM1-BGC).
+Many models are run multiple times with slight perturbed initial
+conditions to produce an ensemble of realizations.
+These ensemble members comprise the third level of the hierarchy.
+The script selects two variables, <var>snc</var> and <var>snd</var> (snow cover
+and snow depth).
<a name="index-_002d_002dgag-1"></a>
<a name="index-aggregation"></a>
<a name="index-group-aggregation-1"></a>
@@ -16284,7 +16535,7 @@ the way).
#
# Method:
# - Create files with groups by ncecat --gag
-# - Append groups level by level using ncks
+# - Append groups level by level using ncks
#
# Input files like:
# snc_LImon_CCSM4_historical_r1i1p1_199001-200512.nc
@@ -16304,7 +16555,7 @@ drc_out='../data/grp/'
# Constants
rlm='LImon' # Realm: LandIce; Time frequency: monthly
-tms='200001-200512' # Timeseris
+tms='200001-200512' # Timeseries
flt='nc' # File Type
# Geographical weights
@@ -17300,7 +17551,7 @@ Next: <a href="#CCSM-Example" accesskey="n" rel="next">CCSM Example</a>, Previou
<p>This section will describe scripting strategies, including the use of
<acronym>GNU</acronym> Parallel, to <acronym>NCO</acronym>.
</p><div class="example">
-<pre class="example">ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" {} 50y/{}
+<pre class="verbatim">ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" {} 50y/{}
</pre></div>
<a name="ccsm"></a> <!-- http://nco.sf.net/nco.html#ccsm --><hr>
@@ -17316,9 +17567,9 @@ Next: <a href="#mybibnode" accesskey="n" rel="next">mybibnode</a>, Previous: <a
<p>This chapter illustrates how to use <acronym>NCO</acronym> to
process and analyze the results of a <acronym>CCSM</acronym> climate simulation.
</p><div class="example">
-<pre class="example">************************************************************************
+<pre class="verbatim">************************************************************************
Task 0: Finding input files
-************************************************************************
+x************************************************************************
The CCSM model outputs files to a local directory like:
/ptmp/zender/archive/T42x1_40
@@ -17874,6 +18125,8 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-_002d_002dgpe-gpe_005fdsc"><code>--gpe <var>gpe_dsc</var></code></a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002d_002dgroup-grp"><code>--group <var>grp</var></code></a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002d_002dgrp-grp"><code>--grp <var>grp</var></code></a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-_002d_002dgrp_005fxtr_005fvar_005fxcl"><code>--grp_xtr_var_xcl</code></a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-_002d_002dgxvx"><code>--gxvx</code></a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002d_002dhdf4">‘<samp>--hdf4</samp>’</a>:</td><td> </td><td valign="top"><a href="#netCDF2_002f3_002f4-and-HDF4_002f5-Support">netCDF2/3/4 and HDF4/5 Support</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002d_002dhdf_005funpack"><code>--hdf_unpack</code></a>:</td><td> </td><td valign="top"><a href="#Packed-data">Packed data</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-_002d_002dhdf_005fupk"><code>--hdf_upk</code></a>:</td><td> </td><td valign="top"><a href="#Packed-data">Packed data</a></td></tr>
@@ -18124,7 +18377,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-64BIT-files"><code>64BIT</code> files</a>:</td><td> </td><td valign="top"><a href="#File-Formats-and-Conversion">File Formats and Conversion</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_symbol-14">:</a></th><td></td><td></td></tr>
-<tr><td></td><td valign="top"><a href="#index-_003a-_0028separator-character_0029"><code>:</code> (separator character)</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-_003a-_0028separator-character_0029"><code>:</code> (separator character)</a>:</td><td> </td><td valign="top"><a href="#Flattening-Groups">Flattening Groups</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_symbol-15">;</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_003b-_0028end-of-statement_0029"><code>;</code> (end of statement)</a>:</td><td> </td><td valign="top"><a href="#Syntax-of-ncap2-statements">Syntax of ncap2 statements</a></td></tr>
@@ -18140,7 +18393,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_symbol-18">@</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_0040-_0028attribute_0029"><code>@</code> (attribute)</a>:</td><td> </td><td valign="top"><a href="#Syntax-of-ncap2-statements">Syntax of ncap2 statements</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-_0040-_0028separator-character_0029"><code>@</code> (separator character)</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-_0040-_0028separator-character_0029"><code>@</code> (separator character)</a>:</td><td> </td><td valign="top"><a href="#Flattening-Groups">Flattening Groups</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_symbol-19">[</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-_005b_005d-_0028array-delimiters_0029"><code>[]</code> (array delimiters)</a>:</td><td> </td><td valign="top"><a href="#Syntax-of-ncap2-statements">Syntax of ncap2 statements</a></td></tr>
@@ -18214,6 +18467,8 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-alternate-invocations">alternate invocations</a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-anchor">anchor</a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-anchoring">anchoring</a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-ancillary-variables-convention">ancillary variables convention</a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-ancillary_005fvariables"><code>ancillary_variables</code></a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Andrea-Cimatoribus">Andrea Cimatoribus</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Andrew-Wittenberg">Andrew Wittenberg</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-annual-average">annual average</a>:</td><td> </td><td valign="top"><a href="#Annual-Average-over-Regions">Annual Average over Regions</a></td></tr>
@@ -18390,13 +18645,13 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-cell-methods-convention">cell methods convention</a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cell_002dbased-grids">cell-based grids</a>:</td><td> </td><td valign="top"><a href="#Auxiliary-Coordinates">Auxiliary Coordinates</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cell_005fmethods"><code>cell_methods</code></a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-CF-compliance-checker"><acronym>CF</acronym> compliance checker</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-CF-compliance-checker"><acronym>CF</acronym> compliance checker</a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CF-conventions"><acronym>CF</acronym> conventions</a>:</td><td> </td><td valign="top"><a href="#Subsetting-Coordinate-Variables">Subsetting Coordinate Variables</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CF-conventions-1"><acronym>CF</acronym> conventions</a>:</td><td> </td><td valign="top"><a href="#Auxiliary-Coordinates">Auxiliary Coordinates</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CF-conventions-2"><acronym>CF</acronym> conventions</a>:</td><td> </td><td valign="top"><a href="#UDUnits-Support">UDUnits Support</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CF-conventions-3"><acronym>CF</acronym> conventions</a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CF-conventions-4"><acronym>CF</acronym> conventions</a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-cfchecker"><code>cfchecker</code></a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-cfchecker"><code>cfchecker</code></a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-change_005fmiss_0028_0029"><code>change_miss()</code></a>:</td><td> </td><td valign="top"><a href="#Missing-values-ncap2">Missing values ncap2</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-char_0028_0029">char()</a>:</td><td> </td><td valign="top"><a href="#Methods-and-functions">Methods and functions</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-characters_002c-special">characters, special</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
@@ -18411,6 +18666,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-chunking-map-1">chunking map</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-chunking-policy">chunking policy</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-chunksize">chunksize</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-citation">citation</a>:</td><td> </td><td valign="top"><a href="#Citation">Citation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-clang"><code>clang</code></a>:</td><td> </td><td valign="top"><a href="#Compatability">Compatability</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-CLASSIC-files"><code>CLASSIC</code> files</a>:</td><td> </td><td valign="top"><a href="#File-Formats-and-Conversion">File Formats and Conversion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-client_002dserver">client-server</a>:</td><td> </td><td valign="top"><a href="#OPeNDAP">OPeNDAP</a></td></tr>
@@ -18433,6 +18689,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-cnk_005flfp">‘<samp>cnk_lfp</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cnk_005fmap"><var>cnk_map</var></a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cnk_005fprd">‘<samp>cnk_prd</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-cnk_005fr1d">‘<samp>cnk_r1d</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cnk_005frd1">‘<samp>cnk_rd1</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cnk_005fscl">‘<samp>cnk_scl</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-cnk_005fxpl">‘<samp>cnk_xpl</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
@@ -18451,7 +18708,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-compatability">compatability</a>:</td><td> </td><td valign="top"><a href="#Compatability">Compatability</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-compilers">compilers</a>:</td><td> </td><td valign="top"><a href="#Specifying-Output-Files">Specifying Output Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-complementary-error-function">complementary error function</a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-compliance-checker">compliance checker</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-compliance-checker">compliance checker</a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-compression">compression</a>:</td><td> </td><td valign="top"><a href="#Deflation">Deflation</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-compression-1">compression</a>:</td><td> </td><td valign="top"><a href="#ncks-netCDF-Kitchen-Sink">ncks netCDF Kitchen Sink</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-concatenation">concatenation</a>:</td><td> </td><td valign="top"><a href="#Appending-Variables">Appending Variables</a></td></tr>
@@ -18534,7 +18791,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-degenerate-dimension-7">degenerate dimension</a>:</td><td> </td><td valign="top"><a href="#ncra-netCDF-Record-Averager">ncra netCDF Record Averager</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-degenerate-dimension-8">degenerate dimension</a>:</td><td> </td><td valign="top"><a href="#ncwa-netCDF-Weighted-Averager">ncwa netCDF Weighted Averager</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-degenerate-dimension-9">degenerate dimension</a>:</td><td> </td><td valign="top"><a href="#Normalization-and-Integration">Normalization and Integration</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-delete-_0028groups_0029">delete (groups)</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-delete-_0028groups_0029">delete (groups)</a>:</td><td> </td><td valign="top"><a href="#Flattening-Groups">Flattening Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-delete_005fmiss_0028_0029"><code>delete_miss()</code></a>:</td><td> </td><td valign="top"><a href="#Missing-values-ncap2">Missing values ncap2</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-demotion">demotion</a>:</td><td> </td><td valign="top"><a href="#Type-Conversion">Type Conversion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Dennis-Heimbigner">Dennis Heimbigner</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
@@ -18546,10 +18803,10 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-dimension-names">dimension names</a>:</td><td> </td><td valign="top"><a href="#ncrename-netCDF-Renamer">ncrename netCDF Renamer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dimension-order">dimension order</a>:</td><td> </td><td valign="top"><a href="#Annual-Average-over-Regions">Annual Average over Regions</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-dimensions_002c-growing">dimensions, growing</a>:</td><td> </td><td valign="top"><a href="#Examples-ncap2">Examples ncap2</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-disaggregate">disaggregate</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-disaggregate">disaggregate</a>:</td><td> </td><td valign="top"><a href="#Dismembering-Files">Dismembering Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-disjoint-files">disjoint files</a>:</td><td> </td><td valign="top"><a href="#Appending-Variables">Appending Variables</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-diskless-files">diskless files</a>:</td><td> </td><td valign="top"><a href="#RAM-disks">RAM disks</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-dismember">dismember</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-dismember">dismember</a>:</td><td> </td><td valign="top"><a href="#Dismembering-Files">Dismembering Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Distributed-Data-Reduction-_0026-Analysis">Distributed Data Reduction & Analysis</a>:</td><td> </td><td valign="top"><a href="#Proposals-for-Institutional-Funding">Proposals for Institutional Funding</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Distributed-Oceanographic-Data-System">Distributed Oceanographic Data System</a>:</td><td> </td><td valign="top"><a href="#OPeNDAP">OPeNDAP</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-divide"><code>divide</code></a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
@@ -18631,7 +18888,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-fixed-dimension-2">fixed dimension</a>:</td><td> </td><td valign="top"><a href="#ncks-netCDF-Kitchen-Sink">ncks netCDF Kitchen Sink</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-fixed-dimension-3">fixed dimension</a>:</td><td> </td><td valign="top"><a href="#ncks-netCDF-Kitchen-Sink">ncks netCDF Kitchen Sink</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-flags">flags</a>:</td><td> </td><td valign="top"><a href="#Examples-ncap2">Examples ncap2</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-flatten-_0028groups_0029">flatten (groups)</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-flatten-_0028groups_0029">flatten (groups)</a>:</td><td> </td><td valign="top"><a href="#Flattening-Groups">Flattening Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-flattening">flattening</a>:</td><td> </td><td valign="top"><a href="#Autoconversion">Autoconversion</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-float"><code>float</code></a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-float_0028_0029">float()</a>:</td><td> </td><td valign="top"><a href="#Methods-and-functions">Methods and functions</a></td></tr>
@@ -18709,6 +18966,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-GNU_002fLinux"><acronym>GNU</acronym>/Linux</a>:</td><td> </td><td valign="top"><a href="#Large-Datasets">Large Datasets</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-GNUmakefile"><samp>GNUmakefile</samp></a>:</td><td> </td><td valign="top"><a href="#Windows-Operating-System">Windows Operating System</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-God">God</a>:</td><td> </td><td valign="top"><a href="#UDUnits-Support">UDUnits Support</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-GODAD"><acronym>GODAD</acronym></a>:</td><td> </td><td valign="top"><a href="#CMIP5-Example">CMIP5 Example</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-grep-_002dE"><code>grep -E</code></a>:</td><td> </td><td valign="top"><a href="#Subsetting-Files">Subsetting Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-group-aggregation">group aggregation</a>:</td><td> </td><td valign="top"><a href="#ncecat-netCDF-Ensemble-Concatenator">ncecat netCDF Ensemble Concatenator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-group-aggregation-1">group aggregation</a>:</td><td> </td><td valign="top"><a href="#Combine-Files">Combine Files</a></td></tr>
@@ -18724,8 +18982,8 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-groups-1">groups</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-groups_002c-averaging">groups, averaging</a>:</td><td> </td><td valign="top"><a href="#Global-Distribution-of-Long_002dterm-Average">Global Distribution of Long-term Average</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-groups_002c-creating">groups, creating</a>:</td><td> </td><td valign="top"><a href="#Combine-Files">Combine Files</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-groups_002c-moving">groups, moving</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-groups_002c-renaming">groups, renaming</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-groups_002c-moving">groups, moving</a>:</td><td> </td><td valign="top"><a href="#Moving-Groups">Moving Groups</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-groups_002c-renaming">groups, renaming</a>:</td><td> </td><td valign="top"><a href="#Moving-Groups">Moving Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-growing-dimensions">growing dimensions</a>:</td><td> </td><td valign="top"><a href="#Examples-ncap2">Examples ncap2</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-GSL"><acronym>GSL</acronym></a>:</td><td> </td><td valign="top"><a href="#Compatability">Compatability</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-GSL-1"><acronym>GSL</acronym></a>:</td><td> </td><td valign="top"><a href="#GSL-special-functions">GSL special functions</a></td></tr>
@@ -18801,7 +19059,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-ID-Quoting">ID Quoting</a>:</td><td> </td><td valign="top"><a href="#ID-Quoting">ID Quoting</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-IDL"><acronym>IDL</acronym></a>:</td><td> </td><td valign="top"><a href="#Philosophy">Philosophy</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-IEEE"><acronym>IEEE</acronym></a>:</td><td> </td><td valign="top"><a href="#Automatic-type-conversion">Automatic type conversion</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-IEEE-NaN">IEEE NaN</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-IEEE-NaN"><acronym>IEEE</acronym> NaN</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-if_0028_0029">if()</a>:</td><td> </td><td valign="top"><a href="#if-statement">if statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ilimit"><code>ilimit</code></a>:</td><td> </td><td valign="top"><a href="#Large-Datasets">Large Datasets</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-illegal-names">illegal names</a>:</td><td> </td><td valign="top"><a href="#netCDF2_002f3_002f4-and-HDF4_002f5-Support">netCDF2/3/4 and HDF4/5 Support</a></td></tr>
@@ -18912,7 +19170,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-Martin-Dix">Martin Dix</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Martin-Otte">Martin Otte</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Martin-Schmidt">Martin Schmidt</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-Martin-Schultz">Martin Schultz</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-Martin-Schultz">Martin Schultz</a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-mask">mask</a>:</td><td> </td><td valign="top"><a href="#Irregular-grids">Irregular grids</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-mask-1">mask</a>:</td><td> </td><td valign="top"><a href="#Examples-ncap2">Examples ncap2</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-mask-condition">mask condition</a>:</td><td> </td><td valign="top"><a href="#Mask-condition">Mask condition</a></td></tr>
@@ -18939,7 +19197,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-metadata-optimization">metadata optimization</a>:</td><td> </td><td valign="top"><a href="#Metadata-Optimization">Metadata Optimization</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-metadata_002c-global">metadata, global</a>:</td><td> </td><td valign="top"><a href="#ncecat-netCDF-Ensemble-Concatenator">ncecat netCDF Ensemble Concatenator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-metadata_002c-global-1">metadata, global</a>:</td><td> </td><td valign="top"><a href="#ncks-netCDF-Kitchen-Sink">ncks netCDF Kitchen Sink</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-Michael-Decker">Michael Decker</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-Michael-Decker">Michael Decker</a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Michael-Prather">Michael Prather</a>:</td><td> </td><td valign="top"><a href="#Promoting-Single_002dprecision-to-Double">Promoting Single-precision to Double</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Michael-Schulz">Michael Schulz</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Microsoft">Microsoft</a>:</td><td> </td><td valign="top"><a href="#Compatability">Compatability</a></td></tr>
@@ -18969,7 +19227,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-monthly-data">monthly data</a>:</td><td> </td><td valign="top"><a href="#Monthly-data-in-one-file">Monthly data in one file</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-monthly-data-1">monthly data</a>:</td><td> </td><td valign="top"><a href="#One-time-point-one-file">One time point one file</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-monthly-data-2">monthly data</a>:</td><td> </td><td valign="top"><a href="#Multiple-files-with-multiple-time-points">Multiple files with multiple time points</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-move-groups">move groups</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-move-groups">move groups</a>:</td><td> </td><td valign="top"><a href="#Moving-Groups">Moving Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-MRO">MRO</a>:</td><td> </td><td valign="top"><a href="#Subcycle">Subcycle</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-MSA"><acronym>MSA</acronym></a>:</td><td> </td><td valign="top"><a href="#Multislabs">Multislabs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-msk_005f_002a"><code>msk_*</code></a>:</td><td> </td><td valign="top"><a href="#CF-Conventions">CF Conventions</a></td></tr>
@@ -19000,6 +19258,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><th><a name="General-Index_cp_letter-N">N</a></th><td></td><td></td></tr>
<tr><td></td><td valign="top"><a href="#index-naked-characters">naked characters</a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NaN">NaN</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-NARR-_0028North-American-Regional-Reanalysis_0029a"><acronym>NARR</acronym> (North American Regional Reanalysis)a</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NASA"><acronym>NASA</acronym></a>:</td><td> </td><td valign="top"><a href="#Proposals-for-Institutional-Funding">Proposals for Institutional Funding</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NASA-EOSDIS"><acronym>NASA EOSDIS</acronym></a>:</td><td> </td><td valign="top"><a href="#Large-Numbers-of-Files">Large Numbers of Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-National-Virtual-Ocean-Data-System">National Virtual Ocean Data System</a>:</td><td> </td><td valign="top"><a href="#OPeNDAP">OPeNDAP</a></td></tr>
@@ -19024,8 +19283,8 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-ncbo-1"><code>ncbo</code></a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ncbo"><code>ncbo</code></a>:</td><td> </td><td valign="top"><a href="#Missing-Values">Missing Values</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ncdiff"><code>ncdiff</code></a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-ncdismember"><code>ncdismember</code></a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-ncdismember-1"><code>ncdismember</code></a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-ncdismember"><code>ncdismember</code></a>:</td><td> </td><td valign="top"><a href="#Dismembering-Files">Dismembering Files</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-ncdismember-1"><code>ncdismember</code></a>:</td><td> </td><td valign="top"><a href="#Checking-CF_002dcompliance">Checking CF-compliance</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ncdivide"><code>ncdivide</code></a>:</td><td> </td><td valign="top"><a href="#ncbo-netCDF-Binary-Operator">ncbo netCDF Binary Operator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ncdmnsz"><code>ncdmnsz</code></a>:</td><td> </td><td valign="top"><a href="#Filters-for-ncks">Filters for <code>ncks</code></a></td></tr>
<tr><td></td><td valign="top"><a href="#index-ncdump"><code>ncdump</code></a>:</td><td> </td><td valign="top"><a href="#Determining-File-Format">Determining File Format</a></td></tr>
@@ -19155,6 +19414,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-non_002drectangular-grids">non-rectangular grids</a>:</td><td> </td><td valign="top"><a href="#Irregular-grids">Irregular grids</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-non_002dstandard-grids">non-standard grids</a>:</td><td> </td><td valign="top"><a href="#Irregular-grids">Irregular grids</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-normalization">normalization</a>:</td><td> </td><td valign="top"><a href="#Normalization-and-Integration">Normalization and Integration</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-North-American-Regional-Reanalysis-_0028NARR_0029">North American Regional Reanalysis (<acronym>NARR</acronym>)</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Not_002da_002dNumber">Not-a-Number</a>:</td><td> </td><td valign="top"><a href="#ncatted-netCDF-Attribute-Editor">ncatted netCDF Attribute Editor</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NO_005fNETCDF_005f2"><code>NO_NETCDF_2</code></a>:</td><td> </td><td valign="top"><a href="#netCDF2_002f3_002f4-and-HDF4_002f5-Support">netCDF2/3/4 and HDF4/5 Support</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-NRA"><acronym>NRA</acronym></a>:</td><td> </td><td valign="top"><a href="#Proposals-for-Institutional-Funding">Proposals for Institutional Funding</a></td></tr>
@@ -19264,6 +19524,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-plc_005fall">‘<samp>plc_all</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-plc_005fg2d">‘<samp>plc_g2d</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-plc_005fg3d">‘<samp>plc_g3d</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-plc_005fr1d">‘<samp>plc_r1d</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-plc_005fxpl">‘<samp>plc_xpl</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-plc_005fxst">‘<samp>plc_xst</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-portability">portability</a>:</td><td> </td><td valign="top"><a href="#Compatability">Compatability</a></td></tr>
@@ -19306,6 +19567,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-quotes-3">quotes</a>:</td><td> </td><td valign="top"><a href="#ncpdq-netCDF-Permute-Dimensions-Quickly">ncpdq netCDF Permute Dimensions Quickly</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_letter-R">R</a></th><td></td><td></td></tr>
+<tr><td></td><td valign="top"><a href="#index-r1d">‘<samp>r1d</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-RAG"><acronym>RAG</acronym></a>:</td><td> </td><td valign="top"><a href="#ncecat-netCDF-Ensemble-Concatenator">ncecat netCDF Ensemble Concatenator</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-RAM"><acronym>RAM</acronym></a>:</td><td> </td><td valign="top"><a href="#Memory-Requirements">Memory Requirements</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-RAM-1"><acronym>RAM</acronym></a>:</td><td> </td><td valign="top"><a href="#RAM-disks">RAM disks</a></td></tr>
@@ -19367,7 +19629,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-Remik-Ziemlinski">Remik Ziemlinski</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-remote-files">remote files</a>:</td><td> </td><td valign="top"><a href="#Windows-Operating-System">Windows Operating System</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-remote-files-1">remote files</a>:</td><td> </td><td valign="top"><a href="#Remote-storage">Remote storage</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-rename-groups">rename groups</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-rename-groups">rename groups</a>:</td><td> </td><td valign="top"><a href="#Moving-Groups">Moving Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-renaming-attributes">renaming attributes</a>:</td><td> </td><td valign="top"><a href="#ncrename-netCDF-Renamer">ncrename netCDF Renamer</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-renaming-attributes-1">renaming attributes</a>:</td><td> </td><td valign="top"><a href="#Regrid-MODIS-Data">Regrid MODIS Data</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-renaming-dimensions">renaming dimensions</a>:</td><td> </td><td valign="top"><a href="#ncrename-netCDF-Renamer">ncrename netCDF Renamer</a></td></tr>
@@ -19385,6 +19647,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-reverse-dimensions-2">reverse dimensions</a>:</td><td> </td><td valign="top"><a href="#ncpdq-netCDF-Permute-Dimensions-Quickly">ncpdq netCDF Permute Dimensions Quickly</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-reverse_0028_0029">reverse()</a>:</td><td> </td><td valign="top"><a href="#Arrays-and-hyperslabs">Arrays and hyperslabs</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-rew">‘<samp>rew</samp>’</a>:</td><td> </td><td valign="top"><a href="#Chunking">Chunking</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-Rich-Signell">Rich Signell</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-rint"><var>rint</var></a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-rms"><code>rms</code></a>:</td><td> </td><td valign="top"><a href="#Operation-Types">Operation Types</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-rmssdn"><code>rmssdn</code></a>:</td><td> </td><td valign="top"><a href="#Operation-Types">Operation Types</a></td></tr>
@@ -19447,6 +19710,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-single_002dprecision">single-precision</a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-sinh"><var>sinh</var></a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-size_0028_0029">size()</a>:</td><td> </td><td valign="top"><a href="#Methods-and-functions">Methods and functions</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-SLD-_0028Swath_002dlike-Data_0029"><acronym>SLD</acronym> (Swath-like Data)</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-SMP"><acronym>SMP</acronym></a>:</td><td> </td><td valign="top"><a href="#OpenMP-Threading">OpenMP Threading</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-sort"><code>sort</code></a>:</td><td> </td><td valign="top"><a href="#Sort-methods">Sort methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-sort-alphabetically">sort alphabetically</a>:</td><td> </td><td valign="top"><a href="#ncks-netCDF-Kitchen-Sink">ncks netCDF Kitchen Sink</a></td></tr>
@@ -19517,6 +19781,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-swap-space">swap space</a>:</td><td> </td><td valign="top"><a href="#Large-Datasets">Large Datasets</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-swap-space-1">swap space</a>:</td><td> </td><td valign="top"><a href="#Memory-Requirements">Memory Requirements</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-swap-space-2">swap space</a>:</td><td> </td><td valign="top"><a href="#RAM-disks">RAM disks</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-Swath_002dlike-Data-_0028SLD_0029">Swath-like Data (<acronym>SLD</acronym>)</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-switches">switches</a>:</td><td> </td><td valign="top"><a href="#Command-Line-Options">Command Line Options</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-symbolic-links">symbolic links</a>:</td><td> </td><td valign="top"><a href="#Symbolic-Links">Symbolic Links</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-symbolic-links-1">symbolic links</a>:</td><td> </td><td valign="top"><a href="#Statistics-vs_002e-Concatenation">Statistics vs. Concatenation</a></td></tr>
@@ -19561,7 +19826,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-TREFHT"><acronym>TREFHT</acronym></a>:</td><td> </td><td valign="top"><a href="#Promoting-Single_002dprecision-to-Double">Promoting Single-precision to Double</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-trunc"><var>trunc</var></a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-trunc_0028_0029"><code>trunc()</code></a>:</td><td> </td><td valign="top"><a href="#Automatic-type-conversion">Automatic type conversion</a></td></tr>
-<tr><td></td><td valign="top"><a href="#index-truncate-_0028groups_0029">truncate (groups)</a>:</td><td> </td><td valign="top"><a href="#Group-Path-Editing">Group Path Editing</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-truncate-_0028groups_0029">truncate (groups)</a>:</td><td> </td><td valign="top"><a href="#Flattening-Groups">Flattening Groups</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-truncation-function">truncation function</a>:</td><td> </td><td valign="top"><a href="#Intrinsic-mathematical-methods">Intrinsic mathematical methods</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-truth-condition">truth condition</a>:</td><td> </td><td valign="top"><a href="#Mask-condition">Mask condition</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-truth-condition-1">truth condition</a>:</td><td> </td><td valign="top"><a href="#Normalization-and-Integration">Normalization and Integration</a></td></tr>
@@ -19621,6 +19886,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-Vista-_0028Microsoft-operating-system_0029">Vista (Microsoft operating system)</a>:</td><td> </td><td valign="top"><a href="#Windows-Operating-System">Windows Operating System</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_letter-W">W</a></th><td></td><td></td></tr>
+<tr><td></td><td valign="top"><a href="#index-Weather-and-Research-Forecast-_0028WRF_0029-Model">Weather and Research Forecast (<acronym>WRF</acronym>) Model</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-weighted-average">weighted average</a>:</td><td> </td><td valign="top"><a href="#ncwa-netCDF-Weighted-Averager">ncwa netCDF Weighted Averager</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-weighted-average-1">weighted average</a>:</td><td> </td><td valign="top"><a href="#Monthly-Cycle">Monthly Cycle</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-Wenshan-Wang">Wenshan Wang</a>:</td><td> </td><td valign="top"><a href="#Contributors">Contributors</a></td></tr>
@@ -19641,6 +19907,7 @@ Previous: <a href="#mybibnode" accesskey="p" rel="previous">mybibnode</a>, Up: <
<tr><td></td><td valign="top"><a href="#index-wrapped-coordinates-3">wrapped coordinates</a>:</td><td> </td><td valign="top"><a href="#Filters-for-ncks">Filters for <code>ncks</code></a></td></tr>
<tr><td></td><td valign="top"><a href="#index-wrapped-filenames">wrapped filenames</a>:</td><td> </td><td valign="top"><a href="#Specifying-Input-Files">Specifying Input Files</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-WRF"><acronym>WRF</acronym></a>:</td><td> </td><td valign="top"><a href="#Irregular-grids">Irregular grids</a></td></tr>
+<tr><td></td><td valign="top"><a href="#index-WRF-_0028Weather-and-Research-Forecast-Model_0029"><acronym>WRF</acronym> (Weather and Research Forecast Model)</a>:</td><td> </td><td valign="top"><a href="#Where-statement">Where statement</a></td></tr>
<tr><td></td><td valign="top"><a href="#index-WWW-documentation">WWW documentation</a>:</td><td> </td><td valign="top"><a href="#Availability">Availability</a></td></tr>
<tr><td colspan="4"> <hr></td></tr>
<tr><th><a name="General-Index_cp_letter-X">X</a></th><td></td><td></td></tr>
@@ -19889,8 +20156,13 @@ results of file globbing) exceeding 4096 characters.</p>
This is <acronym>BSD</acronym>-licensed software available from
<a href="http://www.geocities.com/ResearchTriangle/Node/9405/#my_getopt">http://www.geocities.com/ResearchTriangle/Node/9405/#my_getopt</a>.</p>
<h3><a name="FOOT19" href="#DOCF19">(19)</a></h3>
-<p>The ‘<samp>-n</samp>’ option is a backward compatible superset of the
-<code>NINTAP</code> option from the <acronym>NCAR</acronym> <acronym>CCM</acronym> Processor.</p>
+<p>The ‘<samp>-n</samp>’ option is a backward-compatible superset of the
+<code>NINTAP</code> option from the <acronym>NCAR</acronym> <acronym>CCM</acronym> Processor.
+The <acronym>CCM</acronym> Processor was custom-written Fortran code maintained
+for many years by Lawrence Buja at <acronym>NCAR</acronym>, and phased-out in
+the late 1990s.
+<acronym>NCO</acronym> stole some ideas, like <code>NINTAP</code>-functionality,
+from the <acronym>CCM</acronym> Processor capabilities.</p>
<h3><a name="FOOT20" href="#DOCF20">(20)</a></h3>
<p><acronym>NCO</acronym> does not implement command line options to
specify <acronym>FTP</acronym> logins and passwords because copying those data
@@ -20025,17 +20297,17 @@ called, although the results would be the same if it were.</p>
<h3><a name="FOOT41" href="#DOCF41">(41)</a></h3>
<p>According to Wikipedia’s summary of <acronym>IEEE</acronym> standard
754, “If a decimal string with at most 6 significant digits is
-converted to IEEE 754 single-precision and then converted back to the
+converted to <acronym>IEEE</acronym> 754 single-precision and then converted back to the
same number of significant decimal, then the final string should match
-the original; and if an IEEE 754 single-precision is converted to a
+the original; and if an <acronym>IEEE</acronym> 754 single-precision is converted to a
decimal string with at least 9 significant decimal and then converted
back to single, then the final number must match the original”.</p>
<h3><a name="FOOT42" href="#DOCF42">(42)</a></h3>
<p>According to Wikipedia’s summary of <acronym>IEEE</acronym> standard
754, “If a decimal string with at most 15 significant digits is
-converted to IEEE 754 double-precision representation and then converted
+converted to <acronym>IEEE</acronym> 754 double-precision representation and then converted
back to a string with the same number of significant digits, then the
-final string should match the original; and if an IEEE 754 double
+final string should match the original; and if an <acronym>IEEE</acronym> 754 double
precision is converted to a decimal string with at least 17 significant
digits and then converted back to double, then the final number must
match the original”.</p>
@@ -20110,11 +20382,18 @@ available, and uses the casting method when they are not.
<p>Linux supports more of these intrinsic functions than
other OSs.</p>
<h3><a name="FOOT52" href="#DOCF52">(52)</a></h3>
+<p>Arithmetic comparisons to NaN and NaN-like numbers always
+return False, contrary to the behavior of all other numbers.
+This is difficult to inuit, yet is the behavior defined for NaN by
+<acronym>IEEE</acronym> 754.
+Using NaN for the missing value in datasets is legal.
+We strongly discourage it.</p>
+<h3><a name="FOOT53" href="#DOCF53">(53)</a></h3>
<p>A naked<!-- /@w --> (i.e., unprotected or unquoted) ‘<samp>*</samp>’ is a
wildcard character.
A naked<!-- /@w --> ‘<samp>-</samp>’ may confuse the command line parser.
A naked<!-- /@w --> ‘<samp>+</samp>’ and ‘<samp>/</samp>’ are relatively harmless.</p>
-<h3><a name="FOOT53" href="#DOCF53">(53)</a></h3>
+<h3><a name="FOOT54" href="#DOCF54">(54)</a></h3>
<p>The widely used shell Bash correctly interprets all these
special characters even when they are not quoted.
That is, Bash does not prevent <acronym>NCO</acronym> from correctly interpreting
@@ -20122,30 +20401,30 @@ the intended arithmetic operation when the following arguments are given
(without quotes) to <code>ncbo</code>:
‘<samp>--op_typ=+</samp>’, ‘<samp>--op_typ=-</samp>’, ‘<samp>--op_typ=*</samp>’,
and ‘<samp>--op_typ=/</samp>’</p>
-<h3><a name="FOOT54" href="#DOCF54">(54)</a></h3>
-<p>The command to do this is ‘<samp>ln -s -f ncbo ncadd</samp>’</p>
<h3><a name="FOOT55" href="#DOCF55">(55)</a></h3>
-<p>The command to do this is ‘<samp>alias ncadd='ncbo --op_typ=add'</samp>’</p>
+<p>The command to do this is ‘<samp>ln -s -f ncbo ncadd</samp>’</p>
<h3><a name="FOOT56" href="#DOCF56">(56)</a></h3>
+<p>The command to do this is ‘<samp>alias ncadd='ncbo --op_typ=add'</samp>’</p>
+<h3><a name="FOOT57" href="#DOCF57">(57)</a></h3>
<p>Prior to <acronym>NCO</acronym> version 4.3.1 (May, 2013), <code>ncbo</code>
would only broadcast variables in <var>file_2</var> to conform to
<var>file_1</var>.
Variables in <var>file_1</var> were <em>never</em> broadcast to conform to the
dimensions in <var>file_2</var>.</p>
-<h3><a name="FOOT57" href="#DOCF57">(57)</a></h3>
+<h3><a name="FOOT58" href="#DOCF58">(58)</a></h3>
<p>This is because <code>ncra</code> collapses the record dimension
to a size of 1<!-- /@w --> (making it a <em>degenerate</em> dimension), but does
not remove it, while, unless ‘<samp>-b</samp>’ is given, <code>ncwa</code> removes
all averaged dimensions.
In other words, by default <code>ncra</code> changes variable size though
not rank, while, <code>ncwa</code> changes both variable size and rank.</p>
-<h3><a name="FOOT58" href="#DOCF58">(58)</a></h3>
+<h3><a name="FOOT59" href="#DOCF59">(59)</a></h3>
<p>The old ncea command was deprecated in <acronym>NCO</acronym> version 4.3.9,
released December, 2013.
<acronym>NCO</acronym> will attempt to maintain back-compatibility and work
as expected with invocations of <code>ncea</code> for as long as possible.
Please replace <code>ncea</code> by <code>nces</code> in all future work.</p>
-<h3><a name="FOOT59" href="#DOCF59">(59)</a></h3>
+<h3><a name="FOOT60" href="#DOCF60">(60)</a></h3>
<p>As of <acronym>NCO</acronym> version 4.4.2 (released February, 2014)
<code>nces</code> allows hyperslabs in all dimensions so long as the
hyperslabs resolve to the same size.
@@ -20155,7 +20434,7 @@ the hypserslabs may (and usually do) change the size of the dimensions
from the input to the output files.
Prior to this, <code>nces</code> was only guaranteed to work on hyperslabs
in the record dimension that resolved to the same size.</p>
-<h3><a name="FOOT60" href="#DOCF60">(60)</a></h3>
+<h3><a name="FOOT61" href="#DOCF61">(61)</a></h3>
<p>Those familiar with netCDF mechanics might wish to know what is
happening here: <code>ncks</code> does not attempt to redefine the variable
in <var>output-file</var> to match its definition in <var>input-file</var>,
@@ -20163,10 +20442,10 @@ in <var>output-file</var> to match its definition in <var>input-file</var>,
coordinate dimensions, if any, from <var>input-file</var> to
<var>output-file</var>.
</p>
-<h3><a name="FOOT61" href="#DOCF61">(61)</a></h3>
+<h3><a name="FOOT62" href="#DOCF62">(62)</a></h3>
<p>This limitation, imposed by the netCDF storage layer,
may be relaxed in the future with netCDF4.</p>
-<h3><a name="FOOT62" href="#DOCF62">(62)</a></h3>
+<h3><a name="FOOT63" href="#DOCF63">(63)</a></h3>
<p>Prior to <acronym>NCO</acronym> 4.4.0 and netCDF 4.3.1 (January, 2014),
<acronym>NCO</acronym> requires the ‘<samp>--hdf4</samp>’ switch to correctly read
HDF4 input files.
@@ -20178,38 +20457,38 @@ software necessary to workaround netCDF library flaws handling
<acronym>HDF4</acronym> files to netCDF files.
In those cases, use the <code>ncl_convert2nc</code> command distributed
with <acronym>NCL</acronym> to convert <acronym>HDF4</acronym> files to netCDF.</p>
-<h3><a name="FOOT63" href="#DOCF63">(63)</a></h3>
+<h3><a name="FOOT64" href="#DOCF64">(64)</a></h3>
<p><code>ncpdq</code> does not support packing data using the
<acronym>HDF</acronym> convention.
Although it is now straightforward to support this, we think it might
sow more confusion than it reaps.
Let us know if you disagree and would like <acronym>NCO</acronym> to support
packing data with <acronym>HDF</acronym> algorithm.</p>
-<h3><a name="FOOT64" href="#DOCF64">(64)</a></h3>
+<h3><a name="FOOT65" href="#DOCF65">(65)</a></h3>
<p>The default behavior of (‘<samp>-I</samp>’) changed on
19981201—before this date the default was not to weight or mask
coordinate variables.</p>
-<h3><a name="FOOT65" href="#DOCF65">(65)</a></h3>
+<h3><a name="FOOT66" href="#DOCF66">(66)</a></h3>
<p>If <code>lat_wgt</code> contains Gaussian weights then the value of
<code>latitude</code> in the <var>output-file</var> will be the area-weighted
centroid of the hyperslab.
For the example given, this is about 30 degrees.<!-- /@w --></p>
-<h3><a name="FOOT66" href="#DOCF66">(66)</a></h3>
+<h3><a name="FOOT67" href="#DOCF67">(67)</a></h3>
<p>The three switches ‘<samp>-m</samp>’, ‘<samp>-T</samp>’, and ‘<samp>-M</samp>’ are
maintained for backward compatibility and may be deprecated in the
future.
It is safest to write scripts using ‘<samp>--mask_condition</samp>’.</p>
-<h3><a name="FOOT67" href="#DOCF67">(67)</a></h3>
+<h3><a name="FOOT68" href="#DOCF68">(68)</a></h3>
<p><code>gw</code> stands for <em>Gaussian weight</em> in many
climate models.</p>
-<h3><a name="FOOT68" href="#DOCF68">(68)</a></h3>
+<h3><a name="FOOT69" href="#DOCF69">(69)</a></h3>
<p><code>ORO</code> stands for <em>Orography</em> in some climate models
and in those models <em><var>ORO</var> < 0.5</em> selects ocean gridpoints.</p>
-<h3><a name="FOOT69" href="#DOCF69">(69)</a></h3>
+<h3><a name="FOOT70" href="#DOCF70">(70)</a></h3>
<p>Unfortunately the ‘<samp>-B</samp>’ and ‘<samp>--mask_condition</samp>’
options are unsupported on Windows (with the <acronym>MVS</acronym> compiler),
which lacks a free, standard parser and lexer.</p>
-<h3><a name="FOOT70" href="#DOCF70">(70)</a></h3>
+<h3><a name="FOOT71" href="#DOCF71">(71)</a></h3>
<a name="index-chocolate"></a>
<p>Happy users have sent me a few gifts, though.
This includes a box of imported chocolate.
diff --git a/doc/nco.pdf b/doc/nco.pdf
index 61ddd62..19982c3 100644
Binary files a/doc/nco.pdf and b/doc/nco.pdf differ
diff --git a/doc/nco.ps b/doc/nco.ps
index 0f4aed7..67212dd 100644
--- a/doc/nco.ps
+++ b/doc/nco.ps
@@ -1,8 +1,8 @@
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%%Creator: dvips(k) 5.993 Copyright 2013 Radical Eye Software
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-%%CreationDate: Wed May 21 21:31:06 2014
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%DVIPSWebPage: (www.radicaleye.com)
%DVIPSCommandLine: dvips -o nco.ps nco.dvi
%DVIPSParameters: dpi=600
-%DVIPSSource: TeX output 2014.05.21:2130
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+390 2162 y(else)g({)485 2271 y(time_max=time.max\(\);)485
2381 y(time_min=time.min\(\);)485 2491 y(print\("min)e(value)i(of)g
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(example)390 5230 y(th_nw=\(three_dmn_var_sht)41 b(>=)47
b(0)h(?)f(three_dmn_var_sht.uint\(\))41 b(:)48 b(\\)724
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y Fy(print\(variable_name/attr)o(ibut)o(e)i(name/string,)i(format)i
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(00,)390 2380 y(print\(mss_val_fst at _FillV)o(alue)o(\);)390
2490 y(mss_val_fst at _FillValue,)41 b(size)47 b(=)h(1)f(NC_FLOAT,)e
(value)i(=)g(-999)390 2709 y(print\("This)e(function)g(\\t)i(is)h
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b(monotonic)150 3039 y Fu(4.1.10)63 b(Missing)43 b(v)-7
b(alues)41 b(ncap2)150 3186 y FD(Missing)27 b(v)-5 b(alues)27
b(op)s(erate)g(sligh)m(tly)h(di\013eren)m(tly)f(in)f
@@ -21157,9 +21270,9 @@ b(Consider)f(the)h(variable:)390 5011 y(int)g
o(_Fil)o(lVal)o(ue)g(=)48 b(-999;)390 5340 y(n2=rec_var_int_mss_val_i)o
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@@ -21194,9 +21307,9 @@ b(ariable.)73 b(If)41 b(the)g(v)-5 b(ariable)42 b(exists)g(in)f(Input)f
b(alue)39 b(of)h(the)f(v)-5 b(ariable)40 b(in)e(Output)g(is)i
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-(returned.)150 2839 y Fy(delete_miss\(\))630 2949 y FD(Deletes)i(the)f
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b(a)h(v)-5 b(ariable)31 b(con)m(tains.)390 3367 y Fy
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(;)390 5230 y(print\(three_dmn_var_dbl@)o(_Fil)o(lVal)o(ue\))o(;)390
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b(Metho)s(ds)43 b(and)e(functions)150 749 y FD(The)32
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4451 y(four_time_avg=four_dmn_r)o(ec_v)o(ar\($)o(tim)o(e\);)180
4720 y Fq(P)m(ac)m(king)32 b(Metho)s(ds)174 4830 y FD(F)-8
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y Fy(reverse\(dim)c(args\))630 4860 y FD(Rev)m(erses)k(the)g(dimension)
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39 b(A)24 b(limitation)i(of)e(this)f(p)s(erm)m(ute)h(\(unlik)m(e)g(ncp)
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-739 1176 V 41 w(3j)p 853 1176 V 40 w(e)583 b(N)112 b(gsl)p
-1802 1176 V 40 w(sf)p 1906 1176 V 40 w(coupling)p 2279
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-367 1285 V 39 w(coupling)p 739 1285 V 41 w(6j)p 853 1285
-V 40 w(e)583 b(N)112 b(gsl)p 1802 1285 V 40 w(sf)p 1906
-1285 V 40 w(coupling)p 2279 1285 V 40 w(6j)150 1395 y(gsl)p
-262 1395 V 41 w(sf)p 367 1395 V 39 w(coupling)p 739 1395
-V 41 w(RacahW)p 1121 1395 V 41 w(e)314 b(N)112 b(gsl)p
-1802 1395 V 40 w(sf)p 1906 1395 V 40 w(coupling)p 2279
-1395 V 40 w(RacahW)150 1504 y(gsl)p 262 1504 V 41 w(sf)p
-367 1504 V 39 w(coupling)p 739 1504 V 41 w(9j)p 853 1504
-V 40 w(e)583 b(N)112 b(gsl)p 1802 1504 V 40 w(sf)p 1906
-1504 V 40 w(coupling)p 2279 1504 V 40 w(9j)150 1614 y(gsl)p
-262 1614 V 41 w(sf)p 367 1614 V 39 w(coupling)p 739 1614
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-w(e)-21 b(N)112 b(gsl)p 1802 1614 V 40 w(sf)p 1906 1614
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-w(INCORRECT)150 1724 y(gsl)p 262 1724 V 41 w(sf)p 367
-1724 V 39 w(da)m(wson)p 697 1724 V 40 w(e)739 b(Y)112
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-2399 1724 V 39 w(expr\))150 1833 y(gsl)p 262 1833 V 41
-w(sf)p 367 1833 V 39 w(deb)m(y)m(e)p 630 1833 V 41 w(1)p
-716 1833 V 40 w(e)720 b(Y)112 b(gsl)p 1802 1833 V 40
-w(sf)p 1906 1833 V 40 w(deb)m(y)m(e)p 2170 1833 V 41
-w(1\(dbl)p 2418 1833 V 40 w(expr\))150 1943 y(gsl)p 262
-1943 V 41 w(sf)p 367 1943 V 39 w(deb)m(y)m(e)p 630 1943
-V 41 w(2)p 716 1943 V 40 w(e)720 b(Y)112 b(gsl)p 1802
-1943 V 40 w(sf)p 1906 1943 V 40 w(deb)m(y)m(e)p 2170
-1943 V 41 w(2\(dbl)p 2418 1943 V 40 w(expr\))150 2052
-y(gsl)p 262 2052 V 41 w(sf)p 367 2052 V 39 w(deb)m(y)m(e)p
-630 2052 V 41 w(3)p 716 2052 V 40 w(e)720 b(Y)112 b(gsl)p
-1802 2052 V 40 w(sf)p 1906 2052 V 40 w(deb)m(y)m(e)p
-2170 2052 V 41 w(3\(dbl)p 2418 2052 V 40 w(expr\))150
-2162 y(gsl)p 262 2162 V 41 w(sf)p 367 2162 V 39 w(deb)m(y)m(e)p
-630 2162 V 41 w(4)p 716 2162 V 40 w(e)720 b(Y)112 b(gsl)p
-1802 2162 V 40 w(sf)p 1906 2162 V 40 w(deb)m(y)m(e)p
-2170 2162 V 41 w(4\(dbl)p 2418 2162 V 40 w(expr\))150
-2271 y(gsl)p 262 2271 V 41 w(sf)p 367 2271 V 39 w(deb)m(y)m(e)p
-630 2271 V 41 w(5)p 716 2271 V 40 w(e)720 b(Y)112 b(gsl)p
-1802 2271 V 40 w(sf)p 1906 2271 V 40 w(deb)m(y)m(e)p
-2170 2271 V 41 w(5\(dbl)p 2418 2271 V 40 w(expr\))150
-2381 y(gsl)p 262 2381 V 41 w(sf)p 367 2381 V 39 w(deb)m(y)m(e)p
-630 2381 V 41 w(6)p 716 2381 V 40 w(e)720 b(Y)112 b(gsl)p
-1802 2381 V 40 w(sf)p 1906 2381 V 40 w(deb)m(y)m(e)p
-2170 2381 V 41 w(6\(dbl)p 2418 2381 V 40 w(expr\))150
-2491 y(gsl)p 262 2491 V 41 w(sf)p 367 2491 V 39 w(dilog)p
-597 2491 V 41 w(e)838 b(N)112 b(gsl)p 1802 2491 V 40
-w(sf)p 1906 2491 V 40 w(dilog)150 2600 y(gsl)p 262 2600
-V 41 w(sf)p 367 2600 V 39 w(complex)p 731 2600 V 41 w(dilog)p
-963 2600 V 41 w(xy)p 1100 2600 V 40 w(e)336 b(N)112 b(gsl)p
-1802 2600 V 40 w(sf)p 1906 2600 V 40 w(complex)p 2271
-2600 V 41 w(dilog)p 2503 2600 V 41 w(xy)p 2640 2600 V
-40 w(e)150 2710 y(gsl)p 262 2710 V 41 w(sf)p 367 2710
-V 39 w(complex)p 731 2710 V 41 w(dilog)p 963 2710 V 41
-w(e)472 b(N)112 b(gsl)p 1802 2710 V 40 w(sf)p 1906 2710
-V 40 w(complex)p 2271 2710 V 41 w(dilog)150 2819 y(gsl)p
-262 2819 V 41 w(sf)p 367 2819 V 39 w(complex)p 731 2819
-V 41 w(sp)s(ence)p 1033 2819 V 40 w(xy)p 1169 2819 V
-40 w(e)267 b(N)112 b(gsl)p 1802 2819 V 40 w(sf)p 1906
-2819 V 40 w(complex)p 2271 2819 V 41 w(sp)s(ence)p 2573
-2819 V 39 w(xy)p 2708 2819 V 40 w(e)150 2929 y(gsl)p
-262 2929 V 41 w(sf)p 367 2929 V 39 w(m)m(ultiply)p 739
-2929 V 41 w(e)696 b(N)112 b(gsl)p 1802 2929 V 40 w(sf)p
-1906 2929 V 40 w(m)m(ultiply)150 3039 y(gsl)p 262 3039
-V 41 w(sf)p 367 3039 V 39 w(m)m(ultiply)p 739 3039 V
-41 w(err)p 892 3039 V 39 w(e)545 b(N)112 b(gsl)p 1802
-3039 V 40 w(sf)p 1906 3039 V 40 w(m)m(ultiply)p 2279
-3039 V 40 w(err)150 3148 y(gsl)p 262 3148 V 41 w(sf)p
-367 3148 V 39 w(ellin)m(t)p 604 3148 V 42 w(Kcomp)p 929
-3148 V 40 w(e)507 b(Y)112 b(gsl)p 1802 3148 V 40 w(sf)p
-1906 3148 V 40 w(ellin)m(t)p 2144 3148 V 41 w(Kcomp\(dbl)p
-2630 3148 V 40 w(expr\))150 3258 y(gsl)p 262 3258 V 41
-w(sf)p 367 3258 V 39 w(ellin)m(t)p 604 3258 V 42 w(Ecomp)p
-920 3258 V 40 w(e)516 b(Y)112 b(gsl)p 1802 3258 V 40
-w(sf)p 1906 3258 V 40 w(ellin)m(t)p 2144 3258 V 41 w(Ecomp\(dbl)p
-2621 3258 V 40 w(expr\))150 3367 y(gsl)p 262 3367 V 41
-w(sf)p 367 3367 V 39 w(ellin)m(t)p 604 3367 V 42 w(Pcomp)p
-920 3367 V 40 w(e)516 b(Y)112 b(gsl)p 1802 3367 V 40
-w(sf)p 1906 3367 V 40 w(ellin)m(t)p 2144 3367 V 41 w(Pcomp\(dbl)p
-2621 3367 V 40 w(expr,dbl)p 2988 3367 V 39 w(expr\))150
-3477 y(gsl)p 262 3477 V 41 w(sf)p 367 3477 V 39 w(ellin)m(t)p
-604 3477 V 42 w(Dcomp)p 927 3477 V 40 w(e)509 b(Y)112
-b(gsl)p 1802 3477 V 40 w(sf)p 1906 3477 V 40 w(ellin)m(t)p
-2144 3477 V 41 w(Dcomp\(dbl)p 2628 3477 V 41 w(expr\))150
-3587 y(gsl)p 262 3587 V 41 w(sf)p 367 3587 V 39 w(ellin)m(t)p
-604 3587 V 42 w(F)p 705 3587 V 40 w(e)731 b(Y)112 b(gsl)p
-1802 3587 V 40 w(sf)p 1906 3587 V 40 w(ellin)m(t)p 2144
-3587 V 41 w(F\(dbl)p 2406 3587 V 40 w(expr,dbl)p 2773
-3587 V 39 w(expr\))150 3696 y(gsl)p 262 3696 V 41 w(sf)p
-367 3696 V 39 w(ellin)m(t)p 604 3696 V 42 w(E)p 708 3696
-V 40 w(e)728 b(Y)112 b(gsl)p 1802 3696 V 40 w(sf)p 1906
-3696 V 40 w(ellin)m(t)p 2144 3696 V 41 w(E\(dbl)p 2409
-3696 V 40 w(expr,dbl)p 2776 3696 V 39 w(expr\))150 3806
-y(gsl)p 262 3806 V 41 w(sf)p 367 3806 V 39 w(ellin)m(t)p
-604 3806 V 42 w(P)p 708 3806 V 40 w(e)728 b(Y)112 b(gsl)p
-1802 3806 V 40 w(sf)p 1906 3806 V 40 w(ellin)m(t)p 2144
-3806 V 41 w(P\(dbl)p 2409 3806 V 40 w(expr,dbl)p 2776
-3806 V 39 w(expr,dbl)p 3142 3806 V 39 w(expr\))150 3915
-y(gsl)p 262 3915 V 41 w(sf)p 367 3915 V 39 w(ellin)m(t)p
-604 3915 V 42 w(D)p 715 3915 V 40 w(e)721 b(Y)112 b(gsl)p
-1802 3915 V 40 w(sf)p 1906 3915 V 40 w(ellin)m(t)p 2144
-3915 V 41 w(D\(dbl)p 2416 3915 V 40 w(expr,dbl)p 2783
-3915 V 39 w(expr,dbl)p 3149 3915 V 39 w(expr\))150 4025
-y(gsl)p 262 4025 V 41 w(sf)p 367 4025 V 39 w(ellin)m(t)p
-604 4025 V 42 w(R)m(C)p 776 4025 V 40 w(e)660 b(Y)112
-b(gsl)p 1802 4025 V 40 w(sf)p 1906 4025 V 40 w(ellin)m(t)p
-2144 4025 V 41 w(R)m(C\(dbl)p 2477 4025 V 40 w(expr,dbl)p
-2844 4025 V 39 w(expr\))150 4134 y(gsl)p 262 4134 V 41
-w(sf)p 367 4134 V 39 w(ellin)m(t)p 604 4134 V 42 w(RD)p
-782 4134 V 40 w(e)654 b(Y)112 b(gsl)p 1802 4134 V 40
-w(sf)p 1906 4134 V 40 w(ellin)m(t)p 2144 4134 V 41 w(RD\(dbl)p
-2483 4134 V 40 w(expr,dbl)p 2850 4134 V 39 w(expr,dbl)p
-3216 4134 V 39 w(expr\))150 4244 y(gsl)p 262 4244 V 41
-w(sf)p 367 4244 V 39 w(ellin)m(t)p 604 4244 V 42 w(RF)p
-772 4244 V 40 w(e)664 b(Y)112 b(gsl)p 1802 4244 V 40
-w(sf)p 1906 4244 V 40 w(ellin)m(t)p 2144 4244 V 41 w(RF\(dbl)p
-2473 4244 V 40 w(expr,dbl)p 2840 4244 V 39 w(expr,dbl)p
-3206 4244 V 39 w(expr\))150 4354 y(gsl)p 262 4354 V 41
-w(sf)p 367 4354 V 39 w(ellin)m(t)p 604 4354 V 42 w(RJ)p
-760 4354 V 39 w(e)677 b(Y)112 b(gsl)p 1802 4354 V 40
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-2461 4354 V 40 w(expr,dbl)p 2828 4354 V 39 w(expr,dbl)p
-3194 4354 V 39 w(expr,dbl)p 3560 4354 V 39 w(expr\))150
-4463 y(gsl)p 262 4463 V 41 w(sf)p 367 4463 V 39 w(elljac)p
-609 4463 V 42 w(e)825 b(N)112 b(gsl)p 1802 4463 V 40
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-V 41 w(sf)p 367 4573 V 39 w(erfc)p 550 4573 V 40 w(e)886
-b(Y)112 b(gsl)p 1802 4573 V 40 w(sf)p 1906 4573 V 40
-w(erfc\(dbl)p 2252 4573 V 40 w(expr\))150 4682 y(gsl)p
-262 4682 V 41 w(sf)p 367 4682 V 39 w(log)p 521 4682 V
-41 w(erfc)p 706 4682 V 41 w(e)729 b(Y)112 b(gsl)p 1802
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-w(erfc\(dbl)p 2408 4682 V 40 w(expr\))150 4792 y(gsl)p
-262 4792 V 41 w(sf)p 367 4792 V 39 w(erf)p 510 4792 V
-40 w(e)926 b(Y)112 b(gsl)p 1802 4792 V 40 w(sf)p 1906
-4792 V 40 w(erf\(dbl)p 2212 4792 V 39 w(expr\))150 4902
-y(gsl)p 262 4902 V 41 w(sf)p 367 4902 V 39 w(erf)p 510
-4902 V 40 w(Z)p 606 4902 V 40 w(e)830 b(Y)112 b(gsl)p
-1802 4902 V 40 w(sf)p 1906 4902 V 40 w(erf)p 2050 4902
-V 40 w(Z\(dbl)p 2308 4902 V 39 w(expr\))150 5011 y(gsl)p
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-40 w(Q)p 621 5011 V 40 w(e)815 b(Y)112 b(gsl)p 1802 5011
-V 40 w(sf)p 1906 5011 V 40 w(erf)p 2050 5011 V 40 w(Q\(dbl)p
-2323 5011 V 39 w(expr\))150 5121 y(gsl)p 262 5121 V 41
-w(sf)p 367 5121 V 39 w(hazard)p 674 5121 V 40 w(e)762
-b(Y)112 b(gsl)p 1802 5121 V 40 w(sf)p 1906 5121 V 40
-w(hazard\(dbl)p 2376 5121 V 39 w(expr\))150 5230 y(gsl)p
-262 5230 V 41 w(sf)p 367 5230 V 39 w(exp)p 545 5230 V
-40 w(e)891 b(Y)112 b(gsl)p 1802 5230 V 40 w(sf)p 1906
-5230 V 40 w(exp\(dbl)p 2247 5230 V 39 w(expr\))150 5340
-y(gsl)p 262 5340 V 41 w(sf)p 367 5340 V 39 w(exp)p 545
-5340 V 40 w(e10)p 715 5340 V 41 w(e)720 b(N)112 b(gsl)p
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-w(sf)p 1906 1504 V 40 w(expin)m(t)p 2193 1504 V 40 w(E2\(dbl)p
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-V 41 w(e)357 b(Y)112 b(gsl)p 1802 1833 V 40 w(sf)p 1906
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-V 41 w(scaled\(dbl)p 2780 1833 V 40 w(expr\))150 1943
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-1943 V 39 w(expr\))150 2052 y(gsl)p 262 2052 V 41 w(sf)p
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-611 2929 V 40 w(dirac)p 848 2929 V 40 w(m1)p 1009 2929
-V 40 w(e)427 b(Y)112 b(gsl)p 1802 2929 V 40 w(sf)p 1906
-2929 V 40 w(fermi)p 2151 2929 V 40 w(dirac)p 2388 2929
-V 40 w(m1\(dbl)p 2711 2929 V 40 w(expr\))150 3039 y(gsl)p
-262 3039 V 41 w(sf)p 367 3039 V 39 w(fermi)p 611 3039
-V 40 w(dirac)p 848 3039 V 40 w(0)p 933 3039 V 41 w(e)502
-b(Y)112 b(gsl)p 1802 3039 V 40 w(sf)p 1906 3039 V 40
-w(fermi)p 2151 3039 V 40 w(dirac)p 2388 3039 V 40 w(0\(dbl)p
-2635 3039 V 40 w(expr\))150 3148 y(gsl)p 262 3148 V 41
-w(sf)p 367 3148 V 39 w(fermi)p 611 3148 V 40 w(dirac)p
-848 3148 V 40 w(1)p 933 3148 V 41 w(e)502 b(Y)112 b(gsl)p
-1802 3148 V 40 w(sf)p 1906 3148 V 40 w(fermi)p 2151 3148
-V 40 w(dirac)p 2388 3148 V 40 w(1\(dbl)p 2635 3148 V
-40 w(expr\))150 3258 y(gsl)p 262 3258 V 41 w(sf)p 367
-3258 V 39 w(fermi)p 611 3258 V 40 w(dirac)p 848 3258
-V 40 w(2)p 933 3258 V 41 w(e)502 b(Y)112 b(gsl)p 1802
-3258 V 40 w(sf)p 1906 3258 V 40 w(fermi)p 2151 3258 V
-40 w(dirac)p 2388 3258 V 40 w(2\(dbl)p 2635 3258 V 40
-w(expr\))150 3367 y(gsl)p 262 3367 V 41 w(sf)p 367 3367
-V 39 w(fermi)p 611 3367 V 40 w(dirac)p 848 3367 V 40
-w(in)m(t)p 996 3367 V 41 w(e)439 b(Y)112 b(gsl)p 1802
-3367 V 40 w(sf)p 1906 3367 V 40 w(fermi)p 2151 3367 V
-40 w(dirac)p 2388 3367 V 40 w(in)m(t\(in)m(t)p 2679 3367
-V 41 w(expr,dbl)p 3047 3367 V 39 w(expr\))150 3477 y(gsl)p
-262 3477 V 41 w(sf)p 367 3477 V 39 w(fermi)p 611 3477
-V 40 w(dirac)p 848 3477 V 40 w(mhalf)p 1113 3477 V 40
-w(e)323 b(Y)112 b(gsl)p 1802 3477 V 40 w(sf)p 1906 3477
-V 40 w(fermi)p 2151 3477 V 40 w(dirac)p 2388 3477 V 40
-w(mhalf\(dbl)p 2815 3477 V 39 w(expr\))150 3587 y(gsl)p
-262 3587 V 41 w(sf)p 367 3587 V 39 w(fermi)p 611 3587
-V 40 w(dirac)p 848 3587 V 40 w(half)p 1037 3587 V 40
-w(e)399 b(Y)112 b(gsl)p 1802 3587 V 40 w(sf)p 1906 3587
-V 40 w(fermi)p 2151 3587 V 40 w(dirac)p 2388 3587 V 40
-w(half\(dbl)p 2739 3587 V 39 w(expr\))150 3696 y(gsl)p
-262 3696 V 41 w(sf)p 367 3696 V 39 w(fermi)p 611 3696
-V 40 w(dirac)p 848 3696 V 40 w(3half)p 1082 3696 V 41
-w(e)353 b(Y)112 b(gsl)p 1802 3696 V 40 w(sf)p 1906 3696
-V 40 w(fermi)p 2151 3696 V 40 w(dirac)p 2388 3696 V 40
-w(3half\(dbl)p 2784 3696 V 40 w(expr\))150 3806 y(gsl)p
-262 3806 V 41 w(sf)p 367 3806 V 39 w(fermi)p 611 3806
-V 40 w(dirac)p 848 3806 V 40 w(inc)p 1004 3806 V 40 w(0)p
-1089 3806 V 41 w(e)346 b(Y)112 b(gsl)p 1802 3806 V 40
-w(sf)p 1906 3806 V 40 w(fermi)p 2151 3806 V 40 w(dirac)p
-2388 3806 V 40 w(inc)p 2544 3806 V 40 w(0\(dbl)p 2791
-3806 V 40 w(expr,dbl)p 3158 3806 V 39 w(expr\))150 3915
-y(gsl)p 262 3915 V 41 w(sf)p 367 3915 V 39 w(lngamma)p
-769 3915 V 41 w(e)666 b(Y)112 b(gsl)p 1802 3915 V 40
-w(sf)p 1906 3915 V 40 w(lngamma\(dbl)p 2471 3915 V 40
-w(expr\))150 4025 y(gsl)p 262 4025 V 41 w(sf)p 367 4025
-V 39 w(lngamma)p 769 4025 V 41 w(sgn)p 942 4025 V 40
-w(e)494 b(N)112 b(gsl)p 1802 4025 V 40 w(sf)p 1906 4025
-V 40 w(lngamma)p 2309 4025 V 41 w(sgn)150 4134 y(gsl)p
-262 4134 V 41 w(sf)p 367 4134 V 39 w(gamma)p 693 4134
-V 41 w(e)742 b(Y)112 b(gsl)p 1802 4134 V 40 w(sf)p 1906
-4134 V 40 w(gamma\(dbl)p 2395 4134 V 40 w(expr\))150
-4244 y(gsl)p 262 4244 V 41 w(sf)p 367 4244 V 39 w(gammastar)p
-845 4244 V 41 w(e)590 b(Y)112 b(gsl)p 1802 4244 V 40
-w(sf)p 1906 4244 V 40 w(gammastar\(dbl)p 2547 4244 V
-41 w(expr\))150 4354 y(gsl)p 262 4354 V 41 w(sf)p 367
-4354 V 39 w(gammain)m(v)p 814 4354 V 41 w(e)621 b(Y)112
-b(gsl)p 1802 4354 V 40 w(sf)p 1906 4354 V 40 w(gammain)m(v\(dbl)p
-2516 4354 V 41 w(expr\))150 4463 y(gsl)p 262 4463 V 41
-w(sf)p 367 4463 V 39 w(lngamma)p 769 4463 V 41 w(complex)p
-1135 4463 V 41 w(e)300 b(N)112 b(gsl)p 1802 4463 V 40
-w(sf)p 1906 4463 V 40 w(lngamma)p 2309 4463 V 41 w(complex)150
-4573 y(gsl)p 262 4573 V 41 w(sf)p 367 4573 V 39 w(ta)m(ylorco)s(e\013)p
-818 4573 V 43 w(e)615 b(Y)112 b(gsl)p 1802 4573 V 40
-w(sf)p 1906 4573 V 40 w(ta)m(ylorco)s(e\013\(in)m(t)p
-2501 4573 V 43 w(expr,dbl)p 2871 4573 V 39 w(expr\))150
-4682 y(gsl)p 262 4682 V 41 w(sf)p 367 4682 V 39 w(fact)p
-554 4682 V 41 w(e)881 b(Y)112 b(gsl)p 1802 4682 V 40
-w(sf)p 1906 4682 V 40 w(fact\(uin)m(t)p 2288 4682 V 41
-w(expr\))150 4792 y(gsl)p 262 4792 V 41 w(sf)p 367 4792
-V 39 w(doublefact)p 817 4792 V 41 w(e)618 b(Y)112 b(gsl)p
-1802 4792 V 40 w(sf)p 1906 4792 V 40 w(doublefact\(uin)m(t)p
-2551 4792 V 41 w(expr\))150 4902 y(gsl)p 262 4902 V 41
-w(sf)p 367 4902 V 39 w(lnfact)p 630 4902 V 41 w(e)805
-b(Y)112 b(gsl)p 1802 4902 V 40 w(sf)p 1906 4902 V 40
-w(lnfact\(uin)m(t)p 2364 4902 V 41 w(expr\))150 5011
-y(gsl)p 262 5011 V 41 w(sf)p 367 5011 V 39 w(lndoublefact)p
-893 5011 V 41 w(e)542 b(Y)112 b(gsl)p 1802 5011 V 40
-w(sf)p 1906 5011 V 40 w(lndoublefact\(uin)m(t)p 2627
-5011 V 41 w(expr\))150 5121 y(gsl)p 262 5121 V 41 w(sf)p
-367 5121 V 39 w(lnc)m(ho)s(ose)p 739 5121 V 41 w(e)696
-b(N)112 b(gsl)p 1802 5121 V 40 w(sf)p 1906 5121 V 40
-w(lnc)m(ho)s(ose)150 5230 y(gsl)p 262 5230 V 41 w(sf)p
-367 5230 V 39 w(c)m(ho)s(ose)p 663 5230 V 41 w(e)772
-b(N)112 b(gsl)p 1802 5230 V 40 w(sf)p 1906 5230 V 40
-w(c)m(ho)s(ose)150 5340 y(gsl)p 262 5340 V 41 w(sf)p
-367 5340 V 39 w(lnp)s(o)s(c)m(h)p 672 5340 V 39 w(e)765
+5121 V 40 w(Kn\(in)m(t)p 2482 5121 V 40 w(expr,dbl)p
+2849 5121 V 39 w(expr\))150 5230 y(gsl)p 262 5230 V 41
+w(sf)p 367 5230 V 39 w(b)s(essel)p 637 5230 V 40 w(Kn)p
+799 5230 V 39 w(arra)m(y)471 b(Y)112 b(status=gsl)p 2111
+5230 V 40 w(sf)p 2215 5230 V 40 w(b)s(essel)p 2486 5230
+V 40 w(Kn)p 2648 5230 V 39 w(arra)m(y\(in)m(t,in)m(t,double,&v)-5
+b(ar)p 3678 5230 V 42 w(out\))150 5340 y(gsl)p 262 5340
+V 41 w(sf)p 367 5340 V 39 w(b)s(essel)p 637 5340 V 40
+w(K0)p 793 5340 V 40 w(scaled)p 1070 5340 V 41 w(e)365
b(Y)112 b(gsl)p 1802 5340 V 40 w(sf)p 1906 5340 V 40
-w(lnp)s(o)s(c)m(h\(dbl)p 2374 5340 V 39 w(expr,dbl)p
-2740 5340 V 39 w(expr\))p eop end
+w(b)s(essel)p 2177 5340 V 40 w(K0)p 2333 5340 V 40 w(scaled\(dbl)p
+2772 5340 V 40 w(expr\))p eop end
%%Page: 137 143
TeXDict begin 137 142 bop 150 -116 a FD(Chapter)30 b(4:)41
b(Op)s(erator)30 b(Reference)h(Man)m(ual)1897 b(137)150
-299 y(gsl)p 262 299 28 4 v 41 w(sf)p 367 299 V 39 w(lnp)s(o)s(c)m(h)p
-672 299 V 39 w(sgn)p 843 299 V 40 w(e)593 b(N)112 b(gsl)p
-1802 299 V 40 w(sf)p 1906 299 V 40 w(lnp)s(o)s(c)m(h)p
-2212 299 V 39 w(sgn)150 408 y(gsl)p 262 408 V 41 w(sf)p
-367 408 V 39 w(p)s(o)s(c)m(h)p 596 408 V 40 w(e)840 b(Y)112
-b(gsl)p 1802 408 V 40 w(sf)p 1906 408 V 40 w(p)s(o)s(c)m(h\(dbl)p
-2298 408 V 39 w(expr,dbl)p 2664 408 V 39 w(expr\))150
-518 y(gsl)p 262 518 V 41 w(sf)p 367 518 V 39 w(p)s(o)s(c)m(hrel)p
-697 518 V 40 w(e)739 b(Y)112 b(gsl)p 1802 518 V 40 w(sf)p
-1906 518 V 40 w(p)s(o)s(c)m(hrel\(dbl)p 2399 518 V 39
-w(expr,dbl)p 2765 518 V 39 w(expr\))150 628 y(gsl)p 262
-628 V 41 w(sf)p 367 628 V 39 w(gamma)p 693 628 V 41 w(inc)p
-850 628 V 40 w(Q)p 961 628 V 40 w(e)475 b(Y)112 b(gsl)p
-1802 628 V 40 w(sf)p 1906 628 V 40 w(gamma)p 2233 628
-V 41 w(inc)p 2390 628 V 40 w(Q\(dbl)p 2663 628 V 39 w(expr,dbl)p
-3029 628 V 39 w(expr\))150 737 y(gsl)p 262 737 V 41 w(sf)p
-367 737 V 39 w(gamma)p 693 737 V 41 w(inc)p 850 737 V
-40 w(P)p 952 737 V 40 w(e)484 b(Y)112 b(gsl)p 1802 737
-V 40 w(sf)p 1906 737 V 40 w(gamma)p 2233 737 V 41 w(inc)p
-2390 737 V 40 w(P\(dbl)p 2654 737 V 39 w(expr,dbl)p 3020
-737 V 39 w(expr\))150 847 y(gsl)p 262 847 V 41 w(sf)p
-367 847 V 39 w(gamma)p 693 847 V 41 w(inc)p 850 847 V
-40 w(e)586 b(Y)112 b(gsl)p 1802 847 V 40 w(sf)p 1906
-847 V 40 w(gamma)p 2233 847 V 41 w(inc\(dbl)p 2552 847
-V 40 w(expr,dbl)p 2919 847 V 39 w(expr\))150 956 y(gsl)p
-262 956 V 41 w(sf)p 367 956 V 39 w(ln)m(b)s(eta)p 653
-956 V 41 w(e)782 b(Y)112 b(gsl)p 1802 956 V 40 w(sf)p
-1906 956 V 40 w(ln)m(b)s(eta\(dbl)p 2355 956 V 40 w(expr,dbl)p
-2722 956 V 39 w(expr\))150 1066 y(gsl)p 262 1066 V 41
-w(sf)p 367 1066 V 39 w(ln)m(b)s(eta)p 653 1066 V 41 w(sgn)p
-826 1066 V 40 w(e)610 b(N)112 b(gsl)p 1802 1066 V 40
-w(sf)p 1906 1066 V 40 w(ln)m(b)s(eta)p 2193 1066 V 40
-w(sgn)150 1176 y(gsl)p 262 1176 V 41 w(sf)p 367 1176
-V 39 w(b)s(eta)p 580 1176 V 40 w(e)856 b(Y)112 b(gsl)p
-1802 1176 V 40 w(sf)p 1906 1176 V 40 w(b)s(eta\(dbl)p
-2282 1176 V 40 w(expr,dbl)p 2649 1176 V 39 w(expr\))150
-1285 y(gsl)p 262 1285 V 41 w(sf)p 367 1285 V 39 w(b)s(eta)p
-580 1285 V 40 w(inc)p 736 1285 V 41 w(e)699 b(N)112 b(gsl)p
-1802 1285 V 40 w(sf)p 1906 1285 V 40 w(b)s(eta)p 2120
-1285 V 40 w(inc)150 1395 y(gsl)p 262 1395 V 41 w(sf)p
-367 1395 V 39 w(gegenp)s(oly)p 799 1395 V 41 w(1)p 885
-1395 V 41 w(e)550 b(Y)112 b(gsl)p 1802 1395 V 40 w(sf)p
-1906 1395 V 40 w(gegenp)s(oly)p 2339 1395 V 41 w(1\(dbl)p
-2587 1395 V 40 w(expr,dbl)p 2954 1395 V 39 w(expr\))150
-1504 y(gsl)p 262 1504 V 41 w(sf)p 367 1504 V 39 w(gegenp)s(oly)p
-799 1504 V 41 w(2)p 885 1504 V 41 w(e)550 b(Y)112 b(gsl)p
-1802 1504 V 40 w(sf)p 1906 1504 V 40 w(gegenp)s(oly)p
-2339 1504 V 41 w(2\(dbl)p 2587 1504 V 40 w(expr,dbl)p
-2954 1504 V 39 w(expr\))150 1614 y(gsl)p 262 1614 V 41
-w(sf)p 367 1614 V 39 w(gegenp)s(oly)p 799 1614 V 41 w(3)p
-885 1614 V 41 w(e)550 b(Y)112 b(gsl)p 1802 1614 V 40
-w(sf)p 1906 1614 V 40 w(gegenp)s(oly)p 2339 1614 V 41
-w(3\(dbl)p 2587 1614 V 40 w(expr,dbl)p 2954 1614 V 39
-w(expr\))150 1724 y(gsl)p 262 1724 V 41 w(sf)p 367 1724
-V 39 w(gegenp)s(oly)p 799 1724 V 41 w(n)p 891 1724 V
-40 w(e)545 b(N)112 b(gsl)p 1802 1724 V 40 w(sf)p 1906
-1724 V 40 w(gegenp)s(oly)p 2339 1724 V 41 w(n)150 1833
-y(gsl)p 262 1833 V 41 w(sf)p 367 1833 V 39 w(gegenp)s(oly)p
-799 1833 V 41 w(arra)m(y)469 b(Y)112 b(gsl)p 1802 1833
-V 40 w(sf)p 1906 1833 V 40 w(gegenp)s(oly)p 2339 1833
-V 41 w(arra)m(y)150 1943 y(gsl)p 262 1943 V 41 w(sf)p
-367 1943 V 39 w(h)m(yp)s(erg)p 677 1943 V 40 w(0F1)p
-866 1943 V 41 w(e)569 b(Y)112 b(gsl)p 1802 1943 V 40
-w(sf)p 1906 1943 V 40 w(h)m(yp)s(erg)p 2217 1943 V 39
-w(0F1\(dbl)p 2567 1943 V 41 w(expr,dbl)p 2935 1943 V
-39 w(expr\))150 2052 y(gsl)p 262 2052 V 41 w(sf)p 367
-2052 V 39 w(h)m(yp)s(erg)p 677 2052 V 40 w(1F1)p 866
-2052 V 41 w(in)m(t)p 1015 2052 V 41 w(e)420 b(Y)112 b(gsl)p
-1802 2052 V 40 w(sf)p 1906 2052 V 40 w(h)m(yp)s(erg)p
-2217 2052 V 39 w(1F1)p 2405 2052 V 42 w(in)m(t\(in)m(t)p
-2698 2052 V 41 w(expr,in)m(t)p 3047 2052 V 40 w(expr,dbl)p
-3414 2052 V 39 w(expr\))150 2162 y(gsl)p 262 2162 V 41
-w(sf)p 367 2162 V 39 w(h)m(yp)s(erg)p 677 2162 V 40 w(1F1)p
-866 2162 V 41 w(e)569 b(Y)112 b(gsl)p 1802 2162 V 40
-w(sf)p 1906 2162 V 40 w(h)m(yp)s(erg)p 2217 2162 V 39
-w(1F1\(dbl)p 2567 2162 V 41 w(expr,dbl)p 2935 2162 V
-39 w(expr,dbl)p 3301 2162 V 39 w(expr\))150 2271 y(gsl)p
-262 2271 V 41 w(sf)p 367 2271 V 39 w(h)m(yp)s(erg)p 677
-2271 V 40 w(U)p 785 2271 V 40 w(in)m(t)p 933 2271 V 40
-w(e)503 b(Y)112 b(gsl)p 1802 2271 V 40 w(sf)p 1906 2271
-V 40 w(h)m(yp)s(erg)p 2217 2271 V 39 w(U)p 2324 2271
-V 41 w(in)m(t\(in)m(t)p 2616 2271 V 41 w(expr,in)m(t)p
-2965 2271 V 40 w(expr,dbl)p 3332 2271 V 39 w(expr\))150
-2381 y(gsl)p 262 2381 V 41 w(sf)p 367 2381 V 39 w(h)m(yp)s(erg)p
-677 2381 V 40 w(U)p 785 2381 V 40 w(in)m(t)p 933 2381
-V 40 w(e10)p 1103 2381 V 42 w(e)331 b(N)112 b(gsl)p 1802
-2381 V 40 w(sf)p 1906 2381 V 40 w(h)m(yp)s(erg)p 2217
-2381 V 39 w(U)p 2324 2381 V 41 w(in)m(t)p 2473 2381 V
-40 w(e10)150 2491 y(gsl)p 262 2491 V 41 w(sf)p 367 2491
-V 39 w(h)m(yp)s(erg)p 677 2491 V 40 w(U)p 785 2491 V
-40 w(e)651 b(Y)112 b(gsl)p 1802 2491 V 40 w(sf)p 1906
-2491 V 40 w(h)m(yp)s(erg)p 2217 2491 V 39 w(U\(dbl)p
-2486 2491 V 40 w(expr,dbl)p 2853 2491 V 39 w(expr,dbl)p
-3219 2491 V 39 w(expr\))150 2600 y(gsl)p 262 2600 V 41
-w(sf)p 367 2600 V 39 w(h)m(yp)s(erg)p 677 2600 V 40 w(U)p
-785 2600 V 40 w(e10)p 955 2600 V 41 w(e)480 b(N)112 b(gsl)p
-1802 2600 V 40 w(sf)p 1906 2600 V 40 w(h)m(yp)s(erg)p
-2217 2600 V 39 w(U)p 2324 2600 V 41 w(e10)150 2710 y(gsl)p
-262 2710 V 41 w(sf)p 367 2710 V 39 w(h)m(yp)s(erg)p 677
-2710 V 40 w(2F1)p 866 2710 V 41 w(e)569 b(Y)112 b(gsl)p
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-2935 2710 V 39 w(expr,dbl)p 3301 2710 V 39 w(expr,dbl)p
-3667 2710 V 39 w(expr\))150 2819 y(gsl)p 262 2819 V 41
-w(sf)p 367 2819 V 39 w(h)m(yp)s(erg)p 677 2819 V 40 w(2F1)p
-866 2819 V 41 w(conj)p 1071 2819 V 40 w(e)365 b(Y)112
-b(gsl)p 1802 2819 V 40 w(sf)p 1906 2819 V 40 w(h)m(yp)s(erg)p
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-2819 V 39 w(expr,dbl)p 3139 2819 V 39 w(expr,dbl)p 3505
-2819 V 39 w(expr,dbl)p 3871 2819 V 39 w(expr\))150 2929
-y(gsl)p 262 2929 V 41 w(sf)p 367 2929 V 39 w(h)m(yp)s(erg)p
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-V 39 w(e)246 b(Y)112 b(gsl)p 1802 2929 V 40 w(sf)p 1906
-2929 V 40 w(h)m(yp)s(erg)p 2217 2929 V 39 w(2F1)p 2405
-2929 V 42 w(renorm\(dbl)p 2893 2929 V 39 w(expr,dbl)p
-3259 2929 V 39 w(expr,dbl)p 3625 2929 V 39 w(expr,dbl)p
-3991 2929 V 39 w(expr\))150 3039 y(gsl)p 262 3039 V 41
-w(sf)p 367 3039 V 39 w(h)m(yp)s(erg)p 677 3039 V 40 w(2F1)p
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-3039 V 39 w(e)42 b(Y)112 b(gsl)p 1802 3039 V 40 w(sf)p
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-2935 3148 V 39 w(expr,dbl)p 3301 3148 V 39 w(expr\))150
-3258 y(gsl)p 262 3258 V 41 w(sf)p 367 3258 V 39 w(laguerre)p
-724 3258 V 41 w(1)p 810 3258 V 40 w(e)626 b(Y)112 b(gsl)p
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-3258 V 41 w(1\(dbl)p 2512 3258 V 40 w(expr,dbl)p 2879
-3258 V 39 w(expr\))150 3367 y(gsl)p 262 3367 V 41 w(sf)p
-367 3367 V 39 w(laguerre)p 724 3367 V 41 w(2)p 810 3367
-V 40 w(e)626 b(Y)112 b(gsl)p 1802 3367 V 40 w(sf)p 1906
-3367 V 40 w(laguerre)p 2264 3367 V 41 w(2\(dbl)p 2512
-3367 V 40 w(expr,dbl)p 2879 3367 V 39 w(expr\))150 3477
-y(gsl)p 262 3477 V 41 w(sf)p 367 3477 V 39 w(laguerre)p
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-3477 V 39 w(expr\))150 3587 y(gsl)p 262 3587 V 41 w(sf)p
-367 3587 V 39 w(laguerre)p 724 3587 V 41 w(n)p 816 3587
-V 39 w(e)621 b(Y)112 b(gsl)p 1802 3587 V 40 w(sf)p 1906
-3587 V 40 w(laguerre)p 2264 3587 V 41 w(n\(in)m(t)p 2499
-3587 V 40 w(expr,dbl)p 2866 3587 V 39 w(expr,dbl)p 3232
-3587 V 39 w(expr\))150 3696 y(gsl)p 262 3696 V 41 w(sf)p
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-893 3696 V 40 w(e)543 b(Y)112 b(gsl)p 1802 3696 V 40
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%%Page: 138 144
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%%Page: 139 145
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+b(:)f(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g
+(:)g(:)g(:)g(:)h(:)f(:)g(:)35 b Fs(28,)27 b(43,)g(156,)g(160)2025
+1201 y Fr(WIN32)c Fa(:)13 b(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g
+(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)
+f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)49 b
+Fs(8)2025 1289 y(Windo)n(ws)9 b Fa(:)k(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g
(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)
h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)35 b Fs(6,)27
-b(7)2025 564 y(wrapp)r(ed)f(co)r(ordinates)6 b Fa(:)15
+b(7)2025 1376 y(wrapp)r(ed)f(co)r(ordinates)6 b Fa(:)15
b(:)e(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)33
-b Fs(55,)27 b(62,)g(128,)g(185)2025 652 y(wrapp)r(ed)f(\014lenames)12
+b Fs(56,)27 b(63,)g(130,)g(188)2025 1463 y(wrapp)r(ed)f(\014lenames)12
b Fa(:)h(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)
g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)38 b
-Fs(29)2025 740 y Fp(WRF)13 b Fa(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g
-(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)
-g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)40
-b Fs(129)2025 828 y(WWW)25 b(do)r(cumen)n(tation)12 b
-Fa(:)i(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f
-(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)39 b Fs(5)2025 1067
-y FB(X)2025 1185 y Fr(xargs)9 b Fa(:)14 b(:)f(:)g(:)g(:)h(:)f(:)g(:)g
-(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)
-g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)35 b
-Fs(20,)27 b(30)2025 1273 y Fr(xlc)10 b Fa(:)j(:)h(:)f(:)g(:)g(:)g(:)g
-(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)
-h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g
-(:)g(:)g(:)37 b Fs(6)2025 1362 y Fr(xlC)10 b Fa(:)j(:)h(:)f(:)g(:)g(:)g
-(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)
-g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f
-(:)g(:)g(:)g(:)37 b Fs(6)2025 1450 y Fp(XML)17 b Fa(:)c(:)g(:)g(:)h(:)f
-(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)
+Fs(29)2025 1551 y Fp(WRF)13 b Fa(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)
+g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g
+(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)40
+b Fs(131)2025 1638 y Fp(WRF)26 b Fs(\(W)-6 b(eather)25
+b(and)g(Researc)n(h)h(F)-6 b(orecast)27 b(Mo)r(del\))2200
+1725 y Fa(:)13 b(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)
g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g
-(:)45 b Fs(179)2025 1538 y(XP)25 b(\(Microsoft)j(op)r(erating)f
-(system\))9 b Fa(:)j(:)i(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)
-g(:)g(:)36 b Fs(7)2025 1626 y(`)p Fr(xpl)p Fs(')22 b
-Fa(:)13 b(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f
-(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)
-g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)47 b Fs(72)2025 1715
-y(`)p Fr(xst)p Fs(')10 b Fa(:)k(:)f(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g
+(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)49 b Fs(123)2025 1812
+y(WWW)25 b(do)r(cumen)n(tation)12 b Fa(:)i(:)f(:)g(:)g(:)g(:)g(:)g(:)g
+(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)
+39 b Fs(5)2025 2046 y FB(X)2025 2162 y Fr(xargs)9 b Fa(:)14
+b(:)f(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g
+(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)
+h(:)f(:)35 b Fs(20,)27 b(30)2025 2250 y Fr(xlc)10 b Fa(:)j(:)h(:)f(:)g
+(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)
+g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g
+(:)h(:)f(:)g(:)g(:)g(:)37 b Fs(6)2025 2337 y Fr(xlC)10
+b Fa(:)j(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)
+h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f
+(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)37 b Fs(6)2025
+2425 y Fp(XML)17 b Fa(:)c(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f
+(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)
+g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)45 b Fs(182)2025
+2512 y(XP)25 b(\(Microsoft)j(op)r(erating)f(system\))9
+b Fa(:)j(:)i(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)36
+b Fs(7)2025 2599 y(`)p Fr(xpl)p Fs(')22 b Fa(:)13 b(:)g(:)g(:)g(:)g(:)g
(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)
-f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)36 b Fs(72,)27
-b(73)2025 1970 y FB(Y)2025 2088 y Fs(Y)-6 b(oric)n(k)17
-b Fa(:)c(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)
-g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g
-(:)g(:)g(:)44 b Fs(15,)27 b(24)p eop end
-%%Page: 262 268
-TeXDict begin 262 267 bop eop end
+f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g
+(:)47 b Fs(73)2025 2687 y(`)p Fr(xst)p Fs(')10 b Fa(:)k(:)f(:)g(:)g(:)h
+(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)
+g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)36
+b Fs(73,)27 b(74)2025 2937 y FB(Y)2025 3053 y Fs(Y)-6
+b(oric)n(k)17 b Fa(:)c(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g
+(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)h(:)f(:)g(:)g(:)g(:)g(:)g(:)g(:)h(:)
+f(:)g(:)g(:)g(:)g(:)g(:)44 b Fs(15,)27 b(24)p eop end
+%%Page: 268 274
+TeXDict begin 268 273 bop eop end
%%Trailer
userdict /end-hook known{end-hook}if
diff --git a/doc/nco.texi b/doc/nco.texi
index 1e2831d..0914dee 100644
--- a/doc/nco.texi
+++ b/doc/nco.texi
@@ -7,7 +7,7 @@
@ignore
-$Header: /cvsroot/nco/nco/doc/nco.texi,v 1.993 2014/05/29 18:00:26 zender Exp $
+$Header: /cvsroot/nco/nco/doc/nco.texi,v 1.1017 2014/08/27 04:44:01 zender Exp $
Purpose: TeXInfo documentation for NCO suite
@@ -81,6 +81,7 @@ Legend (defined in "highlighting" section of TeXInfo manual):
@command{}: Commands, e.g., @command{ncra}
@dfn{}: Define use of term, e.g., @dfn{supercalifragilisticexpialidocious}
@email{}: E-mail address, e.g., @email{surname at uci dot edu}
+ at emph{}: Emphasize text, e.g., @emph{important}
@env{}: Environment variable, e.g., @env{HOME}
@file{}: Filename, e.g., @file{in.nc}
@html: Text until @end html passed without translation
@@ -93,6 +94,7 @@ Legend (defined in "highlighting" section of TeXInfo manual):
@url{}: URL, synonym for @uref
@var{}: Metasyntactic variable, e.g., @var{}
@verbatim: Anything goes inside environment (no @'s needed to protect special characters like braces)
+ at verbatiminclude: Insert contents of file here, e.g., @verbatiminclude{nco.sh}
@example: Quoted environment (@'s needed to protect special characters like braces)
@w{}: Unbreakable text, e.g., @w{of 1}
@@ -112,12 +114,12 @@ Octave TeXInfo manual shows clean TeXInfo structure
@setfilename nco.info
@c Define edition, date, ...
- at set nco-edition 4.4.4
- at set doc-edition 4.4.4
+ at set nco-edition 4.4.5
+ at set doc-edition 4.4.5
@set copyright-years 1995--2014
@set update-year 2014
- at set update-date 29 May 2014
- at set update-month May 2014
+ at set update-date 26 August 2014
+ at set update-month August 2014
@settitle @acronym{NCO} @value{nco-edition} User Guide
@@ -479,32 +481,54 @@ March 2008@*
Grenoble, France@*
@sp 2
-The end of the @acronym{NSF} SEI grant in August, 2008 curtailed @acronym{NCO}
-development.
-Fortunately we could justify supporting Henry Butowsky on other research
+The end of the @acronym{NSF} @acronym{SEI} grant in August, 2008 curtailed
+ at acronym{NCO} development.
+Fortunately we could justify supporting Henry Butowsky on other research
grants until May, 2010 while he developed the key @command{ncap2}
features used in our climate research.
-And recently the NASA ACCESS program commenced funding NCO support for
-netCDF4 group functionality.@*
-Thus @acronym{NCO} will grow and evade bit-rot for the foreseeable future.
-
-On a personal level, I continue to receive with gratitude the thanks of
- at acronym{NCO} users at nearly every scientific meeting I attend.
-People introduce themselves, shake my hand and often extol, sometimes
-effusively, @acronym{NCO} as time-saving tools.
+And recently the @acronym{NASA} @acronym{ACCESS} program commenced
+funding us to support netCDF4 group functionality.
+Thus @acronym{NCO} will grow and evade bit-rot for the foreseeable
+future.
+
+I continue to receive with gratitude the thanks of @acronym{NCO} users
+at nearly every scientific meeting I attend.
+People introduce themselves, shake my hand and extol @acronym{NCO},
+often effusively, while I grin in stupid embarassment.
These exchanges lighten me like anti-gravity.
Sometimes I daydream how many hours @acronym{NCO} has turned from grunt
work to productive research for researchers world-wide, or from research
into early happy-hours.
It's a cool feeling.
- at c @uref{http://www.nasa.gov/mission_pages/IPY/main/PolarExploration.html,NNX07AR23G}.@*
@sp 1
@noindent
Charlie Zender@*
April, 2012@*
Irvine, California@*
+ at ignore
+ at sp 2
+The @acronym{NASA} @acronym{ACCESS} 2011 program generously supported
+(Cooperative Agreement NNX12AF48A) @acronym{NCO} from 2012--2014.
+We accomplished our goals and produced the first iteration of a
+Group-oriented Data Analysis and Distribution (@acronym{GODAD}) software
+ecosystem.
+Shifting geoscience data analysis to @acronym{GODAD}, no small task,
+drives our plans.
+Partly due to this success, the @acronym{NASA} @acronym{ACCESS} 2013
+program agreed to support (Cooperative Agreement NNX14AH55A)
+ at acronym{NCO} from 2014--2016.
+This support will allow us to implement support for Swath-like Data
+(@acronym{SLD}) and re-gridding.
+
+ at sp 1
+ at noindent
+Charlie Zender@*
+June, 2014@*
+Irvine, California@*
+ at end ignore
+
@html
<a name="smr"></a> <!-- http://nco.sf.net/nco.html#smr -->
@end html
@@ -1005,7 +1029,7 @@ following @acronym{UNIX} commands in the directory where the
@acronym{NCO} executables are installed.
@example
ln -s -f ncbo ncdiff # ncbo --op_typ='+'
-ln -s -f ncra ncecat # ncra --pseudonym='ncecat'
+ln -s -f ncra nces # ncra --pseudonym='nces'
ln -s -f ncra ncrcat # ncra --pseudonym='ncrcat'
ln -s -f ncbo ncadd # ncbo --op_typ='+'
ln -s -f ncbo ncsubtract # ncbo --op_typ='-'
@@ -1013,7 +1037,7 @@ ln -s -f ncbo ncmultiply # ncbo --op_typ='*'
ln -s -f ncbo ncdivide # ncbo --op_typ='/'
ln -s -f ncpdq ncpack # ncpdq
ln -s -f ncpdq ncunpack # ncpdq --unpack
-# NB: Cygwin executable (and link) names have an '.exe' suffix, e.g.,
+# NB: Windows/Cygwin executable/link names have '.exe' suffix, e.g.,
ln -s -f ncbo.exe ncdiff.exe
...
@end example
@@ -1905,11 +1929,13 @@ Initially the record dimension is @code{time}.
Our goal is to create a single file that contains joins all the
spatially adjacent regions into one single time-evolving dataset.
@example
+ at verbatim
for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
- ncpdq -a x,time x_$@{idx@}.nc foo_$@{idx@}.nc # Make x record dimension
+ ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
done
ncrcat foo_??.nc out.nc # Concatenate along x
ncpdq -a time,x out.nc out.nc # Revert to time as record dimension
+ at end verbatim
@end example
Note that @command{ncrcat} will not concatenate fixed-length variables,
@@ -2016,8 +2042,10 @@ more, typically) of input filenames to the multi-file operators is
to pass the filenames with the @acronym{UNIX} @dfn{standard input}
feature, aka @code{stdin}:
@example
+ at verbatim
# Pipe large numbers of filenames to stdin
-/bin/ls | grep $@{CASEID@}_'......'.nc | ncecat -o foo.nc
+/bin/ls | grep ${CASEID}_'......'.nc | ncecat -o foo.nc
+ at end verbatim
@end example
This method avoids all constraints on command line size imposed by
the operating system.
@@ -2059,8 +2087,10 @@ and to pipe the results to @command{xargs} which, in turn, passes the
matching filenames to an @acronym{NCO} multi-file operator, e.g.,
@command{ncecat}.
@example
+ at verbatim
# Use xargs to transfer filenames on the command line
-/bin/ls | grep $@{CASEID@}_'......'.nc | xargs -x ncecat -o foo.nc
+/bin/ls | grep ${CASEID}_'......'.nc | xargs -x ncecat -o foo.nc
+ at end verbatim
@end example
@cindex pipes
The single quotes protect the only sensitive parts of the extended
@@ -2098,12 +2128,14 @@ directory. If there are 999,999 netCDF files present, the links are
named @file{000001.nc} to @file{999999.nc}:
@cindex @code{-n @var{loop}}
@example
+ at verbatim
# Create enumerated symbolic links
/bin/ls | grep \.nc | perl -e \
-'$idx=1;while(<STDIN>)@{chop;symlink $_,sprintf("%06d.nc",$idx++);@}'
+'$idx=1;while(<STDIN>){chop;symlink $_,sprintf("%06d.nc",$idx++);}'
ncecat -n 999999,6,1 000001.nc foo.nc
# Remove symbolic links when finished
/bin/rm ??????.nc
+ at end verbatim
@end example
The @samp{-n @var{loop}} option tells the @acronym{NCO} operator to
automatically generate the filnames of the symbolic links.
@@ -2501,7 +2533,11 @@ Availability: All operators@*
@cindex L10N
@acronym{NCO} support for @dfn{internationalization} of textual input
and output (e.g., Warning messages) is nascent.
-We hope to produce foreign language string catalogues in 2004.
+We introduced the first foreign language string catalogues (French and
+Spanish) in 2004, yet did not activate these in distributions because
+the catalogues were nearly empty.
+We seek volunteers to populate our templates with translations for their
+favorite languages.
@c fxm: Work on this section
@html
@@ -2812,12 +2848,15 @@ The first method (explicitly specifying all filenames) works by brute
force.
The second method relies on the operating system shell to @dfn{glob}
(expand) the @dfn{regular expression} @code{8[56789].nc}.
-The shell passes valid filenames which match the expansion to
- at command{ncra}.
-The third method uses the @samp{-p @var{input-path}} argument to specify
+The shell then passes the valid filenames (those which match the
+regular expansion) to @command{ncra}.
+In this case @command{ncra} never knows that a regular expression was
+used, because the shell intercepts and expands and matches the regular
+expression before @command{ncra} is actually invoked.
+The third method uses the @samp{-p @var{input-path}} argument to specify
the directory where all the input files reside.
@acronym{NCO} prepends @var{input-path} (e.g.,
- at file{/data/usrname/model}) to all @var{input-files} (though not to
+ at file{/data/username/model}) to all @var{input-files} (though not to
@var{output-file}).
Thus, using @samp{-p}, the path to any number of input files need only
be specified once.
@@ -2826,8 +2865,13 @@ automatically generated if necessary.
The last method passes (with @samp{-n}) syntax concisely describing
the entire set of filenames
- at footnote{The @samp{-n} option is a backward compatible superset of the
- at code{NINTAP} option from the @acronym{NCAR} @acronym{CCM} Processor.}.
+ at footnote{The @samp{-n} option is a backward-compatible superset of the
+ at code{NINTAP} option from the @acronym{NCAR} @acronym{CCM} Processor.
+The @acronym{CCM} Processor was custom-written Fortran code maintained
+for many years by Lawrence Buja at @acronym{NCAR}, and phased-out in
+the late 1990s.
+ at acronym{NCO} stole some ideas, like @code{NINTAP}-functionality,
+from the @acronym{CCM} Processor capabilities.}.
@cindex multi-file operators
@cindex files, multiple
This option is only available with the @dfn{multi-file operators}:
@@ -2844,8 +2888,8 @@ For example, in the file @file{ccm3_h0001.nc}, we have
@var{alphanumeric_prefix} = @file{ccm3_h}, @var{numeric_suffix} =
@file{0001}, and @var{filetype} = @file{nc}.
- at acronym{NCO} is able to decode lists of such filenames encoded using the
- at samp{-n} option.
+ at acronym{NCO} decodes lists of such filenames encoded using the
+ at samp{-n} syntax.
The simpler (3-argument) @samp{-n} usage takes the form
@code{-n @var{file_number}, at var{digit_number}, at var{numeric_increment}}
where @var{file_number} is the number of files, @var{digit_number} is
@@ -2894,12 +2938,12 @@ The first example shows that three arguments to the @samp{-n} option
suffice to specify consecutive months (@code{06, 07, 08}) which do not
``wrap'' back to a minimum value.
The second example shows how to use the optional fourth and fifth
-elements of the @samp{-n} option to specify a wrap value to @acronym{NCO}.
-The fourth argument to @samp{-n}, if present, specifies the maximum
+elements of the @samp{-n} option to specify a wrap value.
+The fourth argument to @samp{-n}, when present, specifies the maximum
integer value of @var{numeric_suffix}.
-In this case the maximum value @w{is 12,} and will be formatted as
+In the example the maximum value @w{is 12,} and will be formatted as
@file{12} in the filename string.
-The fifth argument to @samp{-n}, if present, specifies the minimum
+The fifth argument to @samp{-n}, when present, specifies the minimum
integer value of @var{numeric_suffix}.
The default minimum filename suffix @w{is 1,} which is formatted as
@file{01} in this case.
@@ -3004,16 +3048,18 @@ particular access protocol.
@html
<a name="ftp"></a> <!-- http://nco.sf.net/nco.html#ftp -->
@end html
-To access a file via an anonymous @acronym{FTP} server, supply the
-remote file's @acronym{URL}.
+To access a file via an anonymous @acronym{FTP} server, simply supply
+the remote file's @acronym{URL}.
+Anonymous @acronym{FTP} usually requires no further credentials,
+e.g., no @file{.netrc} file is necessary.
@acronym{FTP} is an intrinsically insecure protocol because it transfers
-passwords in plain text format.
+passwords in plain text format.
Users should access sites using anonymous @acronym{FTP}, or better yet,
-secure @acronym{FTP} when possible.
+secure @acronym{FTP} (@acronym{SFTP}, see below) when possible.
Some @acronym{FTP} servers require a login/password combination for a
valid user account.
- at acronym{NCO} allows these transactions so long as the required
-information is stored in the @file{.netrc} file.
+ at acronym{NCO} allows transactions that require additional credentials
+so long as the required information is stored in the @file{.netrc} file.
Usually this information is the remote machine name, login, and
password, in plain text, separated by those very keywords, e.g.,
@example
@@ -3040,7 +3086,7 @@ specified with a homebrew syntax of the form
sftp://machine.domain.tld:/path/to/filename
@end example
Note the second colon following the top-level-domain, @code{tld}.
-This syntax is a hybrid between an @acronym{FTP URL} and a standard
+This syntax is a hybrid between an @acronym{FTP URL} and standard
remote file syntax.
@html
@@ -3298,7 +3344,7 @@ input and output file format:
one = 1
@end example
And, of course, @acronym{OPeNDAP}-enabled @acronym{NCO} clients continue
-to support other, orthogonal features such as UDUnits
+to support orthogonal features such as UDUnits
(@pxref{UDUnits Support}):
@example
% ncks -u -C -H -v wvl -d wvl,'0.4 micron','0.7 micron' \
@@ -3323,9 +3369,9 @@ http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/su
@cindex unpacking
All with one command!
The data in this particular input file also happen to be packed
-(@pxref{Methods and functions}), although this is completely transparent
-to the user since @acronym{NCO} automatically unpacks data before
-attempting arithmetic.
+(@pxref{Methods and functions}), although this complication is
+transparent to the user since @acronym{NCO} automatically unpacks data
+before attempting arithmetic.
@acronym{NCO} obtains remote files from the @acronym{OPeNDAP} server
(e.g., @file{www.cdc.noaa.gov}) rather than the local machine.
@@ -3871,13 +3917,9 @@ build time.
@cindex @code{--xcl}
@cindex @code{--unn}
@cindex @code{--union}
+ at cindex @code{--gxvx}
+ at cindex @code{--grp_xtr_var_xcl}
@cartouche
-Options @code{--unn}@*
-Availability: @command{ncbo}, @command{nces},
- at command{ncecat}, @command{ncflint}, @command{ncks}, @command{ncpdq},
- at command{ncra}, @command{ncrcat}, @command{ncwa}@*
-Short options: @*
-Long options: @samp{--unn} and @samp{--union}@*
Options @code{-g @var{grp}}@*
Availability: @command{ncbo}, @command{nces},
@command{ncecat}, @command{ncflint}, @command{ncks}, @command{ncpdq},
@@ -3890,6 +3932,16 @@ Availability: (@command{ncap2}), @command{ncbo}, @command{nces},
@command{ncra}, @command{ncrcat}, @command{ncwa}@*
Short options: @samp{-v}, @samp{-x}@*
Long options: @samp{--variable}, @samp{--exclude} or @samp{--xcl}@*
+Options @code{--unn}@*
+Availability: @command{ncbo}, @command{nces},
+ at command{ncecat}, @command{ncflint}, @command{ncks}, @command{ncpdq},
+ at command{ncra}, @command{ncrcat}, @command{ncwa}@*
+Short options: @*
+Long options: @samp{--unn} and @samp{--union}@*
+Options @code{--grp_xtr_var_xcl}@*
+Availability: @command{ncks}@*
+Short options: @*
+Long options: @samp{--gxvx} and @samp{--grp_xtr_var_xcl}@*
@end cartouche
Subsetting variables refers to explicitly specifying variables and
groups to be included or excluded from operator actions.
@@ -3926,6 +3978,25 @@ distinctions.
When learning this syntax it is helpful to keep in mind the similarity
between group hierarchies and directory structures.
+ at html
+<a name="gxvx"></a> <!-- http://nco.sf.net/nco.html#gxvx -->
+<a name="grp_xtr_var_xcl"></a> <!-- http://nco.sf.net/nco.html#grp_xtr_var_xcl -->
+ at end html
+As of @acronym{NCO} 4.4.4 (June, 2014), @command{ncks} (alone) supports
+an option to include specified groups yet exclude specified variables.
+The @samp{--grp_xtr_var_xcl} switch (with long option equivalent
+ at samp{--gxvx}) extracts all contents of groups given as arguments to
+ at samp{-g @var{grp}[, at dots{}]}, except for variables given as arguments
+to @samp{-v @var{var}[, at dots{}]}.
+Use this when one or a few variables in hierarchical files are not to be
+extracted, and all other variables are.
+This is useful when coercing netCDF4 files into netCDF3 files such as
+with converting, flattening, or dismembering files
+(see @ref{Flattening Groups}).
+ at example
+ncks --grp_xtr_var_xcl -g g1 -v v1 # Extract all of group g1 except v1
+ at end example
+
@cindex @command{mv}
@cindex @command{cp}
@cindex recursion
@@ -4170,22 +4241,24 @@ those groups, and file @file{in.nc} with variables @code{Q},
@code{Q01}-- at code{Q99}, @code{Q100}, @code{QAA}-- at code{QZZ},
@code{Q_H2O}, @code{X_H2O}, @code{Q_CO2}, @code{X_CO2}.
@example
+ at verbatim
ncks -v '.+' in.nc # All variables (default)
ncks -v 'Q.?' in.nc # Variables that contain Q
ncks -v '^Q.?' in.nc # Variables that start with Q
ncks -v '^Q+.?.' in.nc # Q, Q0--Q9, Q01--Q99, QAA--QZZ, etc.
ncks -v '^Q..' in.nc # Q01--Q99, QAA--QZZ, etc.
ncks -v '^Q[0-9][0-9]' in.nc # Q01--Q99, Q100
-ncks -v '^Q[[:digit:]]@{2@}' in.nc # Q01--Q99
+ncks -v '^Q[[:digit:]]{2}' in.nc # Q01--Q99
ncks -v 'H2O$' in.nc # Q_H2O, X_H2O
ncks -v 'H2O$|CO2$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
ncks -v '^Q[0-9][0-9]$' in.nc # Q01--Q99
ncks -v '^Q[0-6][0-9]|7[0-3]' in.nc # Q01--Q73, Q100
ncks -v '(Q[0-6][0-9]|7[0-3])$' in.nc # Q01--Q73
-ncks -v '^[a-z]_[a-z]@{3@}$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
+ncks -v '^[a-z]_[a-z]{3}$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
ncks -g 'g.' in_grp.nc # 10 Groups g0-g9
ncks -g 's.' in_grp.nc # 100 sub-groups g0/s0, g0/s1, ... g9/s9
ncks -g 'g.' -v 'v.' in_grp.nc # All variables 'v.' in groups 'g.'
+ at end verbatim
@end example
Beware---two of the most frequently used repetition pattern matching
operators, @samp{*} and @samp{?}, are also valid pattern matching
@@ -4267,12 +4340,15 @@ automatically specifying that @emph{all} coordinate variables in the
Thus @samp{-c} allows the user to select all the coordinate variables
without having to know their names.
@cindex @acronym{CF} conventions
-As of @acronym{NCO} version 3.9.6 (January, 2009)
-both @samp{-c} and @samp{-C} honor the @acronym{CF} @code{coordinates}
-convention described in @ref{CF Conventions}.
+As of @acronym{NCO} version 4.4.5 (July, 2014)
+both @samp{-c} and @samp{-C} honor the @acronym{CF} @code{ancillary_variables}
+convention described in @ref{CF Conventions}.
As of @acronym{NCO} version 4.0.8 (April, 2011)
both @samp{-c} and @samp{-C} honor the @acronym{CF} @code{bounds}
convention described in @ref{CF Conventions}.
+As of @acronym{NCO} version 3.9.6 (January, 2009)
+both @samp{-c} and @samp{-C} honor the @acronym{CF} @code{coordinates}
+convention described in @ref{CF Conventions}.
@html
<a name="gpe"></a> <!-- http://nco.sf.net/nco.html#gpe -->
@@ -4331,6 +4407,14 @@ Hence, @samp{-G :-1} is the same as @samp{-G @@1}.
This is simply a way of making the @var{lvl_nbr} argument
positive-definite.
+ at menu
+* Flattening Groups::
+* Moving Groups::
+* Dismembering Files::
+* Checking CF-compliance::
+ at end menu
+ at node Flattening Groups, Moving Groups, Group Path Editing, Group Path Editing
+ at subsection Deletion, Truncation, and Flattening of Groups
@html
<a name="flatten"></a> <!-- http://nco.sf.net/nco.html#flatten -->
<a name="delete"></a> <!-- http://nco.sf.net/nco.html#delete -->
@@ -4401,6 +4485,7 @@ groups and their placement in the output file as shown by the following
commands.
All commands below may be assumed to end with @samp{in.nc out.nc}.
@example
+ at verbatim
# Prepending paths without editing:
ncks # /g?/v? -> /g?/v?
ncks -v v1 # /g?/v1 -> /g?/v1
@@ -4433,7 +4518,7 @@ ncks -G g2: # /g?/v? -> /g2/v?
ncks -G g2: -g g1/g1 -v v1 # /g1/g1/v1 -> /g2/v1
# Truncate-mode: Truncate from and Append to path tail
# Syntax: -G [apn]:-lvl_nbr = # of levels to truncate
-# NB: -G [apn]:-lvl_nbr is equivalent to -G [apn]@@lvl_nbr
+# NB: -G [apn]:-lvl_nbr is equivalent to -G [apn]@lvl_nbr
ncks -G :-1 -g g1 -v v1 # /g1/v1 -> /v1
ncks -G :-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/v1
ncks -G :-2 -g g1/g2 -v v1 # /g1/g2/v1 -> /v1
@@ -4441,12 +4526,15 @@ ncks -G :-2 -g g1 -v v1 # /g1/v1 -> /v1
ncks -G g2:-1 -v v1 # /g?/v1 -> /g2/v1
ncks -G g2:-1 -g g1 -v v1 # /g1/v1 -> /g2/v1
ncks -G g1:-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/g1/v1
+ at end verbatim
@end example
@html
<a name="mv"></a> <!-- http://nco.sf.net/nco.html#mv -->
<a name="move"></a> <!-- http://nco.sf.net/nco.html#move -->
@end html
+ at node Moving Groups, Dismembering Files, Flattening Groups, Group Path Editing
+ at subsection Moving Groups
@cindex move groups
@cindex groups, moving
@cindex rename groups
@@ -4504,6 +4592,8 @@ all other groups (e.g., @code{ecmwf}, @code{giss}).
<a name="disaggregate"></a> <!-- http://nco.sf.net/nco.html#disaggregate -->
<a name="ncdismember"></a> <!-- http://nco.sf.net/nco.html#ncdismember -->
@end html
+ at node Dismembering Files, Checking CF-compliance, Moving Groups, Group Path Editing
+ at subsection Dismembering Files
@cindex disaggregate
@cindex dismember
@findex ncdismember
@@ -4620,6 +4710,8 @@ as @code{NC_STRING} and @code{NC_UBYTE}) to corresponding netCDF3
atomic types (@code{NC_CHAR} and @code{NC_SHORT}) when the output format
is netCDF3.
+ at node Checking CF-compliance, , Dismembering Files, Group Path Editing
+ at subsection Checking CF-compliance
@cindex @acronym{CF} compliance checker
@findex cfchecker
@findex ncdismember
@@ -4689,15 +4781,15 @@ of the procedure necessary to check @acronym{HDF} files for
@example
@verbatim
cat > ~/ncdismember.txt << 'EOF'
- Preparing an RPM-based OS to Test Hierarchical Files for CF-Compliance
+ Preparing an RPM-based OS to Test HDF & netCDF Files for CF-Compliance
By Charlie Zender, UCI & NASA Dataset Interoperability Working Group (DIWG)
Installation Summary:
-1. HDF4 [with netCDF support _disabled_]
+1. HDF4 [with internal netCDF support _disabled_]
2. HDF5
-3. netCDF version 4.3.1 (or later) [with HDF4 support _enabled_]
-4. NCO version 4.4.0 (or later)
+3. netCDF [with external HDF4 support _enabled_]
+4. NCO
5. numpy
6. netcdf4-python
7. python-lxml
@@ -4728,20 +4820,19 @@ cd hdf5-1.8.11
./configure --enable-shared --prefix=${H5DIR}
make && make check && make install
-# 3. netCDF version 4.3.1. Build in non-default manner with HDF4. No RPM.
+# 3. netCDF version 4.3.1 or later. Build in non-default manner with HDF4.
# Per http://www.unidata.ucar.edu/software/netcdf/docs/build_hdf4.html
# Earlier versions of netCDF may fail checking some HDF4 files
-wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.1.tar.gz
-tar xvzf netcdf-4.3.1.tar.gz
-cd netcdf-4.3.1
+wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz
+tar xvzf netcdf-4.3.2.tar.gz
+cd netcdf-4.3.2
CPPFLAGS="-I${H5DIR}/include -I${H4DIR}/include" \
LDFLAGS="-L${H5DIR}/lib -L${H4DIR}/lib" \
./configure --enable-hdf4 --enable-hdf4-file-tests
-make && make check && make installas
+make && make check && make install
-# 4. NCO version 4.4.4. No RPM for this version. Must install by hand.
-# Earlier versions of NCO are relatively useless for ncdismember
-cd ${DATA}/tmp
+# 4. NCO version 4.4.0 or later. Some RPMs available. Or install by hand.
+# Later versions of NCO have much better support for ncdismember
wget http://nco.sourceforge.net/src/nco-4.4.4.tar.gz .
tar xvzf nco-4.4.4.tar.gz
cd nco-4.4.4
@@ -4759,14 +4850,13 @@ sudo yum install python-lxml -y
# 8. CFunits-python. No RPM available. Must install by hand.
# http://code.google.com/p/cfunits-python/
-cd ${DATA}/tmp
wget http://cfunits-python.googlecode.com/files/cfunits-0.9.6.tar.gz .
+tar xvzf cfunits-0.9.6.tar.gz
cd cfunits-0.9.6
sudo python setup.py install
# 9. CFChecker. No RPM available. Must install by hand.
# https://bitbucket.org/mde_/cfchecker
-cd ${DATA}/tmp
wget https://bitbucket.org/mde_/cfchecker/downloads/CFchecker-1.5.15.tar.bz2 .
tar xvjf CFchecker-1.5.15.tar.bz2
cd CFchecker
@@ -5063,14 +5153,16 @@ concatenate the resulting files together:
@cindex Bourne Shell
@cindex C Shell
@example
+ at verbatim
for idx in 02 14 26 38 50; do # Bourne Shell
- ncks -d time,$@{idx@} 8501_8912.nc foo.$@{idx@}
+ ncks -d time,${idx} 8501_8912.nc foo.${idx}
done
foreach idx (02 14 26 38 50) # C Shell
- ncks -d time,$@{idx@} 8501_8912.nc foo.$@{idx@}
+ ncks -d time,${idx} 8501_8912.nc foo.${idx}
end
ncrcat foo.?? 8589_03.nc
rm foo.??
+ at end verbatim
@end example
With the @var{stride} option, @command{ncks} performs this hyperslab
extraction in one operation:
@@ -5216,13 +5308,15 @@ Traditionally, we would first compute the climatological monthly
mean for each month of summer.
Each of these is a 150-year mean, i.e.,
@example
+ at verbatim
# Step 1: Create climatological monthly files clm06.nc..clm08.nc
-for mth in @{6..8@}; do
+for mth in {6..8}; do
mm=`printf "%02d" $mth`
- ncra -O -F -d time,$@{mm@},,12 -n 150,4,1 1850.nc clm$@{mm@}.nc
+ ncra -O -F -d time,${mm},,12 -n 150,4,1 1850.nc clm${mm}.nc
done
# Step 2: Average climatological monthly files into summertime mean
ncra -O clm06 clm07.nc clm08.nc clm_JJA.nc
+ at end verbatim
@end example
@noindent
So far, nothing is unusual and this task can be performed by any
@@ -5573,7 +5667,7 @@ ranges.
This works on datasets that associate coordinate variables to
grid-mappings using the @acronym{CF}-convention (@pxref{CF Conventions})
@code{coordinates} and @code{standard_name} attributes described
- at uref{http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system, here}.
+ at uref{http://cfconventions.org/1.6.html#coordinate-system, here}.
Currently, @acronym{NCO} understands auxiliary coordinate variables
pointed to by the @code{standard_name} attributes for @var{latitude} and
@var{longitude}.
@@ -6269,30 +6363,33 @@ performance.
The user specifies the desired chunking policy with the @samp{-P} switch
(or its long option equivalents, @samp{--cnk_plc} and
@samp{--chunk_policy}) and its @var{cnk_plc} argument.
-Five chunking policies are currently implemented:@*
+As of August, 2014, six chunking policies are implemented:@*
@cindex @samp{all}
@cindex @samp{g2d}
@cindex @samp{g3d}
+ at cindex @samp{r1d}
@cindex @samp{xpl}
@cindex @samp{xst}
@cindex @samp{cnk_all}
@cindex @samp{cnk_g2d}
@cindex @samp{cnk_g3d}
+ at cindex @samp{cnk_r1d}
@cindex @samp{cnk_xpl}
@cindex @samp{cnk_xst}
@cindex @samp{plc_all}
@cindex @samp{plc_g2d}
@cindex @samp{plc_g3d}
+ at cindex @samp{plc_r1d}
@cindex @samp{plc_xpl}
@cindex @samp{plc_xst}
@table @dfn
- at item Chunk All Variables [@emph{default}]
+ at item Chunk All Variables
Definition: Chunk all variables possible.
For obvious reasons, scalar variables cannot be chunked.@*
Alternate invocation: @code{ncchunk}@*
@var{cnk_plc} key values: @samp{all}, @samp{cnk_all}, @samp{plc_all}@*
Mnemonic: All@*
- at item Chunk Variables with at least Two Dimensions
+ at item Chunk Variables with at least Two Dimensions [@emph{default}]
Definition: Chunk all variables possible with at least two dimensions@*
Alternate invocation: none@*
@var{cnk_plc} key values: @samp{g2d}, @samp{cnk_g2d}, @samp{plc_g2d}@*
@@ -6302,6 +6399,15 @@ Definition: Chunk all variables possible with at least three dimensions@*
Alternate invocation: none@*
@var{cnk_plc} key values: @samp{g3d}, @samp{cnk_g3d}, @samp{plc_g3d}@*
Mnemonic: @emph{G}reater than or equal to @emph{3} @emph{D}imensions@*
+ at item Chunk One-Dimensional Record Variables
+Definition: Chunk all 1-D record variables@*
+Alternate invocation: none@*
+Any specified (with @samp{--cnk_dmn}) record dimension chunksizes will
+be applied to 1-D record variables (and to no other variables).
+Other dimensions may be chunked with their own @samp{--cnk_dmn} options
+that will apply to all variables.
+ at var{cnk_plc} key values: @samp{r1d}, @samp{cnk_r1d}, @samp{plc_r1d}@*
+Mnemonic: @emph{R}ecord @emph{1}- at emph{D} variables@*
@item Chunk Variables Containing Explicitly Chunked Dimensions
Definition: Chunk all variables possible that contain at least one
dimension whose chunksize was explicitly set with the @samp{--cnk_dmn} option.
@@ -6437,6 +6543,14 @@ The option takes two comma-separated arguments,
chunksize, respectively.
The @samp{--cnk_dmn} option may be used as many times as necessary.
+The default behavior of chunking depends on several factors.
+When no chunking options are explicitly specified by the user, then
+output netCDF4 files are chunked with the default behavior of the
+netCDF4 library.
+When any chunking option @emph{except} @samp{cnk_plc} or @samp{cnk_map}
+is specified, then @samp{cnk_plc} and @samp{cnk_map} are set to
+ at samp{g2d} and @samp{rd1}, respectively.
+
@html
<a name="xmp_cnk"></a> <!-- http://nco.sf.net/nco.html#xmp_cnk -->
<a name="xmp_chunk"></a> <!-- http://nco.sf.net/nco.html#xmp_chunk -->
@@ -6476,6 +6590,24 @@ ncwa -O -4 -D 4 -a time --cnk_plc=g2d --cnk_map=rd1 --cnk_dmn lat,32 \
--cnk_dmn lon,128 dstmch90_clm_0112.nc ~/foo.nc
@end example
+ at html
+<a name="r1d"></a> <!-- http://nco.sf.net/nco.html#r1d -->
+ at end html
+Chunking policy @samp{r1d} changes the chunksize of 1-D record variables
+(and no other variables) to the specified (with @samp{--cnk_dmn})
+chunksize.
+Any specified record dimension chunksizes will be applied to 1-D
+record variables only.
+Other dimensions may be chunked with their own @samp{--cnk_dmn} options
+that will apply to all variables.
+For example,
+ at example
+ncks --cnk_plc=r1d --cnk_dmn=time,1000. in.nc out.nc
+ at end example
+This sets @code{time} chunks to 1000 only in 1-D record variables.
+Without the @samp{r1d} policy, @code{time} chunks would change in all
+variables.
+
@cindex record dimension
It is appropriate to conclude by informing users about an aspect of
chunking that may not be expected.
@@ -6802,16 +6934,18 @@ an arbitrary number (set to one hundred thousand) of files are all
symbolically linked to the same file.
Everything is on the local filesystem (not @acronym{DAP}).
@example
+ at verbatim
# Create symbolic links for benchmark
-cd $@{DATA@}/nco # Do all work here
-for idx in @{1..99999@}; do
- idx_fmt=`printf "%05d" $@{idx@}`
- /bin/ln -s $@{DATA@}/nco/LPRM-AMSR_E_L3_D_SOILM3_V002-20120512T111931Z_20020619.nc \
- $@{DATA@}/nco/$@{idx_fmt@}.nc
+cd ${DATA}/nco # Do all work here
+for idx in {1..99999}; do
+ idx_fmt=`printf "%05d" ${idx}`
+ /bin/ln -s ${DATA}/nco/LPRM-AMSR_E_L3_D_SOILM3_V002-20120512T111931Z_20020619.nc \
+ ${DATA}/nco/${idx_fmt}.nc
done
# Benchmark time to ncecat one hundred thousand files
time ncecat --create_ram -O -u time -v ts -d Latitude,40.0 \
- -d Longitude,-105.0 -p $@{DATA@}/nco -n 99999,5,1 00001.nc ~/foo.nc
+ -d Longitude,-105.0 -p ${DATA}/nco -n 99999,5,1 00001.nc ~/foo.nc
+ at end verbatim
@end example
Run normally on a laptop in 201303, this completes in @w{21 seconds}.
The @samp{--create_ram} reduces the elapsed time to @w{9 seconds}.
@@ -7570,7 +7704,7 @@ This is why type conversion is limited to the operators @command{ncap2},
@command{ncwa}.
@item The arithmetic operation could benefit from type conversion.
Operations that could benefit include averaging, summation, or any
-"hard" arithmetic that could overflow or underflow.
+``hard'' arithmetic that could overflow or underflow.
Larger representable sums help avoid overflow, and more precision
helps to avoid underflow.
Type conversion does not benefit searching for minima and maxima
@@ -7641,8 +7775,8 @@ These functions round @var{x} to the nearest integer, halfway cases away
from zero.
The problem with @code{lround()} is that it always rounds real values
ending in @code{.5} away from zero.
-This rounds, for example, @code{1.5d} and @code{2.5d} to @code{1s}
-and @code{2s}, respectively.
+This rounds, for example, @code{1.5d} and @code{2.5d} to @code{2s}
+and @code{3s}, respectively.
@findex @code{lrint()}.
@cindex @acronym{IEEE}
@@ -7688,18 +7822,18 @@ More, err, precisely, the @acronym{IEEE} single-precision representation
gives from @w{6 to 9} significant decimal digits precision
@footnote{According to Wikipedia's summary of @acronym{IEEE} standard
754, ``If a decimal string with at most 6 significant digits is
-converted to IEEE 754 single-precision and then converted back to the
+converted to @acronym{IEEE} 754 single-precision and then converted back to the
same number of significant decimal, then the final string should match
-the original; and if an IEEE 754 single-precision is converted to a
+the original; and if an @acronym{IEEE} 754 single-precision is converted to a
decimal string with at least 9 significant decimal and then converted
back to single, then the final number must match the original''.}.
And the @acronym{IEEE} double-precision representation
gives from @w{15 to 17} significant decimal digits precision
@footnote{According to Wikipedia's summary of @acronym{IEEE} standard
754, ``If a decimal string with at most 15 significant digits is
-converted to IEEE 754 double-precision representation and then converted
+converted to @acronym{IEEE} 754 double-precision representation and then converted
back to a string with the same number of significant digits, then the
-final string should match the original; and if an IEEE 754 double
+final string should match the original; and if an @acronym{IEEE} 754 double
precision is converted to a decimal string with at least 17 significant
digits and then converted back to double, then the final number must
match the original''.}.
@@ -7815,9 +7949,9 @@ seven significant figures for single precision floats (@code{tpt_flt}),
and sixteen significant figures for double precision (@code{tpt_dbl}).
The input precision determines the answer precision.
-IEEE arithmetic guarantees that two methods will produce bit-for-bit
-identical answers only if they compute the same operations in the same
-order.
+ at acronym{IEEE} arithmetic guarantees that two methods will produce
+bit-for-bit identical answers only if they compute the same operations
+in the same order.
Bit-for-bit identical answers may also occur by happenstance when
rounding errors exactly compensate one another.
This is demonstrated by repeating the example above with the
@@ -8274,8 +8408,8 @@ Nevertheless, we refer to all such metadata collectively as @acronym{CF}
metadata.
Skip this section if you never work with @acronym{CF} metadata.
-The @acronym{CF} netCDF conventions are described
- at uref{http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system, here}.
+The latest @acronym{CF} netCDF conventions are described
+ at uref{http://cfconventions.org/1.6.html, here}.
Most @acronym{CF} netCDF conventions are transparent to @acronym{NCO}
@footnote{
The exception is appending/altering the attributes @code{x_op},
@@ -8371,7 +8505,7 @@ or alter the @code{Conventions} attribute.
As of @acronym{NCO} version 4.0.8 (April, 2011), @acronym{NCO}
supports the @acronym{CF} @code{bounds} convention for cell boundaries
described
- at uref{http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#cell-boundaries, here}.
+ at uref{http://cfconventions.org/1.6.html#cell-boundaries, here}.
This convention allows coordinate variables (including multidimensional
coordinates) to describe the boundaries of their cells.
This is done by naming the variable which contains the bounds in
@@ -8381,6 +8515,28 @@ NCO-generated subsets of @acronym{CF}-compliant files with @code{bounds}
attributes will include the coordinates specified by the @code{bounds}
attribute, if any.
Hence the subsets will themselves be @acronym{CF}-compliant.
+Bounds are subject to the user-specified override switches
+(including @samp{-c} and @samp{-C}) described in
+ at ref{Subsetting Coordinate Variables}.
+
+ at html
+<a name="cnv_CF_ncl"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_ncl -->
+<a name="ncl"></a> <!-- http://nco.sf.net/nco.html#ncl -->
+ at end html
+ at cindex @code{ancillary_variables}
+ at cindex ancillary variables convention
+As of @acronym{NCO} version 4.4.5 (July, 2014), @acronym{NCO}
+supports the @acronym{CF} @code{ancillary_variables} convention for
+described
+ at uref{http://cfconventions.org/1.6.html#ancillary-data, here}.
+This convention allows ancillary variables to be associated with one or
+more primary variables.
+ at acronym{NCO} attaches any such variables to the extraction list along
+with the primary variable and its usual (one-dimensional) coordinates,
+if any.
+Ancillary variables are subject to the user-specified override switches
+(including @samp{-c} and @samp{-C}) described in
+ at ref{Subsetting Coordinate Variables}.
@html
<a name="cnv_CF_crd"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_crd -->
@@ -8398,14 +8554,15 @@ Hence the subsets will themselves be @acronym{CF}-compliant.
@cindex @code{--crd}
As of @acronym{NCO} version 3.9.6 (January, 2009), @acronym{NCO}
supports the @acronym{CF} @code{coordinates} convention described
- at uref{http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system, here}.
+ at uref{http://cfconventions.org/1.6.html#coordinate-system, here}.
This convention allows variables to specify additional coordinates
(including multidimensional coordinates) in a space-separated string
attribute named @code{coordinates}.
-NCO attaches any such coordinates to the extraction list along with
-variable and its usual (one-dimensional) coordinates, if any.
-These auxiliary coordinates are subject to the user-specified overrides
-described in @ref{Subsetting Coordinate Variables}.
+ at acronym{NCO} attaches any such coordinates to the extraction list along
+with variable and its usual (one-dimensional) coordinates, if any.
+These auxiliary coordinates are subject to the user-specified override
+switches (including @samp{-c} and @samp{-C}) described in
+ at ref{Subsetting Coordinate Variables}.
@html
<a name="cnv_CF_cll_mth"></a> <!-- http://nco.sf.net/nco.html#cnv_CF_cll_mth -->
@@ -8421,7 +8578,7 @@ described in @ref{Subsetting Coordinate Variables}.
@cindex cell methods convention
As of @acronym{NCO} version 4.4.2 (February, 2014), @acronym{NCO}
supports some of the @acronym{CF} @code{cell_methods}
- at uref{http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.7-draft1/cf-conventions.html#cell-methods, convention}
+ at uref{http://cfconventions.org/1.6.html#cell-methods, convention}
to describe the analysis procedures that have been applied to data.
The convention creates (or appends to an existing) @code{cell_methods}
attribute a space-separated list of couplets of the form @var{dmn: op}
@@ -8575,7 +8732,6 @@ described in any detail in the sections below.
@cindex arithmetic processor
@findex ncap
@findex ncap2
-
@cartouche
@command{ncap2} understands a relatively full-featured
language of operations, including loops, conditionals, arrays,
@@ -8808,6 +8964,7 @@ to precision and rank.@*
Examples:
@example
+ at verbatim
dimensions: time=10, lat=2, lon=4
Suppose we have the two variables:
@@ -8833,11 +8990,12 @@ PZ0 =
Once the expression is evaluated then PZ will be of type double;
Consider now
- start=four-att_var@@double_att; // start =-69 and is of type intger;
+ start=four-att_var at double_att; // start =-69 and is of type intger;
four_pow=four^3.0f // four_pow=64 and is of type float
three_nw=three_dmn_var_sht*1.0f; // type is now float
- start@@n1=att_var@@short_att*att_var@@int_att;
- // start@@n1=5329 and is type int
+ start at n1=att_var at short_att*att_var at int_att;
+ // start at n1=5329 and is type int
+ at end verbatim
@end example
@noindent @strong{Binary Operators} @*
@@ -8911,9 +9069,11 @@ returned else exp3 is returned.
Example:
@example
+ at verbatim
weight_avg=weight.avg();
-weight_avg@@units= (weight_avg == 1 ? "kilo" : "kilos");
+weight_avg at units= (weight_avg == 1 ? "kilo" : "kilos");
PS_nw=PS-(PS.min() > 100000 ? 100000 : 0);
+ at end verbatim
@end example
@html
@@ -9153,8 +9313,9 @@ The number of hyperslab arguments MUST equal the variable's rank.
A simple 1D example:
@example
+ at verbatim
($time.size=10)
-od[$time]=@{20,22,24,26,28,30,32,34,36,38@};
+od[$time]={20,22,24,26,28,30,32,34,36,38};
od(7); // 34
od(7:); // 34,36,38
@@ -9162,13 +9323,15 @@ od(:7); // 20,22,24,26,28,30,32,34
od(::4); // 20,28,36
od(1:6:2) // 22,26,30
od(:) // 20,22,24,26,28,30,32,34,36,38
+ at end verbatim
@end example
A more complex three dimensional example:
@example
+ at verbatim
($lat.size=2,$lon.size=4)
th[$time,$lat,$lon]=
- @{1, 2, 3, 4, 5, 6, 7, 8,
+ {1, 2, 3, 4, 5, 6, 7, 8,
9,10,11,12,13,14,15,16,
17,18,19,20,21,22,23,24,
-99,-99,-99,-99,-99,-99,-99,-99,
@@ -9177,12 +9340,13 @@ th[$time,$lat,$lon]=
49,50,51,52,53,54,55,56,
-99,58,59,60,61,62,63,64,
65,66,67,68,69,70,71,72,
- -99,74,75,76,77,78,79,-99 @};
+ -99,74,75,76,77,78,79,-99 };
th(1,1,3); // 16
th(2,0,:); // 17, 18, 19, 20
th(:,1,3); // 8, 16, 24, -99, 40, 48, 56, 64, 72, -99
th(::5,:,0:3:2); // 1, 3, 5, 7, 41, 43, 45, 47
+ at end verbatim
@end example
If hyperslab arguments collapse to a single value (a cross-section has
@@ -9240,8 +9404,10 @@ Use the @code{reverse()} method to reverse a dimension's elements in a
variable with at least one dimension.
This is equivalent to a negative stride, e.g.,
@example
-th_rv=th(1 ,:,:).reverse($lon); // @{12,11,10,9 @}, @{16,15,14,13@}
-od_rv=od.reverse($time); // @{38,36,34,32,30,28,26,24,22,20@}
+ at verbatim
+th_rv=th(1 ,:,:).reverse($lon); // {12,11,10,9 }, {16,15,14,13}
+od_rv=od.reverse($time); // {38,36,34,32,30,28,26,24,22,20}
+ at end verbatim
@end example
@noindent @strong{Permute method}p@*
@@ -9279,22 +9445,26 @@ three_dmn_var_prm=
@noindent Attributes are referred to by @emph{var_nm@@att_nm} @*
All the following are valid statements:
@example
-global@@text="Test Attributes"; /* Assign a global variable attribute */
+ at verbatim
+global at text="Test Attributes"; /* Assign a global variable attribute */
a1[$time]=time*20;
-a1@@long_name="Kelvin";
-a1@@min=a1.min();
-a1@@max=a1.max();
-a1@@min++;
---a1@@max; q
-a1(0)=a1@@min;
-a1($time.size-1)=a1@@max;
+a1 at long_name="Kelvin";
+a1 at min=a1.min();
+a1 at max=a1.max();
+a1 at min++;
+--a1 at max; q
+a1(0)=a1 at min;
+a1($time.size-1)=a1 at max;
+ at end verbatim
@end example
A @emph{value list} can be used on the RHS of an assign...
@cindex value list
@example
-a1@@trip1=@{1,2,3@} ;
-a1@@triplet=@{a1@@min,(a1@@min+a1@@max)/2,a1@@max@};
+ at verbatim
+a1 at trip1={1,2,3} ;
+a1 at triplet={a1 at min,(a1 at min+a1@max)/2,a1 at max};
+ at end verbatim
@end example
The netCDF specification allows all attribute types to have a size
greater than one.
@@ -9312,8 +9482,10 @@ double a1(time) ;
The @code{size()} method can be used with attributes.
For example, to save an attribute text string in a variable,
@example
-defdim("sng_len", a1@@long_name.size());
-sng_arr[$sng_len]=a1@@long_name; // sng_arr now contains "Kelvin"
+ at verbatim
+defdim("sng_len", a1 at long_name.size());
+sng_arr[$sng_len]=a1 at long_name; // sng_arr now contains "Kelvin"
+ at end verbatim
@end example
Attributes defined in a script are stored in memory and are written to Output after script completion.
To stop the attribute being written use the ram_delete() method or use a bogus variable name.
@@ -9336,7 +9508,9 @@ th_min=1.0 + 2*three_dmn_var_dbl.min($time);
If the attribute name contains non-regular characters use ID quoting. See @pxref{ID Quoting}
@example
-'b..m1@@c--lost'=23;
+ at verbatim
+'b..m1 at c--lost'=23;
+ at end verbatim
@end example
@html
@@ -9351,11 +9525,13 @@ To use the new netCDF4 types @acronym{NCO} must be compiled/linked to
the netCDF4 library and the output file must be @acronym{HDF5}.
@example
+ at verbatim
n1[$time]=1UL; // n1 will now by type @code{NC_UINT}
n2[$lon]=4b; // n2 will be of type @code{NC_BYTE}
n3[$lat]=5ull; // n3 will be of type @code{NC_UINT64}
-n3@@a1=6.0d; // attribute will be type @code{NC_DOUBLE}
-n3@@a2=-666L; // attribute will be type @code{NC_INT}
+n3 at a1=6.0d; // attribute will be type @code{NC_DOUBLE}
+n3 at a2=-666L; // attribute will be type @code{NC_INT}
+ at end verbatim
@end example
A floating point number without a postfix will default to
@@ -9363,13 +9539,15 @@ A floating point number without a postfix will default to
An integer without a postfix will default to type @code{NC_INT}.
There is no postfix for characters, use a quoted string instead.
@example
+ at verbatim
n4[$rlev]=0.1 // n4 will be of type @code{NC_DOUBLE}
n5[$lon_grd]=2.0 // n5 will be of type @code{NC_DOUBLE}
n6[$gds_crd]=2e3; // n6 will be of type @code{NC_DOUBLE}
n7[$gds_crd]=2e3f; // n7 will be of type @code{NC_FLOAT}
-n6@@a1=41; // attribute will be type @code{NC_INT}
-n6@@a2=-21; // attribute will be type @code{NC_INT}
-n6@@units="kelvin" // attribute will be type @code{NC_CHAR}
+n6 at a1=41; // attribute will be type @code{NC_INT}
+n6 at a2=-21; // attribute will be type @code{NC_INT}
+n6 at units="kelvin" // attribute will be type @code{NC_CHAR}
+ at end verbatim
@end example
@table @asis
@@ -9409,6 +9587,7 @@ The syntax of the if statement is similar to its C counterpart.
The @emph{Conditional Operator (ternary operator)} has also been
implemented.
@example
+ at verbatim
if(exp1)
stmt1;
else if(exp2)
@@ -9417,17 +9596,18 @@ else
stmt3;
# Can use code blocks as well:
-if(exp1)@{
+if(exp1){
stmt1;
stmt1a;
stmt1b;
-@} else if(exp2)
+}else if(exp2)
stmt2;
-else @{
+else{
stmt3;
stmt3a;
stmt3b;
-@}
+}
+ at end verbatim
@end example
@comment Truth
@@ -9440,34 +9620,36 @@ OR (@code{||}) and AND (@code{&&}) operators.
The whole expression is evaluated regardless if one of the AND/OR
operands are True/False.
@example
+ at verbatim
# Simple example
if(time>0)
print("All values of time are greater than zero\n");
else if( time<0)
print("All values of time are less than zero\n");
-else @{
+else {
time_max=time.max();
time_min=time.min();
print("min value of time=");print(time_min,"%f");
print("max value of time=");print(time_max,"%f");
-@}
+}
# Example from ddra.nco
-if(fl_typ==fl_typ_gcm)@{
+if(fl_typ==fl_typ_gcm){
var_nbr_apx=32;
lmn_nbr=1.0*var_nbr_apx*varsz_gcm_4D; /* [nbr] Variable size */
- if(nco_op_typ==nco_op_typ_avg)@{
+ if(nco_op_typ==nco_op_typ_avg){
lmn_nbr_avg=1.0*var_nbr_apx*varsz_gcm_4D; // Block size
lmn_nbr_wgt=dmnsz_gcm_lat; /* [nbr] Weight size */
- @} // !nco_op_typ_avg
-@}else if(fl_typ==fl_typ_stl)@{
+ } // !nco_op_typ_avg
+}else if(fl_typ==fl_typ_stl){
var_nbr_apx=8;
lmn_nbr=1.0*var_nbr_apx*varsz_stl_2D; /* [nbr] Variable size */
- if(nco_op_typ==nco_op_typ_avg)@{
+ if(nco_op_typ==nco_op_typ_avg){
lmn_nbr_avg=1.0*var_nbr_apx*varsz_stl_2D; // Block size
lmn_nbr_wgt=dmnsz_stl_lat; /* [nbr] Weight size */
- @} // !nco_op_typ_avg
-@} // !fl_typ
+ } // !nco_op_typ_avg
+} // !fl_typ
+ at end verbatim
@end example
@noindent @strong{Conditional Operator @*}
@@ -9498,6 +9680,7 @@ will be saved and can be printed), and then print the variable.
@noindent examples
@example
+ at verbatim
print(lon);
lon[0]=0
lon[1]=90
@@ -9507,11 +9690,12 @@ lon[3]=270
print(lon_2D_rrg,"%3.2f,");
0.00,0.00,180.00,0.00,180.00,0.00,180.00,0.00,
-print(mss_val_fst@@_FillValue);
-mss_val_fst@@_FillValue, size = 1 NC_FLOAT, value = -999
+print(mss_val_fst at _FillValue);
+mss_val_fst at _FillValue, size = 1 NC_FLOAT, value = -999
print("This function \t is monotonic\n");
This function is monotonic
+ at end verbatim
@end example
@html
@@ -9589,13 +9773,14 @@ They only work on variables in Output.
If the variable has no missing value then an error is returned.
@item delete_miss()
@cindex @code{delete_miss()}
- Deletes the missing value associated with a variable.
+ Delete the missing value associated with a variable.
@item number_miss()
@cindex @code{number_miss()}
- Counts the number of missing values a variable contains.
+ Count the number of missing values a variable contains.
@end table
@example
+ at verbatim
th=three_dmn_var_dbl;
th.change_miss(-1e10d);
/* Set values less than 0 or greater than 50 to missing value */
@@ -9613,10 +9798,11 @@ elsewhere
// Print missing value and variable summary
mss_val_nbr=three_dmn_var_dbl.number_miss();
-print(three_dmn_var_dbl@@_FillValue);
+print(three_dmn_var_dbl at _FillValue);
print("Number of missing values in three_dmn_var_dbl: ");
print(mss_val_nbr,"%d");
print(three_dmn_var_dbl);
+ at end verbatim
@end example
@html
@@ -9853,6 +10039,7 @@ A @code{where()} combines the definition and application of a mask all in one go
The full syntax of a @code{where()} statement is as follows:
@example
+ at verbatim
// Single assign (the 'elsewhere' block is optional)
where(mask)
var1=expr1;
@@ -9860,16 +10047,17 @@ elsewhere
var1=expr2;
// Multiple assigns
-where(mask)@{
+where(mask){
var1=expr1;
var2=expr2;
...
-@}elsewhere@{
+}elsewhere{
var1=expr3
var2=expr4
var3=expr5;
...
-@}
+}
+ at end verbatim
@end example
@itemize @bullet
@@ -9909,24 +10097,92 @@ to set its values less than 8 or greater than 80 @w{to 0}:
where(RDM < 8 || RDM > 80) RDM=0;
@end example
+ at html
+<a name="WRF"></a> <!-- http://nco.sf.net/nco.html#WRF -->
+<a name="SLD"></a> <!-- http://nco.sf.net/nco.html#SLD -->
+<a name="wrf"></a> <!-- http://nco.sf.net/nco.html#wrf -->
+<a name="sld"></a> <!-- http://nco.sf.net/nco.html#sld -->
+ at end html
+ at cindex Weather and Research Forecast (@acronym{WRF}) Model
+ at cindex Swath-like Data (@acronym{SLD})
+ at cindex @acronym{WRF} (Weather and Research Forecast Model)
+ at cindex @acronym{SLD} (Swath-like Data)
Consider irregularly gridded data, described using @w{rank 2} coordinates:
@code{double lat(south_north,east_west)},
@code{double lon(south_north,east_west)},
@code{double temperature(south_north,east_west)}.
+This type of structure is often found in regional weather/climate model
+(such as @acronym{WRF}) output, and in satellite swath data.
+For this reason we call it ``Swath-like Data'', or @acronym{SLD}.
To find the average temperature in a region bounded by
[@var{lat_min}, at var{lat_max}] and [@var{lon_min}, at var{lon_max}]:
@example
+ at verbatim
temperature_msk[$south_north,$east_west]=0.0;
-where(lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max)
+where((lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max))
temperature_msk=temperature;
elsewhere
- temperature_msk=temperature@@_FillValue;
+ temperature_msk=temperature at _FillValue;
temp_avg=temperature_msk.avg();
temp_max=temperature.max();
+ at end verbatim
@end example
@html
+<a name="NARR"></a> <!-- http://nco.sf.net/nco.html#NARR -->
+<a name="narr"></a> <!-- http://nco.sf.net/nco.html#narr -->
+ at end html
+ at cindex @acronym{NARR} (North American Regional Reanalysis)a
+ at cindex North American Regional Reanalysis (@acronym{NARR})
+For North American Regional Reanalysis (@acronym{NARR}) data
+(example
+ at uref{http://dust.ess.uci.edu/diwg/narr_uwnd.199605.nc, dataset})
+the procedure looks like this
+ at example
+ at verbatim
+ncap2 -O -v -S ~/narr.nco ${DATA}/hdf/narr_uwnd.199605.nc ~/foo.nc
+ at end verbatim
+ at end example
+where @file{narr.nco} is an @command{ncap2} script like this:
+ at example
+ at verbatim
+/* North American Regional Reanalysis (NARR) Statistics
+ NARR stores grids with 2-D latitude and longitude, aka Swath-like Data (SLD)
+ Here we work with three variables:
+ lat(y,x), lon(y,x), and uwnd(time,level,y,x);
+ To study sub-regions of SLD, we use masking techniques:
+ 1. Define mask as zero times variable to be masked
+ Then mask automatically inherits variable attributes
+ And average below will inherit mask attributes
+ 2. Optionally, create mask as RAM variable (as below with asterisk *)
+ NCO does not write RAM variable to output
+ Masks are often unwanted, and can be big, so this speeds execution
+ 3. Example could be extended to preserve mean lat and lon of sub-region
+ Follow uwnd example to do this: lat_msk=0.0*lat ... lat_avg=lat.avg($y,$x) */
+*uwnd_msk=0.0*uwnd;
+where((lat >= 35.6 && lat <= 37.0) && (lon >= -100.5 && lon <= -99.0))
+ uwnd_msk=uwnd;
+elsewhere
+ uwnd_msk=uwnd at _FillValue;
+
+// Average only over horizontal dimensions x and y (preserve level and time)
+uwnd_avg=uwnd_msk.avg($y,$x);
+ at end verbatim
+ at end example
+Stripped of comments and formatting, this example is a three-statement
+script executed by a one-line command.
+ at acronym{NCO} needs only this meagre input to unpack and copy the input
+data and attributes, compute the statistics, and then define and write
+the output file.
+Unless the comments pointed out that wind variable (@code{uwnd}) was
+four-dimensional and the latitude/longitude grid variables were both
+two-dimensional, there would be no way to tell.
+This shows how @acronym{NCO} hides from the user the complexity of
+analyzing multi-dimensional @acronym{SLD}.
+We plan to extend such @acronym{SLD} features to more operators soon.
+
+ at html
<a name="ncap_lop"></a> <!-- http://nco.sf.net/nco.html#ncap_lop -->
@end html
@node Loops, Include files, Where statement, ncap2 netCDF Arithmetic Processor
@@ -9940,6 +10196,7 @@ To break out of a loop use the @command{break} command.
To iterate to the next cycle use the @command{continue} command.
@example
+ at verbatim
// Set elements in variable double temp(time,lat)
// If element < 0 set to 0, if element > 100 set to 100
*sz_idx=$time.size;
@@ -9964,13 +10221,14 @@ if(idx == sz) print("lat co-ordinate is monotonic\n");
*sz=$lat_nw.size;
*sum=0.0;
-while(idx<sz)@{
+while(idx<sz){
if(lat(idx)%2) sum+=lat(idx);
idx++;
-@}
+}
ram_write(sum);
print("Total of odd elements ");print(sum);print("\n");
+ at end verbatim
@end example
@html
@@ -10048,17 +10306,19 @@ de-sorting map @var{dsr_map} which is inverse map of the input map
This gives the user access to both the forward and inverse sorting maps
which can be useful in special situations.
@example
-a1[$time]=@{10,2,3,4,6,5,7,3,4,1@};
+ at verbatim
+a1[$time]={10,2,3,4,6,5,7,3,4,1};
a1_sort=sort(a1);
print(a1_sort);
// 1, 2, 3, 3, 4, 4, 5, 6, 7, 10;
-a2[$lon]=@{2,1,4,3@};
+a2[$lon]={2,1,4,3};
a2_sort=sort(a2,&a2_map);
print(a2);
// 1, 2, 3, 4
print(a2_map);
// 1, 0, 3, 2;
+ at end verbatim
@end example
If the map variable does not exist prior to the @command{sort()} call,
@@ -10068,15 +10328,16 @@ If the map variable already exists, then the only restriction is that it
be of at least the same size as the input variable.
To apply a map use @code{remap(var_in,srt_map)}.
@example
+ at verbatim
defdim("nlat",5);
-a3[$lon]=@{2,5,3,7@};
-a4[$nlat,$lon]=@{
+a3[$lon]={2,5,3,7};
+a4[$nlat,$lon]={
1, 2, 3, 4,
5, 6, 7, 8,
9,10,11,12,
13,14,15,16,
- 17,18,19,20@};
+ 17,18,19,20};
a3_sort=sort(a3,&a3_map);
print(a3_map);
@@ -10090,7 +10351,7 @@ print(a4_sort);
// 13,15,14,16,
// 17,19,18,20;
-a3_map2[$nlat]=@{4,3,0,2,1@};
+a3_map2[$nlat]={4,3,0,2,1};
a4_sort2=remap(a4,a3_map2);
print(a4_sort2);
@@ -10098,6 +10359,7 @@ print(a4_sort2);
// 8, 10, 9,7, 6,
// 13,15,14,12,11,
// 18,20,19,17,16
+ at end verbatim
@end example
As in the above example you may create your own sort map.
To sort in descending order, apply the @code{reverse()} method after the
@@ -10389,10 +10651,6 @@ ncap2 -S ncap2.in in.nc out.nc
@end verbatim
@end example
- at html
-<a name="wrf"></a> <!-- http://nco.sf.net/nco.html#wrf -->
-<a name="WRF"></a> <!-- http://nco.sf.net/nco.html#WRF -->
- at end html
@ignore
http://foehn.colorado.edu/wrfout_to_cf/wrfout_to_cf.ncl
ncl 'file_in="wrfout.nc"' 'file_out="wrfpost.nc"' wrfout_to_cf.ncl
@@ -10405,7 +10663,7 @@ one must use global metadata to determine the grid staggering and
offsets to translate @code{XLAT} and @code{XLONG} into real latitudes,
longitudes, and missing points.
The @acronym{WRF} grid documentation should describe this.
-For @acronym{WRF} files creating regional masks looks like
+For @acronym{WRF} files creating regional masks looks, in general, like
@example
mask_var = (XLAT >= lat_min && XLAT <= lat_max) && (XLONG >= lon_min && XLONG <= lon_max);
@end example
@@ -10469,33 +10727,37 @@ After calculations @code{var_out} is converted to the input type of
Suppose the first part of an @command{ncap2} script is
@example
+ at verbatim
defdim("X",4);
defdim("Y",5);
// Temperature
T_in[$X,$Y]=
- @{100, 200, 300, 400, 500,
+ {100, 200, 300, 400, 500,
101, 202, 303, 404, 505,
102, 204, 306, 408, 510,
- 103, 206, 309, 412, 515.0 @};
+ 103, 206, 309, 412, 515.0 };
// Coordinate variables
-x_in[$X]=@{0.0,1.0,2.0,3.01@};
-y_in[$Y]=@{1.0,2.0,3.0,4.0,5@};
+x_in[$X]={0.0,1.0,2.0,3.01};
+y_in[$Y]={1.0,2.0,3.0,4.0,5};
+ at end verbatim
@end example
Now we interpolate with the following variables:
@example
+ at verbatim
defdim("Xn",3);
defdim("Yn",4);
T_out[$Xn,$Yn]=0.0;
-x_out[$Xn]=@{0.0,0.02,3.01@};
-y_out[$Yn]=@{1.1,2.0,3,4@};
+x_out[$Xn]={0.0,0.02,3.01};
+y_out[$Yn]={1.1,2.0,3,4};
var_out=bilinear_interp(T_in,T_out,x_out,y_out,x_in,y_in);
print(var_out);
// 110, 200, 300, 400,
// 110.022, 200.04, 300.06, 400.08,
// 113.3, 206, 309, 412 ;
+ at end verbatim
@end example
It is possible to interpolate a single point:
@@ -10520,27 +10782,28 @@ typically these are in the range (-90,90).
This @command{ncap2} script illustrates both wrapping and extrapolation
of end points:
@example
+ at verbatim
defdim("lat_in",6);
defdim("lon_in",5);
// Coordinate input vars
-lat_in[$lat_in]=@{-80,-40,0,30,60.0,85.0@};
-lon_in[$lon_in]=@{30, 110, 190, 270, 350.0@};
+lat_in[$lat_in]={-80,-40,0,30,60.0,85.0};
+lon_in[$lon_in]={30, 110, 190, 270, 350.0};
T_in[$lat_in,$lon_in]=
- @{10,40,50,30,15,
+ {10,40,50,30,15,
12,43,52,31,16,
14,46,54,32,17,
16,49,56,33,18,
18,52,58,34,19,
- 20,55,60,35,20.0 @};
+ 20,55,60,35,20.0 };
defdim("lat_out",4);
defdim("lon_out",3);
// Coordinate variables
-lat_out[$lat_out]=@{-90,0,70,88.0@};
-lon_out[$lon_out]=@{0,190,355.0@};
+lat_out[$lat_out]={-90,0,70,88.0};
+lon_out[$lon_out]={0,190,355.0};
T_out[$lat_out,$lon_out]=0.0;
@@ -10550,6 +10813,7 @@ print(T_out);
// 16.25, 54, 16.625,
// 19.25, 58.8, 19.325,
// 20.15, 60.24, 20.135 ;
+ at end verbatim
@end example
@html
@@ -10593,9 +10857,11 @@ us know if you find otherwise).
@code{int gsl_sf_gamma_e(const double x, gsl_sf_result * result)}
The @command{ncap2} script would be:
@example
-lon_in[lon]=@{-1,0.1,0,2,0.3@};
+ at verbatim
+lon_in[lon]={-1,0.1,0,2,0.3};
lon_out=gsl_sf_gamma(lon_in);
lon_out= _, 9.5135, 4.5908, 2.9915
+ at end verbatim
@end example
@noindent The first value is set to @code{_FillValue} since the gamma
@@ -10621,9 +10887,11 @@ This computes the Bessel function of order @var{n=2} for every value in
The Bessel order argument, an integer, can also be a non-scalar
variable, i.e., an array.
@example
-n_in[lon]=@{0,1,2,3@};
+ at verbatim
+n_in[lon]={0,1,2,3};
lon_out=gsl_sf_bessel_Jn(n_in,0.5);
lon_out= 0.93846, 0.24226, 0.03060, 0.00256
+ at end verbatim
@end example
@noindent Arguments to @acronym{GSL} wrapper functions in @command{ncap2}
@@ -10997,13 +11265,14 @@ prototypes look at the spreadsheet @strong{doc/nco_gsl.ods}. @* @*
@noindent A simple example
@example
-x_in[$lon]=@{1.0,2.0,3.0,4.0@};
-y_in[$lon]=@{1.1,1.2,1.5,1.8@};
+ at verbatim
+x_in[$lon]={1.0,2.0,3.0,4.0};
+y_in[$lon]={1.1,1.2,1.5,1.8};
// Ram variable is declared and defined here
gsl_interp_cspline(&ram_sp,x_in,y_in);
-x_out[$lon_grd]=@{1.1,2.0,3.0,3.1,3.99@};
+x_out[$lon_grd]={1.1,2.0,3.0,3.1,3.99};
y_out=gsl_spline_eval(ram_sp,x_out);
y2=gsl_spline_eval(ram_sp,1.3);
@@ -11013,6 +11282,7 @@ ram_delete(ram_sp);
print(y_out); // 1.10472, 1.2, 1.4, 1.42658, 1.69680002
print(y2); // 1.12454
print(y3); // '_'
+ at end verbatim
@end example
@noindent Note in the above example y3 is set to 'missing value' because 0.0 isn't within the input X range.
@@ -11089,21 +11359,23 @@ If data_x or data_y is less than type @code{double} then it is converted to type
@noindent The below example shows @strong{gsl_fit_linear()} in action
@example
+ at verbatim
defdim("d1",10);
-xin[d1]=@{1,2,3,4,5,6,7,8,9,10.0@};
-yin[d1]=@{3.1,6.2,9.1,12.2,15.1,18.2,21.3,24.0,27.0,30.0@};
+xin[d1]={1,2,3,4,5,6,7,8,9,10.0};
+yin[d1]={3.1,6.2,9.1,12.2,15.1,18.2,21.3,24.0,27.0,30.0};
gsl_fit_linear(xin,1,yin,1,$d1.size,&c0,&c1,&cov00,&cov01,&cov11,&sumsq);
print(c0); // 0.2
print(c1); // 2.98545454545
defdim("e1",4);
-xout[e1]=@{1.0,3.0,4.0,11@};
+xout[e1]={1.0,3.0,4.0,11};
yout[e1]=0.0;
yout=gsl_fit_linear_est(xout, c0,c1, cov00,cov01, cov11, sumsq);
print(yout); // 3.18545454545 ,9.15636363636, ,12.1418181818 ,33.04
+ at end verbatim
@end example
@* @*
@@ -11142,7 +11414,8 @@ double gsl_stats_quantile_from_sorted_data (var_sorted_data, data_stride, n, var
Some examples
@example
-a1[time]=@{1,2,3,4,5,6,7,8,9,10 @};
+ at verbatim
+a1[time]={1,2,3,4,5,6,7,8,9,10};
a1_avg=gsl_stats_mean(a1,1,10);
print(a1_avg); // 5.5
@@ -11152,7 +11425,7 @@ print(a1_var); // 16.0
// bounding error, vector attempts to access element a1(10)
a1_sd=gsl_stats_sd(a1,5,3);
-
+ at end verbatim
@end example
@noindent For functions with the signature
@@ -11316,7 +11589,9 @@ Define new attribute @var{new} for existing variable @var{one}
as twice the existing attribute @var{double_att} of variable
@var{att_var}:
@example
-ncap2 -s 'one@@new=2*att_var@@double_att' in.nc out.nc
+ at verbatim
+ncap2 -s 'one at new=2*att_var at double_att' in.nc out.nc
+ at end verbatim
@end example
Average variables of mixed types (result is of type @code{double}):
@@ -11496,6 +11771,7 @@ variables in @command{ncap2} command-line scripts
In such cases it may be necessary to use the shell backslash character
@samp{\} to protect the @command{ncap2} meta-character.
+
@cindex appending data
@cindex time-averaging
@findex ncks
@@ -11901,7 +12177,8 @@ rint$(0.1) = 0$
@item round(x)
@dfn{Round}
Nearest integer to @var{x} is returned in floating point format.
-Round halfway cases away from zero, regardless of current IEEE rounding direction.
+Round halfway cases away from zero, regardless of current @acronym{IEEE}
+rounding direction.
Example:
@tex
round$(0.5) = 1.0$
@@ -11968,7 +12245,8 @@ tanh$(1.0) = 0.761594155956$
@item trunc(x)
@dfn{Truncate}
Nearest integer to @var{x} is returned in floating point format.
-Round halfway cases toward zero, regardless of current IEEE rounding direction.
+Round halfway cases toward zero, regardless of current @acronym{IEEE}
+rounding direction.
Example:
@tex
trunc$(0.5) = 0.0$
@@ -12108,24 +12386,27 @@ netcdf-3.6.0-p1 @*
netcdf-3.6.1 @*
netcdf-3.6.2 @*
@example
+ at verbatim
/*
- * ( [a-zA-Z]|[0-9]|'_'|'-'|'+'|'.'|'|':'|'@@'|'('|')' )+
+ * ( [a-zA-Z]|[0-9]|'_'|'-'|'+'|'.'|'|':'|'@'|'('|')' )+
* Verify that name string is valid CDL syntax, i.e., all characters are
* alphanumeric, '-', '_', '+', or '.'.
- * Also permit ':', '@@', '(', or ')' in names for chemists currently making
+ * Also permit ':', '@', '(', or ')' in names for chemists currently making
* use of these characters, but don't document until ncgen and ncdump can
* also handle these characters in names.
*/
+ at end verbatim
@end example
@noindent netcdf-3.6.3@*
netcdf-4.0 Final 2008/08/28@*
@example
+ at verbatim
/*
* Verify that a name string is valid syntax. The allowed name
* syntax (in RE form) is:
*
- * ([a-zA-Z_]|@{UTF8@})([^\x00-\x1F\x7F/]|@{UTF8@})*
+ * ([a-zA-Z_]|{UTF8})([^\x00-\x1F\x7F/]|{UTF8})*
*
* where UTF8 represents a multibyte UTF-8 encoding. Also, no
* trailing spaces are permitted in names. This definition
@@ -12135,6 +12416,7 @@ netcdf-4.0 Final 2008/08/28@*
* character can occur anywhere within an identifier. We later
* normalize UTF-8 strings to NFC to facilitate matching and queries.
*/
+ at end verbatim
@end example
@c End HMB documentation
@@ -12499,22 +12781,29 @@ ncatted -a long_name,T,o,c,temperature in.nc
<a name="NaN"></a> <!-- http://nco.sf.net/nco.html#NaN -->
@end html
@cindex NaN
- at cindex IEEE NaN
+ at cindex @acronym{IEEE} NaN
@cindex Not-a-Number
- at acronym{NCO} arithmetic operators will not work as expected on IEEE
-NaN (short for Not-a-Number) and NaN-like numbers such as positive
-infinity and negative infinity.
-One way to work-around this problem is to change IEEE NaNs to normal
-missing values.
+ at acronym{NCO} arithmetic operators may not work as expected on
+ at acronym{IEEE} NaN (short for Not-a-Number) and NaN-like numbers such as
+positive infinity and negative infinity
+ at footnote{Arithmetic comparisons to NaN and NaN-like numbers always
+return False, contrary to the behavior of all other numbers.
+This is difficult to inuit, yet is the behavior defined for NaN by
+ at acronym{IEEE} 754.
+Using NaN for the missing value in datasets is legal.
+We strongly discourage it.}.
+One way to work-around this problem is to change @acronym{IEEE} NaNs to
+normal missing values.
As of @acronym{NCO} 4.1.0 (March, 2012), @command{ncatted} works with
NaNs.
First set the missing value (i.e., the value of the @code{_FillValue}
-attribute) for the variable(s) in question to the IEEE NaN value.
+attribute) for the variable(s) in question to the @acronym{IEEE} NaN value.
@example
ncatted -a _FillValue,,o,f,NaN in.nc
@end example
-Then change the missing value from the IEEE NaN value to a normal IEEE
-number, like 1.0e36 (or to whatever the original missing value was).
+Then change the missing value from the @acronym{IEEE} NaN value to a
+normal @acronym{IEEE} number, like 1.0e36 (or to whatever the original
+missing value was).
@example
ncatted -a _FillValue,,m,f,1.0e36 in.nc
@end example
@@ -12842,9 +13131,9 @@ In these cases, creating @var{file_2} with @command{ncra} rather than
@command{ncwa} will cause the @command{ncbo} operation to fail.
For concreteness say the record dimension in @code{file_1} is
@code{time}.
-If @var{file_2} were created by averaging @var{file_1} over the
- at code{time} dimension with the @command{ncra} operator rather than with
-the @command{ncwa} operator, then @var{file_2} will have a @code{time}
+If @var{file_2} was created by averaging @var{file_1} over the
+ at code{time} dimension with the @command{ncra} operator (rather than with
+the @command{ncwa} operator), then @var{file_2} will have a @code{time}
dimension of @w{size 1} rather than having no @code{time} dimension at
all
@cindex degenerate dimension
@@ -13025,25 +13314,29 @@ twelve months:
@cindex Bourne Shell
@cindex C Shell
@example
-for idx in @{1..12@}; do # Bash Shell (version 3.0+)
- idx=`printf "%02d" $@{idx@}` # Zero-pad to preserve order
- ncks -F -d time,$@{idx@},,12 t_anm_8501_8912.nc foo.$@{idx@}
- ncra foo.$@{idx@} t_anm_8589_$@{idx@}.nc
+ at verbatim
+for idx in {1..12}; do # Bash Shell (version 3.0+)
+ idx=`printf "%02d" ${idx}` # Zero-pad to preserve order
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
done
for idx in 01 02 03 04 05 06 07 08 09 10 11 12; do # Bourne Shell
- ncks -F -d time,$@{idx@},,12 t_anm_8501_8912.nc foo.$@{idx@}
- ncra foo.$@{idx@} t_anm_8589_$@{idx@}.nc
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
done
foreach idx (01 02 03 04 05 06 07 08 09 10 11 12) # C Shell
- ncks -F -d time,$@{idx@},,12 t_anm_8501_8912.nc foo.$@{idx@}
- ncra foo.$@{idx@} t_anm_8589_$@{idx@}.nc
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
end
+ at end verbatim
@end example
@noindent
Note that @command{ncra} understands the @code{stride} argument so the
two commands inside the loop may be combined into the single command
@example
-ncra -F -d time,$@{idx@},,12 t_anm_8501_8912.nc foo.$@{idx@}
+ at verbatim
+ncra -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ at end verbatim
@end example
@noindent
Finally, use @command{ncrcat} to concatenate the @w{12 average} monthly
@@ -13815,7 +14108,7 @@ SYNTAX
ncks [-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b @var{binary-file}] [-C] [-c] [--cdl]
[--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz]
[-D @var{dbg}] [-d @var{dim},[@var{min}][,[@var{max}][,[@var{stride}]]] [-F] [--fix_rec_dmn @var{dim}]
-[-G @var{gpe_dsc}] [-g @var{grp}[, at dots{}]] [-H] [-h] [--hdn] [--hdr_pad @var{nbr}]
+[-G @var{gpe_dsc}] [-g @var{grp}[, at dots{}]] [--grp_xtr_var_xcl] [-H] [-h] [--hdn] [--hdr_pad @var{nbr}]
[-L @var{dfl_lvl}] [-l @var{path}] [-M] [-m] [--mk_rec_dmn @var{dim}] [--md5_digest]
[--no_blank] [--no_tmp_fl] [-O] [-o @var{output-file}] [-P] [-p @var{path}]
[-Q] [-q] [-R] [-r] [--rad] [--ram_all] [-s @var{format}]
@@ -14099,15 +14392,16 @@ valid @acronym{CDL} (network Common data form Description Language).
@command{ncgen} and excreted by @command{ncdump}.
Compare @command{ncks} ``traditional'' with @acronym{CDL} printing:
@example
-zender@@roulee:~$ ncks -v one ~/nco/data/in.nc
+ at verbatim
+zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
one = 1
-zender@@roulee:~$ ncks --cdl -v one ~/nco/data/in.nc
-netcdf in @{
+zender at roulee:~$ ncks --cdl -v one ~/nco/data/in.nc
+netcdf in {
variables:
float one ;
@@ -14116,7 +14410,8 @@ netcdf in @{
data:
one = 1 ;
-@} // group /
+} // group /
+ at end verbatim
@end example
@command{ncgen} converts @acronym{CDL}-mode output into a netCDF file:
@example
@@ -14436,7 +14731,7 @@ into @acronym{NcML}, including metadata and data, using all
Compare @command{ncks} ``traditional'' with @acronym{XML} printing:
@example
@verbatim
-zender@@roulee:~$ ncks -v one ~/nco/data/in.nc
+zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
@@ -14483,19 +14778,19 @@ variables of character-type and numeric-type, respectively.
Their default separators are "*" and " ":
@example
@verbatim
-zender@@roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
+zender at roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
...
<values separator="*">abc*bcd*cde*def</values>
...
- zender@@roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
+ zender at roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
...
<values separator=", ">abc, bcd, cde, def, efg, fgh, ghi, hij, jkl, klm</values>
...
-zender@@roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
...
<values>1 2 3 4 5 6 7 8 9 10</values>
...
-zender@@roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
...
<values separator=", ">1, 2, 3, 4, 5, 6, 7, 8, 9, 10</values>
...
@@ -14583,7 +14878,9 @@ The filters are clearly too complex to remember on-the-fly so the entire
procedure could be implemented as a shell command or function called,
say, @command{ncattget}
@example
-function ncattget @{ ncks -M -m $@{3@} | grep -E -i "^$@{2@} attribute [0-9]+: $@{1@}" | cut -f 11- -d ' ' | sort ; @}
+ at verbatim
+function ncattget { ncks -M -m ${3} | grep -E -i "^${2} attribute [0-9]+: ${1}" | cut -f 11- -d ' ' | sort ; }
+ at end verbatim
@end example
The shell @command{ncattget} is invoked with three arugments that are,
in order, the names of the attribute, variable, and file to examine.
@@ -14823,19 +15120,21 @@ coordinates, except variable @code{time}, from netCDF @file{in.nc}:
ncks -x -v time in.nc out.nc
@end example
As a special case of this, consider how to remove a
- at acronym{CF} Convention comliant @code{bounds} or @code{coordinates}
-variable (@pxref{CF Conventions}) such as @code{time_bounds}.
- at acronym{NCO} subsetting assumes the user wants all coordinates
-and bounds and axes associated with all extracted variables
+ at acronym{CF} Convention comliant @code{ancillary_variables},
+ at code{bounds}, or @code{coordinates} variable (@pxref{CF Conventions})
+such as @code{time_bounds}.
+ at acronym{NCO} subsetting assumes the user wants all ancillary variables,
+axes, bounds and coordinates associated with all extracted variables
(@pxref{Subsetting Coordinate Variables}).
-Hence to exclude a @code{bounds} or @code{coordinates} variable while
-retaining the ``parent'' variable (here @code{time}), one must use the
- at samp{-C} switch:
+Hence to exclude a @code{ancillary_variables}, @code{bounds}, or
+ at code{coordinates} variable while retaining the ``parent'' variable
+(here @code{time}), one must use the @samp{-C} switch:
@example
ncks -C -x -v time_bounds in.nc out.nc
@end example
The @samp{-C} switch tells the operator @emph{NOT} to necessarily
-include all the @acronym{CF} coordinates and bounds and axes.
+include all the @acronym{CF} ancillary variables, axes, bounds, and
+coordinates.
Hence the output file will contain @code{time} and not
@code{time_bounds}.
@@ -15893,7 +16192,9 @@ ncrename -v p,pressure -v .t,temperature in.nc
Rename the attribute @code{long_name} to @code{largo_nombre} in the
variable @code{u}, and no other variables in netCDF @file{in.nc}.
@example
-ncrename -a u@@long_name,largo_nombre in.nc
+ at verbatim
+ncrename -a u at long_name,largo_nombre in.nc
+ at end verbatim
@end example
Rename the group @code{g8} to @code{g20} in netCDF4 file
@@ -15958,8 +16259,10 @@ those variables which possess it), the attribute @code{hieght} is
changed to @code{height} in the variable @code{tpt}, and in the
variable @code{prs_sfc}, if it exists.
@example
+ at verbatim
ncrename -a _FillValue,missing_value -a .units,CGS_units \
- -a tpt@@hieght,height -a prs_sfc@@.hieght,height in.nc out.nc
+ -a tpt at hieght,height -a prs_sfc at .hieght,height in.nc out.nc
+ at end verbatim
@end example
The presence and absence of the @samp{.} and @samp{@@} features
cause this command to execute successfully only if a number of
@@ -15976,12 +16279,14 @@ The variable @code{prs_sfc} need not exist, and need not contain the
Rename the global or group attribute @code{Convention} to
@code{Conventions}
@example
+ at verbatim
ncrename -a Convention,Conventions in.nc # Variable and global atts.
ncrename -a .Convention,Conventions in.nc # Variable and global atts.
-ncrename -a @@Convention,Conventions in.nc # Global atts. only
-ncrename -a @@.Convention,Conventions in.nc # Global atts. only
-ncrename -a global@@Convention,Conventions in.nc # Global atts. only
-ncrename -a .global@@.Convention,Conventions in.nc # Global atts. only
+ncrename -a @Convention,Conventions in.nc # Global atts. only
+ncrename -a @.Convention,Conventions in.nc # Global atts. only
+ncrename -a global at Convention,Conventions in.nc # Global atts. only
+ncrename -a .global at .Convention,Conventions in.nc # Global atts. only
+ at end verbatim
@end example
The examples without the @code{@@} character attempt to change the
attribute name in both Global or Group and variable attributes.
@@ -16349,7 +16654,8 @@ EXAMPLES
Given file @file{85_0112.nc}:
@example
-netcdf 85_0112 @{
+ at verbatim
+netcdf 85_0112 {
dimensions:
lat = 64 ;
lev = 18 ;
@@ -16365,7 +16671,8 @@ variables:
float two_dmn_var(lat, lev) ;
float mask(lat, lon) ;
float gw(lat) ;
-@}
+}
+ at end verbatim
@end example
Average all variables in @file{in.nc} over all dimensions and store
@@ -16491,14 +16798,16 @@ correctly integrate the cell areas into a total regional area.
Mask a file to contain @var{_FillValue} everywhere except where
@math{@var{thr_min} <= @var{msk_var} <= @var{thr_max}}:
@example
+ at verbatim
# Set masking variable and its scalar thresholds
export msk_var='three_dmn_var_dbl' # Masking variable
export thr_max='20' # Maximum allowed value
export thr_min='10' # Minimum allowed value
ncecat -O in.nc out.nc # Wrap out.nc in degenerate "record" dimension
-ncwa -O -a record -B "$@{msk_var@} <= $@{thr_max@}" out.nc out.nc
+ncwa -O -a record -B "${msk_var} <= ${thr_max}" out.nc out.nc
ncecat -O out.nc out.nc # Wrap out.nc in degenerate "record" dimension
-ncwa -O -a record -B "$@{msk_var@} >= $@{thr_min@}" out.nc out.nc
+ncwa -O -a record -B "${msk_var} >= ${thr_min}" out.nc out.nc
+ at end verbatim
@end example
After the first use of @command{ncwa}, @file{out.nc} contains
@var{_FillValue} where @code{$@{msk_var@} >= $@{thr_max@}}.
@@ -16541,10 +16850,11 @@ So you could be the third!
@end html
@menu
* Contributors::
+* Citation::
* Proposals for Institutional Funding::
@end menu
- at node Contributors, Proposals for Institutional Funding, Contributing, Contributing
+ at node Contributors, Citation, Contributing, Contributing
@section Contributors
@acronym{NCO} would not exist without the dedicated efforts of the
remarkable software engineers who conceive, develop, and
@@ -16587,7 +16897,7 @@ research, releases.
Non-linear operations and @code{min()}, @code{max()}, @code{total()}
support in @command{ncra} and @command{ncwa}.
Type conversion for arithmetic.
-Migration to netCDF3 API.
+Migration to netCDF3 @acronym{API}.
@command{ncap2} parser, lexer, @acronym{GSL}-support, @w{and I/O}.
Multislabbing algorithm.
Variable wildcarding.
@@ -16595,7 +16905,7 @@ Numerous hacks.
@command{ncap2} language.
@cindex Rorik Peterson
@item Rorik Peterson
-Original autotool build support.
+Original autotools build support.
Long command-line options.
Original UDUnits support.
Debianization.
@@ -16617,7 +16927,7 @@ Windows Visual Studio support.
netCDF4 groups.
@cindex Russ Rew
@item Russ Rew
-Advice on NCO structural algorithms
+Advice on @acronym{NCO} structural algorithms
@cindex Brian Mays
@item Brian Mays
Original packaging for Debian @acronym{GNU}/Linux, @command{nroff} man pages.
@@ -16655,11 +16965,12 @@ Large work-load testing
@cindex Martin Schmidt
@cindex Lori Sentman
@cindex Michael Schulz
+ at cindex Rich Signell
@cindex Gary Strand
@cindex Andrew Wittenberg
@cindex George White
@cindex Remik Ziemlinski
- at item Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski
+ at item Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Rich Signell, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski
Excellent bug reports and feature requests.
@cindex Daniel Baumann
@cindex Nick Bower
@@ -16707,6 +17018,33 @@ Single bug reports and fixes
Please let me know if your name was omitted!
@html
+<a name="ctt"></a> <!-- http://nco.sf.net/nco.html#ctt -->
+ at end html
+ at node Citation, Proposals for Institutional Funding, Contributors, Contributing
+ at section Citation
+ at cindex citation
+The recommended citations for @acronym{NCO} software are
+ at example
+ at verbatim
+Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience
+Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10),
+1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+
+Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.3,
+http://nco.sf.net/nco.pdf.
+ at end verbatim
+ at end example
+Use the former when referring to overall design, purpose, and
+optimization of @acronym{NCO}, and use the latter when referring to
+specific features and/or the User Guide itself.
+
+Additional information on citing @acronym{NCO} is in the User Guide at
+ at url{http://nco.sf.net#ctt}.
+A complete list of @acronym{NCO} publications and presentations is at
+ at url{http://nco.sf.net#pub}.
+This list links to the full papers and seminars themselves.
+
+ at html
<a name="prp"></a> <!-- http://nco.sf.net/nco.html#prp -->
<a name="prp_sei"></a> <!-- http://nco.sf.net/nco.html#prp_sei -->
<a name="fnd"></a> <!-- http://nco.sf.net/nco.html#fnd -->
@@ -16715,7 +17053,7 @@ Please let me know if your name was omitted!
* Proposals for Institutional Funding::
@end menu
- at node Proposals for Institutional Funding, , Contributors, Contributing
+ at node Proposals for Institutional Funding, , Citation, Contributing
@section Proposals for Institutional Funding
@cindex funding
@cindex proposals
@@ -16790,18 +17128,20 @@ file of @file{in.nc} with the record dimension as @code{time}.
@cindex average
@cindex time-averaging
@example
-for yyyy in @{1990..2005@}; do # Loop over years
- for moy in @{1..12@}; do # Loop over months
- mm=$( printf "%02d" $@{moy@} ) # Change to 2-digit format
+ at verbatim
+for yyyy in {1990..2005}; do # Loop over years
+ for moy in {1..12}; do # Loop over months
+ mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
# Average specific month yyyy-mm
- ncra -O -d time,"$@{yyyy@}-$@{mm@}-01","$@{yyyy@}-$@{mm@}-31" \
- in.nc in_$@{yyyy@}$@{mm@}.nc
+ ncra -O -d time,"${yyyy}-${mm}-01","${yyyy}-${mm}-31" \
+ in.nc in_${yyyy}${mm}.nc
done
done
# Concatenate monthly files together
ncrcat -O in_??????.nc out.nc
+ at end verbatim
@end example
@noindent
@@ -16810,12 +17150,14 @@ ncrcat -O in_??????.nc out.nc
@cindex average
@cindex time-averaging
@example
-for yyyy in @{1990..2005@}; do # Loop over years
- ncra -O -d time,"$@{yyyy@}-01-01","$@{yyyy@}-12-31" in.nc in_$@{yyyy@}.nc
+ at verbatim
+for yyyy in {1990..2005}; do # Loop over years
+ ncra -O -d time,"${yyyy}-01-01","${yyyy}-12-31" in.nc in_${yyyy}.nc
done
# Concatenate annual files together
ncrcat -O in_????.nc out.nc
+ at end verbatim
@end example
The @option{-O} switch means to overwrite the pre-existing files (@pxref{Batch Mode}).
The @option{-d} option is to specify the range of hyperslabs (@pxref{Hyperslabs}).
@@ -16878,11 +17220,13 @@ ncra -O snd_199001??.nc out.nc
@end example
You might want to use loop if you need the average of each month.
@example
-for moy in @{1..12@}; do # Loop over months
- mm=$( printf "%02d" $@{moy@} ) # Change to 2-digit format
+ at verbatim
+for moy in {1..12}; do # Loop over months
+ mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
- ncra -O snd_????$@{mm@}??.nc out_$@{mm@}.nc
+ ncra -O snd_????${mm}??.nc out_${mm}.nc
done
+ at end verbatim
@end example
@node Multiple files with multiple time points, , One time point one file, Quick Start
@@ -16896,10 +17240,12 @@ And for seasonal averages, you can specify the three months by shell scripts.
@html
<a name="cmip5"></a> <!-- http://nco.sf.net/nco.html#cmip5 -->
+<a name="godad"></a> <!-- http://nco.sf.net/nco.html#godad -->
@end html
@node CMIP5 Example, Parallel, Quick Start, Top
@chapter @acronym{CMIP5} Example
@cindex @acronym{CMIP5}
+ at cindex @acronym{GODAD}
@ignore
This @uref{http://nco.sf.net/xmp_cesm.html,Wonderful CMIP5 Documentation}
shows complete processing of the @acronym{CMIP5} dataset.
@@ -16912,11 +17258,37 @@ responses of climate models from around the world.
However, it is a tremendous workload to retrieve a single climate
statistic from all these models, each of which includes several ensemble
members.
-Not only that, it is too often a repetitive process which impedes new
+Not only that, it is too often a tedious process that impedes new
research and hypothesis testing.
-Our @acronym{NASA} @acronym{ACCESS} project is designed to simplify and
-accelerate this process.
-To begin, we document below a prototypical example of @acronym{CMIP5}
+Our @acronym{NASA} @acronym{ACCESS} 2011 project simplified and
+accelerated this process.
+
+Traditional geoscience data analysis requires users to work with
+numerous flat (data in one level or namespace) files.
+In that paradigm instruments or models produce, and then repositories
+archive and distribute, and then researchers request and analyze,
+collections of flat files.
+ at acronym{NCO} works well with that paradigm, yet it also embodies the
+necessary algorithms to transition geoscience data analysis from relying
+solely on traditional (or ``flat'') datasets to allowing newer
+hierarchical (or ``nested'') datasets.
+
+Hierarchical datasets support and enable combining all datastreams that
+meet user-specified criteria into a single or small number of files that
+hold @emph{all} the science-relevant data.
+ at acronym{NCO} (and no other software to our knowledge) exploits this
+capability now.
+Data and metadata may be aggregated into and analyzed in hierarchical
+structures.
+We call the resulting data storage, distribution, and analysis
+paradigm Group-Oriented Data Analysis and Distribution
+(@acronym{GODAD}).
+ at acronym{GODAD} lets the scientific question organize the data, not the
+ at emph{ad hoc} granularity of all relevant datasets.
+This chapter illustrates @acronym{GODAD} techniques applied to
+analysis of the @acronym{CMIP5} dataset.
+
+To begin, we document below a prototypical example of @acronym{CMIP5}
analysis and evaluation using traditional @acronym{NCO} commands on
netCDF3-format model and @acronym{HDF-EOS} format observational
(@acronym{NASA} @acronym{MODIS} satellite instrument) datasets.
@@ -16951,8 +17323,8 @@ group-based processing as well.
@cindex file combination
Sometimes, the data of one ensemble member will be stored in several
files to reduce single file size.
-But it is not convenient to process in a batch mode.
-The following script illustrates how to concatenate these files into one.
+It is more convenient to concatenate these files into a single
+timeseries, and the following script illustrates how.
Key steps include:
@enumerate
@item Obtain number and names (or partial names) of files in a directory
@@ -16963,20 +17335,20 @@ Key steps include:
@verbatiminclude xmp/cmb_fl.sh
@end example
-Right now, @acronym{CMIP5} model data downloaded from Earth System Grid
+ at acronym{CMIP5} model data downloaded from the Earth System Grid
Federation (@uref{http://pcmdi9.llnl.gov/esgf-web-fe/, @acronym{ESGF}})
-will not contain @key{group} features yet.
-Therefore users can aggregate the flat files into groups themselves.
-The following script shows how to aggregate models to one file.
+does not contain group features yet.
+Therefore users must aggregate flat files into hierarchical ones themselves.
+The following script shows how.
Each dataset becomes a group in the output file.
There can be several levels of groups.
-In this example, we employ two experiments as the top-level.
-The second-level comprises different models.
-Some models have more than one ensemble member.
-These ensemble members are on the third level.
-In each sub-group of ensemble members, we appended two variables,
- at var{snc} and @var{snd} (these stand for snow cover and snow depth, by
-the way).
+In this example, we employ two experiments (``scenarios'') as the top-level.
+The second-level comprises different models (e.g., CCSM4, CESM1-BGC).
+Many models are run multiple times with slight perturbed initial
+conditions to produce an ensemble of realizations.
+These ensemble members comprise the third level of the hierarchy.
+The script selects two variables, @var{snc} and @var{snd} (snow cover
+and snow depth).
@cindex @option{--gag}
@cindex aggregation
@cindex group aggregation
@@ -17216,7 +17588,9 @@ Here is an example showing:
This section will describe scripting strategies, including the use of
@acronym{GNU} Parallel, to @acronym{NCO}.
@example
-ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" @{@} 50y/@{@}
+ at verbatim
+ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" {} 50y/{}
+ at end verbatim
@end example
@html
@@ -17229,9 +17603,10 @@ ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" @{@} 50y
This chapter illustrates how to use @acronym{NCO} to
process and analyze the results of a @acronym{CCSM} climate simulation.
@example
+ at verbatim
************************************************************************
Task 0: Finding input files
-************************************************************************
+x************************************************************************
The CCSM model outputs files to a local directory like:
/ptmp/zender/archive/T42x1_40
@@ -17273,44 +17648,44 @@ Each month in the output file is the mean of 100 input files.
Normally, we store the "reduced" data in a smaller, local directory.
caseid='T42x1_40'
-#drc_in="$@{DATA@}/archive/$@{caseid@}/atm"
-drc_in="$@{DATA@}/$@{caseid@}"
-drc_out="$@{DATA@}/$@{caseid@}"
-mkdir -p $@{drc_out@}
-cd $@{drc_out@}
+#drc_in="${DATA}/archive/${caseid}/atm"
+drc_in="${DATA}/${caseid}"
+drc_out="${DATA}/${caseid}"
+mkdir -p ${drc_out}
+cd ${drc_out}
Method 1: Assume all data in directory applies
-for mth in @{1..12@}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
- ncra -O -D 1 -o $@{drc_out@}/$@{caseid@}_clm$@{mm@}.nc \
- $@{drc_in@}/$@{caseid@}.cam2.h0.*-$@{mm@}.nc
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.*-${mm}.nc
done # end loop over mth
Method 2: Use shell 'globbing' to construct input filenames
-for mth in @{1..12@}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
- ncra -O -D 1 -o $@{drc_out@}/$@{caseid@}_clm$@{mm@}.nc \
- $@{drc_in@}/$@{caseid@}.cam2.h0.00??-$@{mm@}.nc \
- $@{drc_in@}/$@{caseid@}.cam2.h0.0100-$@{mm@}.nc
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.00??-${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.0100-${mm}.nc
done # end loop over mth
Method 3: Construct input filename list explicitly
-for mth in @{1..12@}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
fl_lst_in=''
- for yr in @{1..100@}; do
+ for yr in {1..100}; do
yyyy=`printf "%04d" $yr`
- fl_in=$@{caseid@}.cam2.h0.$@{yyyy@}-$@{mm@}.nc
- fl_lst_in="$@{fl_lst_in@} $@{caseid@}.cam2.h0.$@{yyyy@}-$@{mm@}.nc"
+ fl_in=${caseid}.cam2.h0.${yyyy}-${mm}.nc
+ fl_lst_in="${fl_lst_in} ${caseid}.cam2.h0.${yyyy}-${mm}.nc"
done # end loop over yr
- ncra -O -D 1 -o $@{drc_out@}/$@{caseid@}_clm$@{mm@}.nc -p $@{drc_in@} \
- $@{fl_lst_in@}
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc -p ${drc_in} \
+ ${fl_lst_in}
done # end loop over mth
Make sure the output file averages correct input files!
ncks -M prints global metadata:
- ncks -M $@{drc_out@}/$@{caseid@}_clm01.nc
+ ncks -M ${drc_out}/${caseid}_clm01.nc
The input files ncra used to create the climatological monthly mean
will appear in the global attribute named 'history'.
@@ -17318,23 +17693,23 @@ will appear in the global attribute named 'history'.
Use ncrcat to aggregate the climatological monthly means
ncrcat -O -D 1 \
- $@{drc_out@}/$@{caseid@}_clm??.nc $@{drc_out@}/$@{caseid@}_clm_0112.nc
+ ${drc_out}/${caseid}_clm??.nc ${drc_out}/${caseid}_clm_0112.nc
Finally, create climatological means for reference.
The climatological time-mean:
ncra -O -D 1 \
- $@{drc_out@}/$@{caseid@}_clm_0112.nc $@{drc_out@}/$@{caseid@}_clm.nc
+ ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm.nc
The climatological zonal-mean:
ncwa -O -D 1 -a lon \
- $@{drc_out@}/$@{caseid@}_clm.nc $@{drc_out@}/$@{caseid@}_clm_x.nc
+ ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_x.nc
The climatological time- and spatial-mean:
ncwa -O -D 1 -a lon,lat,time -w gw \
- $@{drc_out@}/$@{caseid@}_clm.nc $@{drc_out@}/$@{caseid@}_clm_xyt.nc
+ ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_xyt.nc
This file contains only scalars, e.g., "global mean temperature",
used for summarizing global results of a climate experiment.
@@ -17343,8 +17718,8 @@ Climatological monthly anomalies = Annual Cycle:
Subtract climatological mean from climatological monthly means.
Result is annual cycle, i.e., climate-mean has been removed.
- ncbo -O -D 1 -o $@{drc_out@}/$@{caseid@}_clm_0112_anm.nc \
- $@{drc_out@}/$@{caseid@}_clm_0112.nc $@{drc_out@}/$@{caseid@}_clm_xyt.nc
+ ncbo -O -D 1 -o ${drc_out}/${caseid}_clm_0112_anm.nc \
+ ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm_xyt.nc
************************************************************************
Task 2: Correcting monthly averages
@@ -17360,29 +17735,29 @@ declare -a dpm
dpm=(0 31 28.25 31 30 31 30 31 31 30 31 30 31) # Allows 1-based indexing
Method 1: Create dpm directly in climatological monthly means
-for mth in @{1..12@}; do
- mm=`printf "%02d" $@{mth@}`
- ncap2 -O -s "dpm=0.0*date+$@{dpm[$@{mth@}]@}" \
- $@{drc_out@}/$@{caseid@}_clm$@{mm@}.nc $@{drc_out@}/$@{caseid@}_clm$@{mm@}.nc
+for mth in {1..12}; do
+ mm=`printf "%02d" ${mth}`
+ ncap2 -O -s "dpm=0.0*date+${dpm[${mth}]}" \
+ ${drc_out}/${caseid}_clm${mm}.nc ${drc_out}/${caseid}_clm${mm}.nc
done # end loop over mth
Method 2: Create dpm by aggregating small files
-for mth in @{1..12@}; do
- mm=`printf "%02d" $@{mth@}`
- ncap2 -O -v -s "dpm=$@{dpm[$@{mth@}]@}" ~/nco/data/in.nc \
- $@{drc_out@}/foo_$@{mm@}.nc
+for mth in {1..12}; do
+ mm=`printf "%02d" ${mth}`
+ ncap2 -O -v -s "dpm=${dpm[${mth}]}" ~/nco/data/in.nc \
+ ${drc_out}/foo_${mm}.nc
done # end loop over mth
-ncecat -O -D 1 -p $@{drc_out@} -n 12,2,2 foo_$@{mm@}.nc foo.nc
-ncrename -O -D 1 -d record,time $@{drc_out@}/foo.nc
+ncecat -O -D 1 -p ${drc_out} -n 12,2,2 foo_${mm}.nc foo.nc
+ncrename -O -D 1 -d record,time ${drc_out}/foo.nc
ncatted -O -h \
-a long_name,dpm,o,c,"Days per month" \
-a units,dpm,o,c,"days" \
- $@{drc_out@}/$@{caseid@}_clm_0112.nc
-ncks -A -v dpm $@{drc_out@}/foo.nc $@{drc_out@}/$@{caseid@}_clm_0112.nc
+ ${drc_out}/${caseid}_clm_0112.nc
+ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
Method 3: Create small netCDF file using ncgen
cat > foo.cdl << 'EOF'
-netcdf foo @{
+netcdf foo {
dimensions:
time=unlimited;
variables:
@@ -17391,10 +17766,10 @@ variables:
dpm:units="days";
data:
dpm=31,28.25,31,30,31,30,31,31,30,31,30,31;
-@}
+}
EOF
ncgen -b -o foo.nc foo.cdl
-ncks -A -v dpm $@{drc_out@}/foo.nc $@{drc_out@}/$@{caseid@}_clm_0112.nc
+ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
Another way to get correct monthly weighting is to average daily
output files, if available.
@@ -17406,8 +17781,8 @@ Let's say you are interested in examining the California region.
Hyperslab your dataset to isolate the appropriate latitude/longitudes.
ncks -O -D 1 -d lat,30.0,37.0 -d lon,240.0,270.0 \
- $@{drc_out@}/$@{caseid@}_clm_0112.nc \
- $@{drc_out@}/$@{caseid@}_clm_0112_Cal.nc
+ ${drc_out}/${caseid}_clm_0112.nc \
+ ${drc_out}/${caseid}_clm_0112_Cal.nc
The dataset is now much smaller!
To examine particular metrics.
@@ -17435,7 +17810,7 @@ http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/su
pres.sfc.1969.nc ~/foo.nc
LLNL PCMDI IPCC OPeNDAP Data Portal:
-ncks -M -p http://username:password@@esgcet.llnl.gov/cgi-bin/dap-cgi.py/ipcc4/sresa1b/ncar_ccsm3_0 pcmdi.ipcc4.ncar_ccsm3_0.sresa1b.run1.atm.mo.xml
+ncks -M -p http://username:password@esgcet.llnl.gov/cgi-bin/dap-cgi.py/ipcc4/sresa1b/ncar_ccsm3_0 pcmdi.ipcc4.ncar_ccsm3_0.sresa1b.run1.atm.mo.xml
Earth System Grid (ESG): http://www.earthsystemgrid.org
@@ -17463,7 +17838,7 @@ iap_fgoals1_0_g inmcm3_0 ipsl_cm4 miroc3_2_hires miroc3_2_medres \
miub_echo_g mpi_echam5 mri_cgcm2_3_2a ncar_ccsm3_0 ncar_pcm1 \
ukmo_hadcm3 ukmo_hadgem1'; do
for run in '1'; do
- ncks -R -O -D 3 -p ftp://climate.llnl.gov/$@{scn@}/atm/mo/$@{var@}/$@{mdl@}/run$@{run@} -l $@{DATA@}/$@{scn@}/atm/mo/$@{var@}/$@{mdl@}/run$@{run@} '*' $@{scn@}_$@{mdl@}_$@{run@}_$@{var@}_$@{yyyymm@}_$@{yyyymm@}.nc
+ ncks -R -O -D 3 -p ftp://climate.llnl.gov/${scn}/atm/mo/${var}/${mdl}/run${run} -l ${DATA}/${scn}/atm/mo/${var}/${mdl}/run${run} '*' ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
done # end loop over run
done # end loop over mdl
done # end loop over scn
@@ -17471,31 +17846,31 @@ done # end loop over var
cd sresa1b/atm/mo/tas/ukmo_hadcm3/run1/
ncks -H -m -v lat,lon,lat_bnds,lon_bnds -M tas_A1.nc | m
-bds -x 096 -y 073 -m 33 -o $@{DATA@}/data/dst_3.75x2.5.nc # ukmo_hadcm3
-ncview $@{DATA@}/data/dst_3.75x2.5.nc
+bds -x 096 -y 073 -m 33 -o ${DATA}/data/dst_3.75x2.5.nc # ukmo_hadcm3
+ncview ${DATA}/data/dst_3.75x2.5.nc
# msk_rgn is California mask on ukmo_hadcm3 grid
# area is correct area weight on ukmo_hadcm3 grid
-ncks -A -v area,msk_rgn $@{DATA@}/data/dst_3.75x2.5.nc \
-$@{DATA@}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/area_msk_ukmo_hadcm3.nc
+ncks -A -v area,msk_rgn ${DATA}/data/dst_3.75x2.5.nc \
+${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/area_msk_ukmo_hadcm3.nc
Template for standardized data:
-$@{scn@}_$@{mdl@}_$@{run@}_$@{var@}_$@{yyyymm@}_$@{yyyymm@}.nc
+${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
e.g., raw data
-$@{DATA@}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/tas_A1.nc
+${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/tas_A1.nc
becomes standardized data
Level 0: raw from IPCC site--no changes except for name
Make symbolic link name match raw data
-Template: $@{scn@}_$@{mdl@}_$@{run@}_$@{var@}_$@{yyyymm@}_$@{yyyymm@}.nc
+Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
ln -s -f tas_A1.nc sresa1b_ukmo_hadcm3_run1_tas_200101_209911.nc
area_msk_ukmo_hadcm3.nc
Level I: Add all variables (not standardized in time)
to file containing msk_rgn and area
-Template: $@{scn@}_$@{mdl@}_$@{run@}_$@{yyyymm@}_$@{yyyymm@}.nc
+Template: ${scn}_${mdl}_${run}_${yyyymm}_${yyyymm}.nc
/bin/cp area_msk_ukmo_hadcm3.nc sresa1b_ukmo_hadcm3_run1_200101_209911.nc
ncks -A -v tas sresa1b_ukmo_hadcm3_run1_tas_200101_209911.nc \
@@ -17509,7 +17884,7 @@ mv sresa1b_ukmo_hadcm3_run1_200101_209911.nc foo.nc
ncks -A -v tas,pr foo.nc sresa1b_ukmo_hadcm3_run1_200101_209911.nc
Level II: Correct # years, months
-Template: $@{scn@}_$@{mdl@}_$@{run@}_$@{var@}_$@{yyyymm@}_$@{yyyymm@}.nc
+Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
ncks -d time,....... file1.nc file2.nc
ncrcat file2.nc file3.nc sresa1b_ukmo_hadcm3_run1_200001_209912.nc
@@ -17525,6 +17900,7 @@ Level III: Many derived products from level II, e.g.,
ncwa -m msk_rgn -w area -a lat,lon \
sresa1b_ukmo_hadcm3_run1_200001_209912.nc \
sresa1b_ukmo_hadcm3_run1_200001_209912_xy_Cal.nc
+ at end verbatim
@end example
@html
diff --git a/doc/nco.txt b/doc/nco.txt
index 63a35e5..3ff8521 100644
--- a/doc/nco.txt
+++ b/doc/nco.txt
@@ -68,6 +68,10 @@ Summary
3.11 Subsetting Files
3.12 Subsetting Coordinate Variables
3.13 Group Path Editing
+ 3.13.1 Deletion, Truncation, and Flattening of Groups
+ 3.13.2 Moving Groups
+ 3.13.3 Dismembering Files
+ 3.13.4 Checking CF-compliance
3.14 C and Fortran Index conventions
3.15 Hyperslabs
3.16 Stride
@@ -149,7 +153,8 @@ Summary
4.12.2 Normalization and Integration
5 Contributing
5.1 Contributors
- 5.2 Proposals for Institutional Funding
+ 5.2 Citation
+ 5.3 Proposals for Institutional Funding
6 Quick Start
6.1 Daily data in one file
6.2 Monthly data in one file
@@ -191,8 +196,8 @@ illustrates NCO use with examples from the field of climate modeling and
analysis. The NCO homepage is <http://nco.sf.net>, and there is a
mirror at <http://dust.ess.uci.edu/nco>.
- This documentation is for NCO version 4.4.4. It was last updated 20
-May 2014. Corrections, additions, and rewrites of this documentation
+ This documentation is for NCO version 4.4.5. It was last updated 8
+July 2014. Corrections, additions, and rewrites of this documentation
are very welcome.
Enjoy,
@@ -262,17 +267,17 @@ Grenoble, France
The end of the NSF SEI grant in August, 2008 curtailed NCO
development. Fortunately we could justify supporting Henry Butowsky on
other research grants until May, 2010 while he developed the key 'ncap2'
-features used in our climate research. And recentely the NASA ACCESS
-program commenced funding NCO support for netCDF4 group functionality.
+features used in our climate research. And recently the NASA ACCESS
+program commenced funding us to support netCDF4 group functionality.
Thus NCO will grow and evade bit-rot for the foreseeable future.
- On a personal level, I continue to receive with gratitude the thanks
-of NCO users at nearly every scientific meeting I attend. People
-introduce themselves, shake my hand and extol, sometimes rather
-effusively, these time-saving tools. These exchanges lighten me like
-anti-gravity. Sometimes I daydream how many hours NCO has turned from
-grunt work to productive research for researchers world-wide, or from
-research into early happy hours. It's a cool feeling.
+ I continue to receive with gratitude the thanks of NCO users at
+nearly every scientific meeting I attend. People introduce themselves,
+shake my hand and extol NCO, often effusively, while I grin in stupid
+embarassment. These exchanges lighten me like anti-gravity. Sometimes
+I daydream how many hours NCO has turned from grunt work to productive
+research for researchers world-wide, or from research into early
+happy-hours. It's a cool feeling.
Charlie Zender
@@ -353,7 +358,7 @@ Detailed instructions about how to download the newest version
descriptions of Known Problems (http://nco.sf.net/#bug) etc. are on our
homepage (<http://nco.sf.net/>).
- There are twelve operators in the current version (4.4.4). The
+ There are twelve operators in the current version (4.4.5). The
function of each is explained in *note Operator Reference Manual:
Operator Reference Manual. Many of the tasks that NCO can accomplish
are described during the explanation of common NCO Features (*note
@@ -534,7 +539,7 @@ different switches. For example, 'ncdiff' is the same as 'ncbo' and
synonyms by the executing the following UNIX commands in the directory
where the NCO executables are installed.
ln -s -f ncbo ncdiff # ncbo --op_typ='+'
- ln -s -f ncra ncecat # ncra --pseudonym='ncecat'
+ ln -s -f ncra nces # ncra --pseudonym='nces'
ln -s -f ncra ncrcat # ncra --pseudonym='ncrcat'
ln -s -f ncbo ncadd # ncbo --op_typ='+'
ln -s -f ncbo ncsubtract # ncbo --op_typ='-'
@@ -542,7 +547,7 @@ where the NCO executables are installed.
ln -s -f ncbo ncdivide # ncbo --op_typ='/'
ln -s -f ncpdq ncpack # ncpdq
ln -s -f ncpdq ncunpack # ncpdq --unpack
- # NB: Cygwin executable (and link) names have an '.exe' suffix, e.g.,
+ # NB: Windows/Cygwin executable/link names have '.exe' suffix, e.g.,
ln -s -f ncbo.exe ncdiff.exe
...
The imputed command called by the link is given after the comment.
@@ -1134,7 +1139,7 @@ respectively. Initially the record dimension is 'time'. Our goal is to
create a single file that contains joins all the spatially adjacent
regions into one single time-evolving dataset.
for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
- ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
+ ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
done
ncrcat foo_??.nc out.nc # Concatenate along x
ncpdq -a time,x out.nc out.nc # Revert to time as record dimension
@@ -1482,8 +1487,11 @@ controlled by the user.
Availability: All operators
NCO support for "internationalization" of textual input and output
-(e.g., Warning messages) is nascent. We hope to produce foreign
-language string catalogues in 2004.
+(e.g., Warning messages) is nascent. We introduced the first foreign
+language string catalogues (French and Spanish) in 2004, yet did not
+activate these in distributions because the catalogues were nearly
+empty. We seek volunteers to populate our templates with translations
+for their favorite languages.
3.2 Metadata Optimization
=========================
@@ -1670,14 +1678,17 @@ They produce identical answers.
ncra -n 5,2,1 85.nc 8589.nc
The first method (explicitly specifying all filenames) works by brute
force. The second method relies on the operating system shell to "glob"
-(expand) the "regular expression" '8[56789].nc'. The shell passes valid
-filenames which match the expansion to 'ncra'. The third method uses
-the '-p INPUT-PATH' argument to specify the directory where all the
-input files reside. NCO prepends INPUT-PATH (e.g.,
-'/data/usrname/model') to all INPUT-FILES (though not to OUTPUT-FILE).
-Thus, using '-p', the path to any number of input files need only be
-specified once. Note INPUT-PATH need not end with '/'; the '/' is
-automatically generated if necessary.
+(expand) the "regular expression" '8[56789].nc'. The shell then passes
+the valid filenames (those which match the regular expansion) to 'ncra'.
+In this case 'ncra' never knows that a regular expression was used,
+because the shell intercepts and expands and matches the regular
+expression before 'ncra' is actually invoked. The third method uses the
+'-p INPUT-PATH' argument to specify the directory where all the input
+files reside. NCO prepends INPUT-PATH (e.g., '/data/username/model') to
+all INPUT-FILES (though not to OUTPUT-FILE). Thus, using '-p', the path
+to any number of input files need only be specified once. Note
+INPUT-PATH need not end with '/'; the '/' is automatically generated if
+necessary.
The last method passes (with '-n') syntax concisely describing the
entire set of filenames (1). This option is only available with the
@@ -1692,8 +1703,8 @@ standard filetype indicator. For example, in the file 'ccm3_h0001.nc',
we have ALPHANUMERIC_PREFIX = 'ccm3_h', NUMERIC_SUFFIX = '0001', and
FILETYPE = 'nc'.
- NCO is able to decode lists of such filenames encoded using the '-n'
-option. The simpler (3-argument) '-n' usage takes the form '-n
+ NCO decodes lists of such filenames encoded using the '-n' syntax.
+The simpler (3-argument) '-n' usage takes the form '-n
FILE_NUMBER,DIGIT_NUMBER,NUMERIC_INCREMENT' where FILE_NUMBER is the
number of files, DIGIT_NUMBER is the fixed number of numeric digits
comprising the NUMERIC_SUFFIX, and NUMERIC_INCREMENT is the constant,
@@ -1731,10 +1742,10 @@ June-July-August, and December-January-February, respectively:
suffice to specify consecutive months ('06, 07, 08') which do not "wrap"
back to a minimum value. The second example shows how to use the
optional fourth and fifth elements of the '-n' option to specify a wrap
-value to NCO. The fourth argument to '-n', if present, specifies the
-maximum integer value of NUMERIC_SUFFIX. In this case the maximum value
-is 12, and will be formatted as '12' in the filename string. The fifth
-argument to '-n', if present, specifies the minimum integer value of
+value. The fourth argument to '-n', when present, specifies the maximum
+integer value of NUMERIC_SUFFIX. In the example the maximum value is 12,
+and will be formatted as '12' in the filename string. The fifth
+argument to '-n', when present, specifies the minimum integer value of
NUMERIC_SUFFIX. The default minimum filename suffix is 1, which is
formatted as '01' in this case. Thus the second and third examples have
the same effect, that is, they automatically generate, in order, the
@@ -1742,8 +1753,11 @@ filenames '85_12.nc', '85_01.nc', and '85_02.nc' as input to NCO.
---------- Footnotes ----------
- (1) The '-n' option is a backward compatible superset of the 'NINTAP'
-option from the NCAR CCM Processor.
+ (1) The '-n' option is a backward-compatible superset of the 'NINTAP'
+option from the NCAR CCM Processor. The CCM Processor was
+custom-written Fortran code maintained for many years by Lawrence Buja
+at NCAR, and phased-out in the late 1990s. NCO stole some ideas, like
+'NINTAP'-functionality, from the CCM Processor capabilities.
3.6 Specifying Output Files
===========================
@@ -1790,15 +1804,17 @@ privileges, NCAR's Mass Storage System (MSS), or an OPeNDAP server.
Examples of each are given below, following a brief description of the
particular access protocol.
- To access a file via an anonymous FTP server, supply the remote
-file's URL. FTP is an intrinsically insecure protocol because it
-transfers passwords in plain text format. Users should access sites
-using anonymous FTP, or better yet, secure FTP when possible. Some FTP
-servers require a login/password combination for a valid user account.
-NCO allows these transactions so long as the required information is
-stored in the '.netrc' file. Usually this information is the remote
-machine name, login, and password, in plain text, separated by those
-very keywords, e.g.,
+ To access a file via an anonymous FTP server, simply supply the
+remote file's URL. Anonymous FTP usually requires no further
+credentials, e.g., no '.netrc' file is necessary. FTP is an
+intrinsically insecure protocol because it transfers passwords in plain
+text format. Users should access sites using anonymous FTP, or better
+yet, secure FTP (SFTP, see below) when possible. Some FTP servers
+require a login/password combination for a valid user account. NCO
+allows transactions that require additional credentials so long as the
+required information is stored in the '.netrc' file. Usually this
+information is the remote machine name, login, and password, in plain
+text, separated by those very keywords, e.g.,
machine dust.ess.uci.edu login zender password bushlied
Eschew using valuable passwords for FTP transactions, since '.netrc'
passwords are potentially exposed to eavesdropping software (1).
@@ -1808,7 +1824,7 @@ the security issues associated with plain FTP. NCO supports SFTP
protocol access to files specified with a homebrew syntax of the form
sftp://machine.domain.tld:/path/to/filename
Note the second colon following the top-level-domain, 'tld'. This
-syntax is a hybrid between an FTP URL and a standard remote file syntax.
+syntax is a hybrid between an FTP URL and standard remote file syntax.
To access a file using 'rcp' or 'scp', specify the Internet address
of the remote file. Of course in this case you must have 'rcp' or 'scp'
@@ -1939,7 +1955,7 @@ format:
% ncks -H -v one ~/foo.nc
one = 1
And, of course, OPeNDAP-enabled NCO clients continue to support
-other, orthogonal features such as UDUnits (*note UDUnits Support::):
+orthogonal features such as UDUnits (*note UDUnits Support::):
% ncks -u -C -H -v wvl -d wvl,'0.4 micron','0.7 micron' \
-p http://thredds-test.ucar.edu/thredds/dodsC/testdods in_4.nc
% wvl[0]=5e-07 meter
@@ -1954,9 +1970,9 @@ mean surface pressure (in Pa).
http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/surface \
pres.sfc.1969.nc ~/foo.nc
All with one command! The data in this particular input file also
-happen to be packed (*note Methods and functions::), although this is
-completely transparent to the user since NCO automatically unpacks data
-before attempting arithmetic.
+happen to be packed (*note Methods and functions::), although this
+complication is transparent to the user since NCO automatically unpacks
+data before attempting arithmetic.
NCO obtains remote files from the OPeNDAP server (e.g.,
'www.cdc.noaa.gov') rather than the local machine. Input files are
@@ -2348,11 +2364,6 @@ to configure LFS at build time.
3.11 Subsetting Files
=====================
-Options '--unn'
-Availability: 'ncbo', 'nces', 'ncecat', 'ncflint', 'ncks', 'ncpdq',
-'ncra', 'ncrcat', 'ncwa'
-Short options:
-Long options: '--unn' and '--union'
Options '-g GRP'
Availability: 'ncbo', 'nces', 'ncecat', 'ncflint', 'ncks', 'ncpdq',
'ncra', 'ncrcat', 'ncwa'
@@ -2363,6 +2374,15 @@ Availability: ('ncap2'), 'ncbo', 'nces', 'ncecat', 'ncflint', 'ncks',
'ncpdq', 'ncra', 'ncrcat', 'ncwa'
Short options: '-v', '-x'
Long options: '--variable', '--exclude' or '--xcl'
+Options '--unn'
+Availability: 'ncbo', 'nces', 'ncecat', 'ncflint', 'ncks', 'ncpdq',
+'ncra', 'ncrcat', 'ncwa'
+Short options:
+Long options: '--unn' and '--union'
+Options '--grp_xtr_var_xcl'
+Availability: 'ncks'
+Short options:
+Long options: '--gxvx' and '--grp_xtr_var_xcl'
Subsetting variables refers to explicitly specifying variables and
groups to be included or excluded from operator actions. Subsetting is
controlled by the '-v VAR[,...]' and '-x' options for directly
@@ -2390,6 +2410,17 @@ controlled by a few powerful yet subtle syntactical distinctions. When
learning this syntax it is helpful to keep in mind the similarity
between group hierarchies and directory structures.
+ As of NCO 4.4.4 (June, 2014), 'ncks' (alone) supports an option to
+include specified groups yet exclude specified variables. The
+'--grp_xtr_var_xcl' switch (with long option equivalent '--gxvx')
+extracts all contents of groups given as arguments to '-g GRP[,...]',
+except for variables given as arguments to '-v VAR[,...]'. Use this
+when one or a few variables in hierarchical files are not to be
+extracted, and all other variables are. This is useful when coercing
+netCDF4 files into netCDF3 files such as with converting, flattening, or
+dismembering files (see *note Flattening Groups::).
+ ncks --grp_xtr_var_xcl -g g1 -v v1 # Extract all of group g1 except v1
+
Two properties of subsetting, recursion and anchoring, are best
illustrated by reminding the user of their UNIX equivalents. The UNIX
command 'mv src dst' moves 'src' _and all its subdirectories_ (and all
@@ -2608,10 +2639,12 @@ simply by explicitly selecting the coordinates with the -V option. The
specifying that _all_ coordinate variables in the INPUT-FILES should
appear in the OUTPUT-FILE. Thus '-c' allows the user to select all the
coordinate variables without having to know their names. As of NCO
+version 4.4.5 (July, 2014) both '-c' and '-C' honor the CF
+'ancillary_variables' convention described in *note CF Conventions::.
+As of NCO version 4.0.8 (April, 2011) both '-c' and '-C' honor the CF
+'bounds' convention described in *note CF Conventions::. As of NCO
version 3.9.6 (January, 2009) both '-c' and '-C' honor the CF
-'coordinates' convention described in *note CF Conventions::. As of NCO
-version 4.0.8 (April, 2011) both '-c' and '-C' honor the CF 'bounds'
-convention described in *note CF Conventions::.
+'coordinates' convention described in *note CF Conventions::.
3.13 Group Path Editing
=======================
@@ -2654,10 +2687,12 @@ positive and it will be assumed to refer to Truncation-Mode. Hence, '-G
:-1' is the same as '-G @1'. This is simply a way of making the LVL_NBR
argument positive-definite.
- GPE has three editing modes: Delete, Truncate, and Flatten. Select
-one of GPE's three editing modes by supplying a LVL_NBR that is
-positive, negative, or zero for Delete-, Truncate- and Flatten-mode,
-respectively.
+3.13.1 Deletion, Truncation, and Flattening of Groups
+-----------------------------------------------------
+
+GPE has three editing modes: Delete, Truncate, and Flatten. Select one
+of GPE's three editing modes by supplying a LVL_NBR that is positive,
+negative, or zero for Delete-, Truncate- and Flatten-mode, respectively.
In Delete-mode, LVL_NBR is a positive integer which specifies the
maximum number of group path components (i.e., groups) that GPE will try
@@ -2742,12 +2777,15 @@ commands. All commands below may be assumed to end with 'in.nc out.nc'.
ncks -G g2:-1 -g g1 -v v1 # /g1/v1 -> /g2/v1
ncks -G g1:-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/g1/v1
- Until fall 2013 (netCDF version 4.3.1-pre1), netCDF contained no
-library function for renaming groups, and therefore 'ncrename' cannot
-rename groups. However, NCO built on earlier versions of netCDF than
-4.3.1 can use a GPE-based workaround mechanism to "rename" groups. The
-GPE mechanism actually _moves_ (i.e., copies to a new location) groups,
-a more arduous procedure than simply renaming them. GPE applies to all
+3.13.2 Moving Groups
+--------------------
+
+Until fall 2013 (netCDF version 4.3.1-pre1), netCDF contained no library
+function for renaming groups, and therefore 'ncrename' cannot rename
+groups. However, NCO built on earlier versions of netCDF than 4.3.1 can
+use a GPE-based workaround mechanism to "rename" groups. The GPE
+mechanism actually _moves_ (i.e., copies to a new location) groups, a
+more arduous procedure than simply renaming them. GPE applies to all
selected groups, so, in the general case, one must move only the desired
group to a new file, and then merge that new file with the original to
obtain a file where the desired group has been "renamed" and all else is
@@ -2773,7 +2811,16 @@ format, the '-G :' option flattens all extracted groups, and the '-g
cesm' option extracts only the 'cesm' group and leaves all other groups
(e.g., 'ecmwf', 'giss').
- Let us show how to completely disaggregate (or, more memorably)
+ ---------- Footnotes ----------
+
+ (1) Note that the '-3' switch should appear _after_ the '-G' and '-g'
+switches. This is due to an artifact of the GPE implementation which we
+wish to remove in the future.
+
+3.13.3 Dismembering Files
+-------------------------
+
+Let us show how to completely disaggregate (or, more memorably)
_dismember_ a hierarchical dataset. For now we take this to mean: store
each group as a standalone flat dataset in netCDF3 format. This can be
accomplished by looping the previous example over all groups. This
@@ -2839,7 +2886,8 @@ specified by the second argument:
eval ${cmd}
if [ ${flg_cf} = 'cf' ]; then
# cfchecker needs Conventions <= 1.5
- ncatted -h -a Conventions,global,o,c,"CF-${cf_vrs}" ${drc_out}/${grp_out}.nc
+ no_bck_sls=`echo ${drc_out}/${grp_out} | sed 's/\\\ / /g'`
+ ncatted -h -a Conventions,global,o,c,CF-${cf_vrs} ${no_bck_sls}.nc
else # !flg_cf
echo ${drc_out}/${grp_out}.nc
fi # !flg_cf
@@ -2876,9 +2924,12 @@ autoconverts netCDF4-only atomic-types (such as 'NC_STRING' and
'NC_UBYTE') to corresponding netCDF3 atomic types ('NC_CHAR' and
'NC_SHORT') when the output format is netCDF3.
- One application of dismembering is to check the CF-compliance of each
+3.13.4 Checking CF-compliance
+-----------------------------
+
+One application of dismembering is to check the CF-compliance of each
group in a file. When invoked with the optional third argumnt 'cf',
-'ncdismember' passes each file it generates to the freely available (2)
+'ncdismember' passes each file it generates to the freely available (1)
'cfchecker' command.
zender at roulee:~$ ncdismember ~/nco/data/mdl_1.nc /data/zender/nco/tmp cf
NCO dismembering file /home/zender/nco/data/mdl_1.nc
@@ -2920,15 +2971,15 @@ conventions.
NASA asked the DIWG to prepare a one-page summary of the procedure
necessary to check HDF files for CF-compliance:
cat > ~/ncdismember.txt << 'EOF'
- Preparing an RPM-based OS to Test Hierarchical Files for CF-Compliance
+ Preparing an RPM-based OS to Test HDF & netCDF Files for CF-Compliance
By Charlie Zender, UCI & NASA Dataset Interoperability Working Group (DIWG)
Installation Summary:
- 1. HDF4 [with netCDF support _disabled_]
+ 1. HDF4 [with internal netCDF support _disabled_]
2. HDF5
- 3. netCDF version 4.3.1 (or later) [with HDF4 support _enabled_]
- 4. NCO version 4.4.0 (or later)
+ 3. netCDF [with external HDF4 support _enabled_]
+ 4. NCO
5. numpy
6. netcdf4-python
7. python-lxml
@@ -2959,20 +3010,19 @@ necessary to check HDF files for CF-compliance:
./configure --enable-shared --prefix=${H5DIR}
make && make check && make install
- # 3. netCDF version 4.3.1. Build in non-default manner with HDF4. No RPM.
+ # 3. netCDF version 4.3.1 or later. Build in non-default manner with HDF4.
# Per http://www.unidata.ucar.edu/software/netcdf/docs/build_hdf4.html
# Earlier versions of netCDF may fail checking some HDF4 files
- wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.1.tar.gz
- tar xvzf netcdf-4.3.1.tar.gz
- cd netcdf-4.3.1
+ wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz
+ tar xvzf netcdf-4.3.2.tar.gz
+ cd netcdf-4.3.2
CPPFLAGS="-I${H5DIR}/include -I${H4DIR}/include" \
LDFLAGS="-L${H5DIR}/lib -L${H4DIR}/lib" \
./configure --enable-hdf4 --enable-hdf4-file-tests
- make && make check && make installas
+ make && make check && make install
- # 4. NCO version 4.4.4. No RPM for this version. Must install by hand.
- # Earlier versions of NCO are relatively useless for ncdismember
- cd ${DATA}/tmp
+ # 4. NCO version 4.4.0 or later. Some RPMs available. Or install by hand.
+ # Later versions of NCO have much better support for ncdismember
wget http://nco.sourceforge.net/src/nco-4.4.4.tar.gz .
tar xvzf nco-4.4.4.tar.gz
cd nco-4.4.4
@@ -2990,14 +3040,13 @@ necessary to check HDF files for CF-compliance:
# 8. CFunits-python. No RPM available. Must install by hand.
# http://code.google.com/p/cfunits-python/
- cd ${DATA}/tmp
wget http://cfunits-python.googlecode.com/files/cfunits-0.9.6.tar.gz .
+ tar xvzf cfunits-0.9.6.tar.gz
cd cfunits-0.9.6
sudo python setup.py install
# 9. CFChecker. No RPM available. Must install by hand.
# https://bitbucket.org/mde_/cfchecker
- cd ${DATA}/tmp
wget https://bitbucket.org/mde_/cfchecker/downloads/CFchecker-1.5.15.tar.bz2 .
tar xvjf CFchecker-1.5.15.tar.bz2
cd CFchecker
@@ -3024,11 +3073,7 @@ necessary to check HDF files for CF-compliance:
---------- Footnotes ----------
- (1) Note that the '-3' switch should appear _after_ the '-G' and '-g'
-switches. This is due to an artifact of the GPE implementation which we
-wish to remove in the future.
-
- (2) CFchecker is developed by Michael Decker and Martin Schultz at
+ (1) CFchecker is developed by Michael Decker and Martin Schultz at
Forschungszentrum Ju"lich and distributed at
<https://bitbucket.org/mde_/cfchecker>.
@@ -3558,9 +3603,9 @@ supports hyperslabbing cell-based grids over coordinate ranges. This
works on datasets that associate coordinate variables to grid-mappings
using the CF-convention (*note CF Conventions::) 'coordinates' and
'standard_name' attributes described here
-(http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system).
-Currently, NCO understands auxiliary coordinate variables pointed to by
-the 'standard_name' attributes for LATITUDE and LONGITUDE. Cells that
+(http://cfconventions.org/1.6.html#coordinate-system). Currently, NCO
+understands auxiliary coordinate variables pointed to by the
+'standard_name' attributes for LATITUDE and LONGITUDE. Cells that
contain a value within the user-specified range
[LON_MIN,LON_MAX,LAT_MIN,LAT_MAX] are included in the output hyperslab.
@@ -4044,14 +4089,15 @@ can tune the three switches in tandem to obtain optimal performance.
The user specifies the desired chunking policy with the '-P' switch
(or its long option equivalents, '--cnk_plc' and '--chunk_policy') and
-its CNK_PLC argument. Five chunking policies are currently implemented:
-"Chunk All Variables [_default_]"
+its CNK_PLC argument. As of August, 2014, six chunking policies are
+currently implemented:
+"Chunk All Variables"
Definition: Chunk all variables possible. For obvious reasons,
scalar variables cannot be chunked.
Alternate invocation: 'ncchunk'
CNK_PLC key values: 'all', 'cnk_all', 'plc_all'
Mnemonic: All
-"Chunk Variables with at least Two Dimensions"
+"Chunk Variables with at least Two Dimensions [_default_]"
Definition: Chunk all variables possible with at least two
dimensions
Alternate invocation: none
@@ -4063,6 +4109,15 @@ its CNK_PLC argument. Five chunking policies are currently implemented:
Alternate invocation: none
CNK_PLC key values: 'g3d', 'cnk_g3d', 'plc_g3d'
Mnemonic: _G_reater than or equal to _3_ _D_imensions
+"Chunk One-Dimensional Record Variables"
+ Definition: Chunk all 1-D record variables
+ Alternate invocation: none
+ Any specified (with '--cnk_dmn') record dimension chunksizes will
+ be applied to 1-D record variables (and to no other variables).
+ Other dimensions may be chunked with their own '--cnk_dmn' options
+ that will apply to all variables. CNK_PLC key values: 'r1d',
+ 'cnk_r1d', 'plc_r1d'
+ Mnemonic: _R_ecord _1_-_D_ variables
"Chunk Variables Containing Explicitly Chunked Dimensions"
Definition: Chunk all variables possible that contain at least one
dimension whose chunksize was explicitly set with the '--cnk_dmn'
@@ -4192,6 +4247,15 @@ many times as necessary.
ncwa -O -4 -D 4 -a time --cnk_plc=g2d --cnk_map=rd1 --cnk_dmn lat,32 \
--cnk_dmn lon,128 dstmch90_clm_0112.nc ~/foo.nc
+ Chunking policy 'r1d' changes the chunksize of 1-D record variables
+(and no other variables) to the specified (with '--cnk_dmn') chunksize.
+Any specified record dimension chunksizes will be applied to 1-D record
+variables only. Other dimensions may be chunked with their own
+'--cnk_dmn' options that will apply to all variables. For example,
+ ncks --cnk_plc=r1d --cnk_dmn=time,1000. in.nc out.nc
+ This sets 'time' chunks to 1000 only in 1-D record variables.
+Without the 'r1d' policy, 'time' chunks would change in all variables.
+
It is appropriate to conclude by informing users about an aspect of
chunking that may not be expected. Three types of variables are
_always_ chunked: Record variables, Deflated (compressed) variables, and
@@ -4823,7 +4887,7 @@ employed the C library family of rounding functions, 'lround()'. These
functions round X to the nearest integer, halfway cases away from zero.
The problem with 'lround()' is that it always rounds real values ending
in '.5' away from zero. This rounds, for example, '1.5d' and '2.5d' to
-'1s' and '2s', respectively.
+'2s' and '3s', respectively.
Since April, 2013 (version 4.3.0), NCO has employed the other C library
family of rounding functions, 'lrint()'. This algorithm rounds X to the
@@ -5296,14 +5360,14 @@ datasets may not contain an explicit 'Conventions' attribute (e.g.,
'CF-1.0'). Nevertheless, we refer to all such metadata collectively as
CF metadata. Skip this section if you never work with CF metadata.
- The CF netCDF conventions are described here
-(http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system).
-Most CF netCDF conventions are transparent to NCO (1). There are no
-known pitfalls associated with using any NCO operator on files adhering
-to these conventions (2). However, to facilitate maximum user
-friendliness, NCO applies special rules to certain variables in CF
-files. The special functions are not required by the CF netCDF
-conventions, yet experience shows that they simplify data analysis.
+ The latest CF netCDF conventions are described here
+(http://cfconventions.org/1.6.html). Most CF netCDF conventions are
+transparent to NCO (1). There are no known pitfalls associated with
+using any NCO operator on files adhering to these conventions (2).
+However, to facilitate maximum user friendliness, NCO applies special
+rules to certain variables in CF files. The special functions are not
+required by the CF netCDF conventions, yet experience shows that they
+simplify data analysis.
Currently, NCO determines whether a datafile is a CF output datafile
simply by checking (case-insensitively) whether the value of the global
@@ -5342,32 +5406,44 @@ first with 'ncrename', or alter the 'Conventions' attribute.
As of NCO version 4.0.8 (April, 2011), NCO supports the CF 'bounds'
convention for cell boundaries described here
-(http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#cell-boundaries).
-This convention allows coordinate variables (including multidimensional
-coordinates) to describe the boundaries of their cells. This is done by
-naming the variable which contains the bounds in in the 'bounds'
-attribute. Note that coordinates of rank N have bounds of rank N+1.
-NCO-generated subsets of CF-compliant files with 'bounds' attributes
-will include the coordinates specified by the 'bounds' attribute, if
-any. Hence the subsets will themselves be CF-compliant.
+(http://cfconventions.org/1.6.html#cell-boundaries). This convention
+allows coordinate variables (including multidimensional coordinates) to
+describe the boundaries of their cells. This is done by naming the
+variable which contains the bounds in in the 'bounds' attribute. Note
+that coordinates of rank N have bounds of rank N+1. NCO-generated
+subsets of CF-compliant files with 'bounds' attributes will include the
+coordinates specified by the 'bounds' attribute, if any. Hence the
+subsets will themselves be CF-compliant. Bounds are subject to the
+user-specified override switches (including '-c' and '-C') described in
+*note Subsetting Coordinate Variables::.
+
+ As of NCO version 4.4.5 (July, 2014), NCO supports the CF
+'ancillary_variables' convention for described here
+(http://cfconventions.org/1.6.html#ancillary-data). This convention
+allows ancillary variables to be associated with one or more primary
+variables. NCO attaches any such variables to the extraction list along
+with the primary variable and its usual (one-dimensional) coordinates,
+if any. Ancillary variables are subject to the user-specified override
+switches (including '-c' and '-C') described in *note Subsetting
+Coordinate Variables::.
As of NCO version 3.9.6 (January, 2009), NCO supports the CF
'coordinates' convention described here
-(http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system).
-This convention allows variables to specify additional coordinates
-(including multidimensional coordinates) in a space-separated string
-attribute named 'coordinates'. NCO attaches any such coordinates to the
+(http://cfconventions.org/1.6.html#coordinate-system). This convention
+allows variables to specify additional coordinates (including
+multidimensional coordinates) in a space-separated string attribute
+named 'coordinates'. NCO attaches any such coordinates to the
extraction list along with variable and its usual (one-dimensional)
coordinates, if any. These auxiliary coordinates are subject to the
-user-specified overrides described in *note Subsetting Coordinate
-Variables::.
+user-specified override switches (including '-c' and '-C') described in
+*note Subsetting Coordinate Variables::.
As of NCO version 4.4.2 (February, 2014), NCO supports some of the CF
'cell_methods' convention
-(http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.7-draft1/cf-conventions.html#cell-methods)
-to describe the analysis procedures that have been applied to data. The
-convention creates (or appends to an existing) 'cell_methods' attribute
-a space-separated list of couplets of the form DMN: OP where DMN is a
+(http://cfconventions.org/1.6.html#cell-methods) to describe the
+analysis procedures that have been applied to data. The convention
+creates (or appends to an existing) 'cell_methods' attribute a
+space-separated list of couplets of the form DMN: OP where DMN is a
comma-separated list of dimensions previously contained in the variable
that have been reduced by the arithmetic operation OP. For example, the
'cell_methods' value 'time: mean' says that the variable in question was
@@ -6027,23 +6103,23 @@ The table below lists the postfix character(s) to add to a number
literal for type cohesion. To use the new netCDF4 types NCO must be
compiled/linked to the netCDF4 library and the output file must be HDF5.
- n1[$time]=1UL; // n1 will now by type NC_UINT
- n2[$lon]=4b; // n2 will be of type NC_BYTE
- n3[$lat]=5ull; // n3 will be of type NC_UINT64
- n3 at a1=6.0d; // attribute will be type NC_DOUBLE
- n3 at a2=-666L; // attribute will be type NC_INT
+ n1[$time]=1UL; // n1 will now by type @code{NC_UINT}
+ n2[$lon]=4b; // n2 will be of type @code{NC_BYTE}
+ n3[$lat]=5ull; // n3 will be of type @code{NC_UINT64}
+ n3 at a1=6.0d; // attribute will be type @code{NC_DOUBLE}
+ n3 at a2=-666L; // attribute will be type @code{NC_INT}
A floating point number without a postfix will default to
'NC_DOUBLE'. An integer without a postfix will default to type
'NC_INT'. There is no postfix for characters, use a quoted string
instead.
- n4[$rlev]=0.1 // n4 will be of type NC_DOUBLE
- n5[$lon_grd]=2.0 // n5 will be of type NC_DOUBLE
- n6[$gds_crd]=2e3; // n6 will be of type NC_DOUBLE
- n7[$gds_crd]=2e3f; // n7 will be of type NC_FLOAT
- n6 at a1=41; // attribute will be type NC_INT
- n6 at a2=-21; // attribute will be type NC_INT
- n6 at units="kelvin" // attribute will be type NC_CHAR
+ n4[$rlev]=0.1 // n4 will be of type @code{NC_DOUBLE}
+ n5[$lon_grd]=2.0 // n5 will be of type @code{NC_DOUBLE}
+ n6[$gds_crd]=2e3; // n6 will be of type @code{NC_DOUBLE}
+ n7[$gds_crd]=2e3f; // n7 will be of type @code{NC_FLOAT}
+ n6 at a1=41; // attribute will be type @code{NC_INT}
+ n6 at a2=-21; // attribute will be type @code{NC_INT}
+ n6 at units="kelvin" // attribute will be type @code{NC_CHAR}
*netCDF3/4 Types*
b|B
@@ -6087,9 +6163,9 @@ _Conditional Operator (ternary operator)_ has also been implemented.
stmt1;
stmt1a;
stmt1b;
- } else if(exp2)
+ }else if(exp2)
stmt2;
- else {
+ else{
stmt3;
stmt3a;
stmt3b;
@@ -6216,9 +6292,9 @@ with a variable. They only work on variables in Output.
is returned. If the variable has no missing value then an error is
returned.
'delete_miss()'
- Deletes the missing value associated with a variable.
+ Delete the missing value associated with a variable.
'number_miss()'
- Counts the number of missing values a variable contains.
+ Count the number of missing values a variable contains.
th=three_dmn_var_dbl;
th.change_miss(-1e10d);
@@ -6479,10 +6555,13 @@ set its values less than 8 or greater than 80 to 0:
Consider irregularly gridded data, described using rank 2
coordinates: 'double lat(south_north,east_west)', 'double
lon(south_north,east_west)', 'double
-temperature(south_north,east_west)'. To find the average temperature in
-a region bounded by [LAT_MIN,LAT_MAX] and [LON_MIN,LON_MAX]:
+temperature(south_north,east_west)'. This type of structure is often
+found in regional weather/climate model (such as WRF) output, and in
+satellite swath data. For this reason we call it "Swath-like Data", or
+SLD. To find the average temperature in a region bounded by
+[LAT_MIN,LAT_MAX] and [LON_MIN,LON_MAX]:
temperature_msk[$south_north,$east_west]=0.0;
- where(lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max)
+ where((lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max))
temperature_msk=temperature;
elsewhere
temperature_msk=temperature at _FillValue;
@@ -6490,6 +6569,42 @@ a region bounded by [LAT_MIN,LAT_MAX] and [LON_MIN,LON_MAX]:
temp_avg=temperature_msk.avg();
temp_max=temperature.max();
+ For North American Regional Reanalysis (NARR) data (example dataset
+(http://dust.ess.uci.edu/diwg/narr_uwnd.199605.nc)) the procedure looks
+like this
+ ncap2 -O -v -S ~/narr.nco ${DATA}/hdf/narr_uwnd.199605.nc ~/foo.nc
+ where 'narr.nco' is an 'ncap2' script like this:
+ /* North American Regional Reanalysis (NARR) Statistics
+ NARR stores grids with 2-D latitude and longitude, aka Swath-like Data (SLD)
+ Here we work with three variables:
+ lat(y,x), lon(y,x), and uwnd(time,level,y,x);
+ To study sub-regions of SLD, we use masking techniques:
+ 1. Define mask as zero times variable to be masked
+ Then mask automatically inherits variable attributes
+ And average below will inherit mask attributes
+ 2. Optionally, create mask as RAM variable (as below with asterisk *)
+ NCO does not write RAM variable to output
+ Masks are often unwanted, and can be big, so this speeds execution
+ 3. Example could be extended to preserve mean lat and lon of sub-region
+ Follow uwnd example to do this: lat_msk=0.0*lat ... lat_avg=lat.avg($y,$x) */
+ *uwnd_msk=0.0*uwnd;
+ where((lat >= 35.6 && lat <= 37.0) && (lon >= -100.5 && lon <= -99.0))
+ uwnd_msk=uwnd;
+ elsewhere
+ uwnd_msk=uwnd at _FillValue;
+
+ // Average only over horizontal dimensions x and y (preserve level and time)
+ uwnd_avg=uwnd_msk.avg($y,$x);
+ Stripped of comments and formatting, this example is a
+three-statement script executed by a one-line command. NCO needs only
+this meagre input to unpack and copy the input data and attributes,
+compute the statistics, and then define and write the output file.
+Unless the comments pointed out that wind variable ('uwnd') was
+four-dimensional and the latitude/longitude grid variables were both
+two-dimensional, there would be no way to tell. This shows how NCO
+hides from the user the complexity of analyzing multi-dimensional SLD.
+We plan to extend such SLD features to more operators soon.
+
4.1.14 Loops
------------
@@ -6882,7 +6997,7 @@ document the procedure:
must use global metadata to determine the grid staggering and offsets to
translate 'XLAT' and 'XLONG' into real latitudes, longitudes, and
missing points. The WRF grid documentation should describe this. For
-WRF files creating regional masks looks like
+WRF files creating regional masks looks, in general, like
mask_var = (XLAT >= lat_min && XLAT <= lat_max) && (XLONG >= lon_min && XLONG <= lon_max);
A few notes: Irregular regions are the union of arrays
@@ -7580,7 +7695,7 @@ final value in the vector.
Some examples
- a1[time]={1,2,3,4,5,6,7,8,9,10 };
+ a1[time]={1,2,3,4,5,6,7,8,9,10};
a1_avg=gsl_stats_mean(a1,1,10);
print(a1_avg); // 5.5
@@ -8320,9 +8435,9 @@ sequences.
whatever it currently is to "temperature":
ncatted -a long_name,T,o,c,temperature in.nc
- NCO arithmetic operators will not work as expected on IEEE NaN (short
+ NCO arithmetic operators may not work as expected on IEEE NaN (short
for Not-a-Number) and NaN-like numbers such as positive infinity and
-negative infinity. One way to work-around this problem is to change
+negative infinity (1). One way to work-around this problem is to change
IEEE NaNs to normal missing values. As of NCO 4.1.0 (March, 2012),
'ncatted' works with NaNs. First set the missing value (i.e., the value
of the '_FillValue' attribute) for the variable(s) in question to the
@@ -8392,6 +8507,13 @@ other special characters (e.g., '\"')
quotes. These outer single quotes are necessary for interactive use,
but may be omitted in batch scripts.
+ ---------- Footnotes ----------
+
+ (1) Arithmetic comparisons to NaN and NaN-like numbers always return
+False, contrary to the behavior of all other numbers. This is difficult
+to inuit, yet is the behavior defined for NaN by IEEE 754. Using NaN
+for the missing value in datasets is legal. We strongly discourage it.
+
4.3 'ncbo' netCDF Binary Operator
=================================
@@ -8508,13 +8630,14 @@ FILE_2 was created by applying an averaging operator to a file with
initially the same dimensions as FILE_1 (often FILE_1 itself). In these
cases, creating FILE_2 with 'ncra' rather than 'ncwa' will cause the
'ncbo' operation to fail. For concreteness say the record dimension in
-'file_1' is 'time'. If FILE_2 were created by averaging FILE_1 over the
-'time' dimension with the 'ncra' operator rather than with the 'ncwa'
-operator, then FILE_2 will have a 'time' dimension of size 1 rather than
-having no 'time' dimension at all (6). In this case the input files to
-'ncbo', FILE_1 and FILE_2, will have unequally sized 'time' dimensions
-which causes 'ncbo' to fail. To prevent this from occuring, use 'ncwa'
-to remove the 'time' dimension from FILE_2. See the example below.
+'file_1' is 'time'. If FILE_2 was created by averaging FILE_1 over the
+'time' dimension with the 'ncra' operator (rather than with the 'ncwa'
+operator), then FILE_2 will have a 'time' dimension of size 1 rather
+than having no 'time' dimension at all (6). In this case the input
+files to 'ncbo', FILE_1 and FILE_2, will have unequally sized 'time'
+dimensions which causes 'ncbo' to fail. To prevent this from occuring,
+use 'ncwa' to remove the 'time' dimension from FILE_2. See the example
+below.
'ncbo' never operates on coordinate variables or variables of type
'NC_CHAR' or 'NC_STRING'. This ensures that coordinates like (e.g.,
@@ -9130,7 +9253,7 @@ SYNTAX
ncks [-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b BINARY-FILE] [-C] [-c] [--cdl]
[--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz]
[-D DBG] [-d DIM,[MIN][,[MAX][,[STRIDE]]] [-F] [--fix_rec_dmn DIM]
- [-G GPE_DSC] [-g GRP[,...]] [-H] [-h] [--hdn] [--hdr_pad NBR]
+ [-G GPE_DSC] [-g GRP[,...]] [--grp_xtr_var_xcl] [-H] [-h] [--hdn] [--hdr_pad NBR]
[-L DFL_LVL] [-l PATH] [-M] [-m] [--mk_rec_dmn DIM] [--md5_digest]
[--no_blank] [--no_tmp_fl] [-O] [-o OUTPUT-FILE] [-P] [-p PATH]
[-Q] [-q] [-R] [-r] [--rad] [--ram_all] [-s FORMAT]
@@ -9502,7 +9625,7 @@ features::.
netCDF4 files into NcML, including metadata and data, using all
NCO's subsetting and hyperslabbing capabilities. Compare 'ncks'
"traditional" with XML printing:
- zender@@roulee:~$ ncks -v one ~/nco/data/in.nc
+ zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
@@ -9536,19 +9659,19 @@ features::.
used as NcML separators for attributes and variables of
character-type and numeric-type, respectively. Their default
separators are "*" and " ":
- zender@@roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
+ zender at roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
...
<values separator="*">abc*bcd*cde*def</values>
...
- zender@@roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
+ zender at roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
...
<values separator=", ">abc, bcd, cde, def, efg, fgh, ghi, hij, jkl, klm</values>
...
- zender@@roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
+ zender at roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
...
<values>1 2 3 4 5 6 7 8 9 10</values>
...
- zender@@roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
+ zender at roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
...
<values separator=", ">1, 2, 3, 4, 5, 6, 7, 8, 9, 10</values>
...
@@ -9757,16 +9880,17 @@ thus not technically strings) is likely to result in a core dump.
coordinates, except variable 'time', from netCDF 'in.nc':
ncks -x -v time in.nc out.nc
As a special case of this, consider how to remove a CF Convention
-comliant 'bounds' or 'coordinates' variable (*note CF Conventions::)
-such as 'time_bounds'. NCO subsetting assumes the user wants all
-coordinates and bounds and axes associated with all extracted variables
-(*note Subsetting Coordinate Variables::). Hence to exclude a 'bounds'
-or 'coordinates' variable while retaining the "parent" variable (here
+comliant 'ancillary_variables', 'bounds', or 'coordinates' variable
+(*note CF Conventions::) such as 'time_bounds'. NCO subsetting assumes
+the user wants all ancillary variables, axes, bounds and coordinates
+associated with all extracted variables (*note Subsetting Coordinate
+Variables::). Hence to exclude a 'ancillary_variables', 'bounds', or
+'coordinates' variable while retaining the "parent" variable (here
'time'), one must use the '-C' switch:
ncks -C -x -v time_bounds in.nc out.nc
The '-C' switch tells the operator _NOT_ to necessarily include all
-the CF coordinates and bounds and axes. Hence the output file will
-contain 'time' and not 'time_bounds'.
+the CF ancillary variables, axes, bounds, and coordinates. Hence the
+output file will contain 'time' and not 'time_bounds'.
Extract variables 'time' and 'pressure' from netCDF 'in.nc'. If
'out.nc' does not exist it will be created. Otherwise the you will be
@@ -10784,11 +10908,11 @@ Charlie Zender
Henry Butowsky
Non-linear operations and 'min()', 'max()', 'total()' support in
'ncra' and 'ncwa'. Type conversion for arithmetic. Migration to
- netCDF3 API. 'ncap2' parser, lexer, GSL-support, and I/O.
+ netCDF3 API. 'ncap2' parser, lexer, GSL-support, and I/O.
Multislabbing algorithm. Variable wildcarding. Numerous hacks.
'ncap2' language.
Rorik Peterson
- Original autotool build support. Long command-line options.
+ Original autotools build support. Long command-line options.
Original UDUnits support. Debianization. Numerous bug-fixes.
Joe Hamman
Python bindings (NCOpy).
@@ -10818,7 +10942,7 @@ Gayathri Venkitachalam
MPI implementation.
Scott Capps
Large work-load testing
-Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski
+Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Rich Signell, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski
Excellent bug reports and feature requests.
Daniel Baumann, Nick Bower, Luk Claebs, Barry deFreese, Aleksandar Jelenak, Francesco Lovergine, Matej Vela
Debian packaging
@@ -10842,7 +10966,26 @@ Wenshan Wang
CMIP5 and MODIS processing documentation.
Please let me know if your name was omitted!
-5.2 Proposals for Institutional Funding
+5.2 Citation
+============
+
+The recommended citations for NCO software are
+ Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience
+ Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10),
+ 1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+
+ Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.3,
+ http://nco.sf.net/nco.pdf.
+ Use the former when referring to overall design, purpose, and
+optimization of NCO, and use the latter when referring to specific
+features and/or the User Guide itself.
+
+ Additional information on citing NCO is in the User Guide at
+<http://nco.sf.net#ctt>. A complete list of NCO publications and
+presentations is at <http://nco.sf.net#pub>. This list links to the
+full papers and seminars themselves.
+
+5.3 Proposals for Institutional Funding
=======================================
NSF has funded a project (http://nco.sf.net#prp_sei) to improve
@@ -10970,26 +11113,48 @@ a multi-model framework for comparing the mechanisms and responses of
climate models from around the world. However, it is a tremendous
workload to retrieve a single climate statistic from all these models,
each of which includes several ensemble members. Not only that, it is
-too often a repetitive process which impedes new research and hypothesis
-testing. Our NASA ACCESS project is designed to simplify and accelerate
-this process. To begin, we document below a prototypical example of
-CMIP5 analysis and evaluation using traditional NCO commands on
-netCDF3-format model and HDF-EOS format observational (NASA MODIS
-satellite instrument) datasets. These examples complement the NCO User
-Guide by detailing in-depth data analysis in a frequently encountered
-"real world" context. Graphical representations of the results (NCL
-scripts available upon request) are provided to illustrate physical
-meaning of the analysis. Since NCO can process hierarchical datasets,
-i.e., datasets stored with netCDF4 groups, we present sample scripts
-illustrating group-based processing as well.
+too often a tedious process that impedes new research and hypothesis
+testing. Our NASA ACCESS 2011 project simplified and accelerated this
+process.
+
+ Traditional geoscience data analysis requires users to work with
+numerous flat (data in one level or namespace) files. In that paradigm
+instruments or models produce, and then repositories archive and
+distribute, and then researchers request and analyze, collections of
+flat files. NCO works well with that paradigm, yet it also embodies the
+necessary algorithms to transition geoscience data analysis from relying
+solely on traditional (or "flat") datasets to allowing newer
+hierarchical (or "nested") datasets.
+
+ Hierarchical datasets support and enable combining all datastreams
+that meet user-specified criteria into a single or small number of files
+that hold _all_ the science-relevant data. NCO (and no other software
+to our knowledge) exploits this capability now. Data and metadata may
+be aggregated into and analyzed in hierarchical structures. We call the
+resulting data storage, distribution, and analysis paradigm
+Group-Oriented Data Analysis and Distribution (GODAD). GODAD lets the
+scientific question organize the data, not the _ad hoc_ granularity of
+all relevant datasets. This chapter illustrates GODAD techniques
+applied to analysis of the CMIP5 dataset.
+
+ To begin, we document below a prototypical example of CMIP5 analysis
+and evaluation using traditional NCO commands on netCDF3-format model
+and HDF-EOS format observational (NASA MODIS satellite instrument)
+datasets. These examples complement the NCO User Guide by detailing
+in-depth data analysis in a frequently encountered "real world" context.
+Graphical representations of the results (NCL scripts available upon
+request) are provided to illustrate physical meaning of the analysis.
+Since NCO can process hierarchical datasets, i.e., datasets stored with
+netCDF4 groups, we present sample scripts illustrating group-based
+processing as well.
7.1 Combine Files
=================
Sometimes, the data of one ensemble member will be stored in several
-files to reduce single file size. But it is not convenient to process
-in a batch mode. The following script illustrates how to concatenate
-these files into one. Key steps include:
+files to reduce single file size. It is more convenient to concatenate
+these files into a single timeseries, and the following script
+illustrates how. Key steps include:
1. Obtain number and names (or partial names) of files in a directory
2. Concatenate files along the record dimension (usually time) using
'ncrcat' (*note ncrcat netCDF Record Concatenator::).
@@ -11082,17 +11247,17 @@ these files into one. Key steps include:
done
done
- Right now, CMIP5 model data downloaded from Earth System Grid
-Federation (ESGF (http://pcmdi9.llnl.gov/esgf-web-fe/)) will not contain
-<group> features yet. Therefore users can aggregate the flat files into
-groups themselves. The following script shows how to aggregate models
-to one file. Each dataset becomes a group in the output file. There
-can be several levels of groups. In this example, we employ two
-experiments as the top-level. The second-level comprises different
-models. Some models have more than one ensemble member. These ensemble
-members are on the third level. In each sub-group of ensemble members,
-we appended two variables, SNC and SND (these stand for snow cover and
-snow depth, by the way).
+ CMIP5 model data downloaded from the Earth System Grid Federation
+(ESGF (http://pcmdi9.llnl.gov/esgf-web-fe/)) does not contain group
+features yet. Therefore users must aggregate flat files into
+hierarchical ones themselves. The following script shows how. Each
+dataset becomes a group in the output file. There can be several levels
+of groups. In this example, we employ two experiments ("scenarios") as
+the top-level. The second-level comprises different models (e.g.,
+CCSM4, CESM1-BGC). Many models are run multiple times with slight
+perturbed initial conditions to produce an ensemble of realizations.
+These ensemble members comprise the third level of the hierarchy. The
+script selects two variables, SNC and SND (snow cover and snow depth).
#!/bin/bash
#
#============================================================
@@ -11100,7 +11265,7 @@ snow depth, by the way).
#
# Method:
# - Create files with groups by ncecat --gag
- # - Append groups level by level using ncks
+ # - Append groups level by level using ncks
#
# Input files like:
# snc_LImon_CCSM4_historical_r1i1p1_199001-200512.nc
@@ -11120,7 +11285,7 @@ snow depth, by the way).
# Constants
rlm='LImon' # Realm: LandIce; Time frequency: monthly
- tms='200001-200512' # Timeseris
+ tms='200001-200512' # Timeseries
flt='nc' # File Type
# Geographical weights
@@ -12019,7 +12184,7 @@ This chapter illustrates how to use NCO to process and analyze the
results of a CCSM climate simulation.
************************************************************************
Task 0: Finding input files
- ************************************************************************
+ x************************************************************************
The CCSM model outputs files to a local directory like:
/ptmp/zender/archive/T42x1_40
@@ -12371,2895 +12536,2906 @@ General Index
* Menu:
* '"' (double quote): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '#include': Syntax of ncap2 statements.
- (line 5594)
-* '$' (wildcard character): Subsetting Files. (line 2537)
+ (line 5669)
+* '$' (wildcard character): Subsetting Files. (line 2567)
* '%' (modulus): Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* ''' (end quote): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '*': ncbo netCDF Binary Operator.
- (line 8468)
-* '*' (filename expansion): Subsetting Files. (line 2537)
+ (line 8589)
+* '*' (filename expansion): Subsetting Files. (line 2567)
* '*' (multiplication): Intrinsic mathematical methods.
- (line 7926)
-* '*' (wildcard character): Subsetting Files. (line 2544)
+ (line 8040)
+* '*' (wildcard character): Subsetting Files. (line 2574)
* '+': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* '+' (addition): Intrinsic mathematical methods.
- (line 7926)
-* '+' (wildcard character): Subsetting Files. (line 2544)
+ (line 8040)
+* '+' (wildcard character): Subsetting Files. (line 2574)
* '-': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* '-' (subtraction): Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* '--3': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--4': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--6': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--64bit': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--7': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--abc': ncks netCDF Kitchen Sink.
- (line 9294)
+ (line 9416)
* '--alphabetize': ncks netCDF Kitchen Sink.
- (line 9294)
+ (line 9416)
* '--apn': Temporary Output Files.
- (line 991)
-* '--apn' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '--apn' <1>: Batch Mode. (line 5315)
* '--apn' <2>: Filters for 'ncks'.
- (line 9744)
+ (line 9866)
* '--append': Temporary Output Files.
- (line 991)
-* '--append' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '--append' <1>: Batch Mode. (line 5315)
* '--append' <2>: Filters for 'ncks'.
- (line 9744)
+ (line 9866)
* '--auxiliary': Auxiliary Coordinates.
- (line 3584)
+ (line 3628)
* '--auxiliary LON_MIN,LON_MAX,LAT_MIN,LAT_MAX': Auxiliary Coordinates.
- (line 3584)
-* '--bfr_sz_hnt': Buffer sizes. (line 4355)
+ (line 3628)
+* '--bfr_sz_hnt': Buffer sizes. (line 4418)
* '--binary': ncks netCDF Kitchen Sink.
- (line 9304)
+ (line 9426)
* '--bnr': ncks netCDF Kitchen Sink.
- (line 9304)
+ (line 9426)
* '--cdl': ncks netCDF Kitchen Sink.
- (line 9357)
-* '--cell_methods': CF Conventions. (line 5408)
-* '--chunk_byte': Chunking. (line 4052)
-* '--chunk_dimension': Chunking. (line 4052)
-* '--chunk_map': Chunking. (line 4052)
-* '--chunk_policy': Chunking. (line 4052)
-* '--chunk_scalar': Chunking. (line 4052)
-* '--cll_mth': CF Conventions. (line 5408)
-* '--cnk_byt': Chunking. (line 4052)
-* '--cnk_dmn': Chunking. (line 4052)
-* '--cnk_map': Chunking. (line 4052)
-* '--cnk_map CNK_MAP': Chunking. (line 4129)
-* '--cnk_plc': Chunking. (line 4052)
-* '--cnk_scl': Chunking. (line 4052)
+ (line 9479)
+* '--cell_methods': CF Conventions. (line 5483)
+* '--chunk_byte': Chunking. (line 4096)
+* '--chunk_dimension': Chunking. (line 4096)
+* '--chunk_map': Chunking. (line 4096)
+* '--chunk_policy': Chunking. (line 4096)
+* '--chunk_scalar': Chunking. (line 4096)
+* '--cll_mth': CF Conventions. (line 5483)
+* '--cnk_byt': Chunking. (line 4096)
+* '--cnk_dmn': Chunking. (line 4096)
+* '--cnk_map': Chunking. (line 4096)
+* '--cnk_map CNK_MAP': Chunking. (line 4183)
+* '--cnk_plc': Chunking. (line 4096)
+* '--cnk_scl': Chunking. (line 4096)
* '--coords': Subsetting Coordinate Variables.
- (line 2614)
-* '--coords' <1>: CF Conventions. (line 5397)
+ (line 2644)
+* '--coords' <1>: CF Conventions. (line 5472)
* '--crd': Subsetting Coordinate Variables.
- (line 2614)
-* '--crd' <1>: CF Conventions. (line 5397)
+ (line 2644)
+* '--crd' <1>: CF Conventions. (line 5472)
* '--create_ram': Temporary Output Files.
- (line 949)
-* '--create_ram' <1>: RAM disks. (line 4386)
+ (line 954)
+* '--create_ram' <1>: RAM disks. (line 4449)
* '--data': ncks netCDF Kitchen Sink.
- (line 9405)
+ (line 9527)
* '--dbg_lvl DEBUG-LEVEL': Help Requests and Bug Reports.
- (line 864)
-* '--dbg_lvl DEBUG-LEVEL' <1>: Large Datasets. (line 1323)
+ (line 869)
+* '--dbg_lvl DEBUG-LEVEL' <1>: Large Datasets. (line 1328)
* '--dbg_lvl DEBUG-LEVEL' <2>: Command Line Options.
- (line 1606)
+ (line 1614)
* '--dbl': Promoting Single-precision to Double.
- (line 4899)
+ (line 4962)
* '--debug-level DEBUG-LEVEL': Help Requests and Bug Reports.
- (line 864)
-* '--debug-level DEBUG-LEVEL' <1>: Large Datasets. (line 1323)
-* '--deflate': Deflation. (line 4248)
-* '--dfl_lvl': Deflation. (line 4248)
-* '--dimension DIM,[MIN],[MAX],STRIDE': Stride. (line 3202)
+ (line 869)
+* '--debug-level DEBUG-LEVEL' <1>: Large Datasets. (line 1328)
+* '--deflate': Deflation. (line 4311)
+* '--dfl_lvl': Deflation. (line 4311)
+* '--dimension DIM,[MIN],[MAX],STRIDE': Stride. (line 3246)
* '--dimension DIM,[MIN],[MAX],[STRIDE],[SUBCYCLE]': Subcycle.
- (line 3314)
-* '--dimension DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3098)
+ (line 3358)
+* '--dimension DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3142)
* '--dimension DIM,[MIN][,[MAX][,[STRIDE]]]' <1>: Multislabs.
- (line 3390)
+ (line 3434)
* '--dimension DIM,[MIN][,[MAX][,[STRIDE]]]' <2>: Wrapped Coordinates.
- (line 3534)
+ (line 3578)
* '--dimension DIM,[MIN][,[MAX][,[STRIDE]]]' <3>: UDUnits Support.
- (line 3694)
+ (line 3738)
* '--diskless_all': Memory Requirements.
- (line 1334)
-* '--diskless_all' <1>: RAM disks. (line 4386)
-* '--dmn DIM,[MIN],[MAX],STRIDE': Stride. (line 3202)
-* '--dmn DIM,[MIN],[MAX],[STRIDE],SUBCYCLE]': Subcycle. (line 3314)
-* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3098)
-* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]' <1>: Multislabs. (line 3390)
+ (line 1339)
+* '--diskless_all' <1>: RAM disks. (line 4449)
+* '--dmn DIM,[MIN],[MAX],STRIDE': Stride. (line 3246)
+* '--dmn DIM,[MIN],[MAX],[STRIDE],SUBCYCLE]': Subcycle. (line 3358)
+* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3142)
+* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]' <1>: Multislabs. (line 3434)
* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]' <2>: Wrapped Coordinates.
- (line 3534)
+ (line 3578)
* '--dmn DIM,[MIN][,[MAX][,[STRIDE]]]' <3>: UDUnits Support.
- (line 3694)
+ (line 3738)
* '--ensemble_file': nces netCDF Ensemble Statistics.
- (line 8759)
+ (line 8881)
* '--ensemble_group': nces netCDF Ensemble Statistics.
- (line 8759)
+ (line 8881)
* '--ensemble_suffix': nces netCDF Ensemble Statistics.
- (line 8759)
-* '--exclude': Subsetting Files. (line 2371)
+ (line 8881)
+* '--exclude': Subsetting Files. (line 2386)
* '--exclude' <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* '--file_format': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--file_list': File List Attributes.
- (line 5300)
-* '--fix_rec_dmn all': Autoconversion. (line 2302)
+ (line 5363)
+* '--fix_rec_dmn all': Autoconversion. (line 2317)
* '--fix_rec_dmn DIM': ncks netCDF Kitchen Sink.
- (line 9320)
+ (line 9442)
* '--flt': Promoting Single-precision to Double.
- (line 4899)
+ (line 4962)
* '--fl_bnr': ncks netCDF Kitchen Sink.
- (line 9304)
+ (line 9426)
* '--fl_fmt': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--fl_lst_in': File List Attributes.
- (line 5300)
+ (line 5363)
* '--fl_out FL_OUT': Specifying Output Files.
- (line 1765)
+ (line 1778)
* '--fl_spt': ncap2 netCDF Arithmetic Processor.
- (line 5532)
+ (line 5607)
* '--fnc_tbl': Intrinsic mathematical methods.
- (line 8033)
+ (line 8147)
* '--fortran': C and Fortran Index Conventions.
- (line 3061)
+ (line 3105)
* '--gag': ncecat netCDF Ensemble Concatenator.
- (line 8931)
-* '--gag' <1>: Combine Files. (line 11158)
+ (line 9053)
+* '--gag' <1>: Combine Files. (line 11322)
* '--glb_mtd_spp': ncecat netCDF Ensemble Concatenator.
- (line 8957)
+ (line 9079)
* '--gpe GPE_DSC': Group Path Editing.
- (line 2639)
-* '--group GRP': Subsetting Files. (line 2371)
-* '--grp GRP': Subsetting Files. (line 2371)
+ (line 2671)
+* '--group GRP': Subsetting Files. (line 2386)
+* '--grp GRP': Subsetting Files. (line 2386)
+* '--grp_xtr_var_xcl': Subsetting Files. (line 2386)
+* '--gxvx': Subsetting Files. (line 2386)
* '--hdf4': netCDF2/3/4 and HDF4/5 Support.
- (line 674)
-* '--hdf_unpack': Packed data. (line 4473)
-* '--hdf_upk': Packed data. (line 4473)
+ (line 679)
+* '--hdf_unpack': Packed data. (line 4536)
+* '--hdf_upk': Packed data. (line 4536)
* '--hdn': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '--hdr_pad HDR_PAD': Metadata Optimization.
- (line 1504)
+ (line 1512)
* '--header_pad HDR_PAD': Metadata Optimization.
- (line 1504)
+ (line 1512)
* '--hidden': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '--hieronymus': ncks netCDF Kitchen Sink.
- (line 9405)
-* '--history': History Attribute. (line 5272)
-* '--hst': History Attribute. (line 5272)
-* '--intersection': Subsetting Files. (line 2462)
-* '--lcl OUTPUT-PATH': Remote storage. (line 1797)
-* '--local OUTPUT-PATH': Remote storage. (line 1797)
-* '--map CNK_MAP': Chunking. (line 4129)
+ (line 9527)
+* '--history': History Attribute. (line 5335)
+* '--hst': History Attribute. (line 5335)
+* '--intersection': Subsetting Files. (line 2492)
+* '--lcl OUTPUT-PATH': Remote storage. (line 1810)
+* '--local OUTPUT-PATH': Remote storage. (line 1810)
+* '--map CNK_MAP': Chunking. (line 4183)
* '--map PCK_MAP': ncpdq netCDF Permute Dimensions Quickly.
- (line 9953)
-* '--mask-value MASK_VAL': Mask condition. (line 10661)
+ (line 10076)
+* '--mask-value MASK_VAL': Mask condition. (line 10784)
* '--mask-variable MASK_VAR': ncwa netCDF Weighted Averager.
- (line 10593)
-* '--mask_comparator MASK_COMP': Mask condition. (line 10647)
+ (line 10716)
+* '--mask_comparator MASK_COMP': Mask condition. (line 10770)
* '--mask_condition MASK_COND': ncwa netCDF Weighted Averager.
- (line 10593)
-* '--mask_condition MASK_COND' <1>: Mask condition. (line 10647)
-* '--mask_value MASK_VAL': Mask condition. (line 10661)
+ (line 10716)
+* '--mask_condition MASK_COND' <1>: Mask condition. (line 10770)
+* '--mask_value MASK_VAL': Mask condition. (line 10784)
* '--mask_variable MASK_VAR': ncwa netCDF Weighted Averager.
- (line 10593)
-* '--md5_dgs': MD5 digests. (line 4285)
-* '--md5_digest': MD5 digests. (line 4285)
-* '--md5_write_attribute': MD5 digests. (line 4285)
-* '--md5_wrt_att': MD5 digests. (line 4285)
+ (line 10716)
+* '--md5_dgs': MD5 digests. (line 4348)
+* '--md5_digest': MD5 digests. (line 4348)
+* '--md5_write_attribute': MD5 digests. (line 4348)
+* '--md5_wrt_att': MD5 digests. (line 4348)
* '--Metadata': ncks netCDF Kitchen Sink.
- (line 9450)
+ (line 9572)
* '--metadata': ncks netCDF Kitchen Sink.
- (line 9493)
+ (line 9615)
* '--mk_rec_dmn DIM': ncecat netCDF Ensemble Concatenator.
- (line 9016)
+ (line 9138)
* '--mk_rec_dmn DIM' <1>: ncks netCDF Kitchen Sink.
- (line 9397)
+ (line 9519)
* '--mrd': Multiple Record Dimensions.
- (line 3901)
-* '--mro': Subcycle. (line 3314)
-* '--msa': Multislabs. (line 3390)
-* '--msa_user_order': Multislabs. (line 3390)
-* '--msa_usr_rdr': Multislabs. (line 3390)
-* '--msk_cmp_typ MASK_COMP': Mask condition. (line 10647)
+ (line 3945)
+* '--mro': Subcycle. (line 3358)
+* '--msa': Multislabs. (line 3434)
+* '--msa_user_order': Multislabs. (line 3434)
+* '--msa_usr_rdr': Multislabs. (line 3434)
+* '--msk_cmp_typ MASK_COMP': Mask condition. (line 10770)
* '--msk_cnd MASK_COND': ncwa netCDF Weighted Averager.
- (line 10593)
-* '--msk_cnd_sng MASK_COND': Mask condition. (line 10647)
+ (line 10716)
+* '--msk_cnd_sng MASK_COND': Mask condition. (line 10770)
* '--msk_nm MASK_VAR': ncwa netCDF Weighted Averager.
- (line 10593)
-* '--msk_val MASK_VAL': Mask condition. (line 10661)
+ (line 10716)
+* '--msk_val MASK_VAL': Mask condition. (line 10784)
* '--msk_var MASK_VAR': ncwa netCDF Weighted Averager.
- (line 10593)
+ (line 10716)
* '--Mtd': ncks netCDF Kitchen Sink.
- (line 9450)
+ (line 9572)
* '--mtd': ncks netCDF Kitchen Sink.
- (line 9493)
+ (line 9615)
* '--multiple_record_dimensions': Multiple Record Dimensions.
- (line 3901)
+ (line 3945)
* '--ncml': ncks netCDF Kitchen Sink.
- (line 9553)
+ (line 9675)
* '--netcdf4': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '--nintap LOOP': Specifying Input Files.
- (line 1662)
+ (line 1670)
* '--no-blank': ncks netCDF Kitchen Sink.
- (line 9506)
+ (line 9628)
* '--no-coords': Subsetting Coordinate Variables.
- (line 2614)
-* '--no-coords' <1>: CF Conventions. (line 5397)
+ (line 2644)
+* '--no-coords' <1>: CF Conventions. (line 5472)
* '--no-crd': Subsetting Coordinate Variables.
- (line 2614)
-* '--no-crd' <1>: CF Conventions. (line 5397)
+ (line 2644)
+* '--no-crd' <1>: CF Conventions. (line 5472)
* '--noblank': ncks netCDF Kitchen Sink.
- (line 9506)
+ (line 9628)
* '--no_blank': ncks netCDF Kitchen Sink.
- (line 9506)
-* '--no_cell_methods': CF Conventions. (line 5408)
-* '--no_cll_mth': CF Conventions. (line 5408)
+ (line 9628)
+* '--no_cell_methods': CF Conventions. (line 5483)
+* '--no_cll_mth': CF Conventions. (line 5483)
* '--no_rec_dmn DIM': ncks netCDF Kitchen Sink.
- (line 9320)
+ (line 9442)
* '--no_tmp_fl': Temporary Output Files.
- (line 949)
-* '--no_tmp_fl' <1>: RAM disks. (line 4466)
+ (line 954)
+* '--no_tmp_fl' <1>: RAM disks. (line 4529)
* '--nsm_fl': nces netCDF Ensemble Statistics.
- (line 8759)
+ (line 8881)
* '--nsm_grp': nces netCDF Ensemble Statistics.
- (line 8759)
+ (line 8881)
* '--nsm_sfx': nces netCDF Ensemble Statistics.
- (line 8759)
-* '--nsx': Subsetting Files. (line 2462)
-* '--omp_num_threads THR_NBR': OpenMP Threading. (line 1525)
+ (line 8881)
+* '--nsx': Subsetting Files. (line 2492)
+* '--omp_num_threads THR_NBR': OpenMP Threading. (line 1533)
* '--open_ram': Temporary Output Files.
- (line 949)
+ (line 954)
* '--open_ram' <1>: Memory Requirements.
- (line 1334)
-* '--open_ram' <2>: RAM disks. (line 4386)
-* '--operation OP_TYP': Operation Types. (line 4610)
+ (line 1339)
+* '--open_ram' <2>: RAM disks. (line 4449)
+* '--operation OP_TYP': Operation Types. (line 4673)
* '--operation OP_TYP' <1>: ncbo netCDF Binary Operator.
- (line 8468)
-* '--op_rlt MASK_COMP': Mask condition. (line 10647)
-* '--op_typ OP_TYP': Operation Types. (line 4610)
+ (line 8589)
+* '--op_rlt MASK_COMP': Mask condition. (line 10770)
+* '--op_typ OP_TYP': Operation Types. (line 4673)
* '--op_typ OP_TYP' <1>: ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* '--orphan_dimensions': ncks netCDF Kitchen Sink.
- (line 9534)
+ (line 9656)
* '--output FL_OUT': Specifying Output Files.
- (line 1765)
+ (line 1778)
* '--overwrite': Temporary Output Files.
- (line 991)
-* '--overwrite' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '--overwrite' <1>: Batch Mode. (line 5315)
* '--ovr': Temporary Output Files.
- (line 991)
-* '--ovr' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '--ovr' <1>: Batch Mode. (line 5315)
* '--pack_policy PCK_PLC': ncpdq netCDF Permute Dimensions Quickly.
- (line 9886)
+ (line 10009)
* '--path INPUT-PATH': Specifying Input Files.
- (line 1662)
-* '--path INPUT-PATH' <1>: Remote storage. (line 1797)
+ (line 1670)
+* '--path INPUT-PATH' <1>: Remote storage. (line 1810)
* '--pck_map PCK_MAP': ncpdq netCDF Permute Dimensions Quickly.
- (line 9953)
+ (line 10076)
* '--pck_plc PCK_PLC': ncpdq netCDF Permute Dimensions Quickly.
- (line 9886)
+ (line 10009)
* '--print': ncks netCDF Kitchen Sink.
- (line 9514)
+ (line 9636)
* '--prn': ncks netCDF Kitchen Sink.
- (line 9514)
+ (line 9636)
* '--prn_fnc_tbl': Intrinsic mathematical methods.
- (line 8033)
-* '--pseudonym': Symbolic Links. (line 534)
+ (line 8147)
+* '--pseudonym': Symbolic Links. (line 539)
* '--pth INPUT-PATH': Specifying Input Files.
- (line 1662)
-* '--pth INPUT-PATH' <1>: Remote storage. (line 1797)
+ (line 1670)
+* '--pth INPUT-PATH' <1>: Remote storage. (line 1810)
* '--quiet': ncks netCDF Kitchen Sink.
- (line 9526)
+ (line 9648)
* '--rad': ncks netCDF Kitchen Sink.
- (line 9534)
+ (line 9656)
* '--ram_all': Memory Requirements.
- (line 1334)
-* '--ram_all' <1>: RAM disks. (line 4386)
+ (line 1339)
+* '--ram_all' <1>: RAM disks. (line 4449)
* '--rcd_nm ULM_NM': ncecat netCDF Ensemble Concatenator.
- (line 8906)
-* '--record_append': Record Appending. (line 3263)
-* '--rec_apn': Record Appending. (line 3263)
+ (line 9028)
+* '--record_append': Record Appending. (line 3307)
+* '--rec_apn': Record Appending. (line 3307)
* '--retain': Retaining Retrieved Files.
- (line 2049)
+ (line 2064)
* '--retain_all_dimensions': ncks netCDF Kitchen Sink.
- (line 9534)
+ (line 9656)
* '--revision': Help Requests and Bug Reports.
- (line 864)
-* '--revision' <1>: Operator Version. (line 5482)
+ (line 869)
+* '--revision' <1>: Operator Version. (line 5557)
* '--rph_dmn': ncks netCDF Kitchen Sink.
- (line 9534)
+ (line 9656)
* '--rth_dbl': Promoting Single-precision to Double.
- (line 4899)
+ (line 4962)
* '--rth_flt': Promoting Single-precision to Double.
- (line 4899)
+ (line 4962)
* '--rtn': Retaining Retrieved Files.
- (line 2049)
+ (line 2064)
* '--script': ncap2 netCDF Arithmetic Processor.
- (line 5532)
+ (line 5607)
* '--script-file': ncap2 netCDF Arithmetic Processor.
- (line 5532)
+ (line 5607)
* '--sng_fmt': ncks netCDF Kitchen Sink.
- (line 9545)
+ (line 9667)
* '--spt': ncap2 netCDF Arithmetic Processor.
- (line 5532)
+ (line 5607)
* '--string': ncks netCDF Kitchen Sink.
- (line 9545)
-* '--threads THR_NBR': OpenMP Threading. (line 1525)
-* '--thr_nbr THR_NBR': OpenMP Threading. (line 1525)
+ (line 9667)
+* '--threads THR_NBR': OpenMP Threading. (line 1533)
+* '--thr_nbr THR_NBR': OpenMP Threading. (line 1533)
* '--ulm_nm ULM_NM': ncecat netCDF Ensemble Concatenator.
- (line 8906)
-* '--union': Subsetting Files. (line 2371)
-* '--union' <1>: Subsetting Files. (line 2462)
+ (line 9028)
+* '--union': Subsetting Files. (line 2386)
+* '--union' <1>: Subsetting Files. (line 2492)
* '--units': ncks netCDF Kitchen Sink.
- (line 9549)
-* '--unn': Subsetting Files. (line 2371)
-* '--unn' <1>: Subsetting Files. (line 2462)
+ (line 9671)
+* '--unn': Subsetting Files. (line 2386)
+* '--unn' <1>: Subsetting Files. (line 2492)
* '--unpack': ncpdq netCDF Permute Dimensions Quickly.
- (line 9937)
+ (line 10060)
* '--upk': ncpdq netCDF Permute Dimensions Quickly.
- (line 9937)
-* '--variable VAR': Subsetting Files. (line 2371)
+ (line 10060)
+* '--variable VAR': Subsetting Files. (line 2386)
* '--variable VAR' <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* '--version': Help Requests and Bug Reports.
- (line 864)
-* '--version' <1>: Operator Version. (line 5482)
+ (line 869)
+* '--version' <1>: Operator Version. (line 5557)
* '--vrs': Help Requests and Bug Reports.
- (line 864)
-* '--vrs' <1>: Operator Version. (line 5482)
+ (line 869)
+* '--vrs' <1>: Operator Version. (line 5557)
* '--weight WEIGHT': ncwa netCDF Weighted Averager.
- (line 10593)
+ (line 10716)
* '--weight WGT1[,WGT2]': ncflint netCDF File Interpolator.
- (line 9056)
+ (line 9178)
* '--wgt_var WEIGHT': ncwa netCDF Weighted Averager.
- (line 10593)
+ (line 10716)
* '--wgt_var WGT1[,WGT2]': ncflint netCDF File Interpolator.
- (line 9056)
+ (line 9178)
* '--write_tmp_fl': Temporary Output Files.
- (line 949)
+ (line 954)
* '--wrt_tmp_fl': Temporary Output Files.
- (line 949)
-* '--xcl': Subsetting Files. (line 2371)
+ (line 954)
+* '--xcl': Subsetting Files. (line 2386)
* '--xcl' <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* '--xml': ncks netCDF Kitchen Sink.
- (line 9553)
+ (line 9675)
* '--xml_no_location': ncks netCDF Kitchen Sink.
- (line 9583)
+ (line 9705)
* '--xml_spr_chr': ncks netCDF Kitchen Sink.
- (line 9583)
+ (line 9705)
* '--xml_spr_nmr': ncks netCDF Kitchen Sink.
- (line 9583)
+ (line 9705)
* '-3': netCDF2/3/4 and HDF4/5 Support.
- (line 667)
+ (line 672)
* '-3' <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '-4': netCDF2/3/4 and HDF4/5 Support.
- (line 667)
+ (line 672)
* '-4' <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '-5': ncks netCDF Kitchen Sink.
- (line 9287)
+ (line 9409)
* '-6': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '-7': File Formats and Conversion.
- (line 2089)
+ (line 2104)
* '-A': Temporary Output Files.
- (line 991)
-* '-A' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '-A' <1>: Batch Mode. (line 5315)
* '-a': ncks netCDF Kitchen Sink.
- (line 9294)
+ (line 9416)
* '-a' <1>: Filters for 'ncks'.
- (line 9732)
+ (line 9854)
* '-A' <2>: Filters for 'ncks'.
- (line 9744)
+ (line 9866)
* '-A' <3>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10069)
-* '-b': Examples ncap2. (line 7904)
+ (line 10192)
+* '-b': Examples ncap2. (line 8018)
* '-b' <1>: ncbo netCDF Binary Operator.
- (line 8566)
+ (line 8687)
* '-b' <2>: ncks netCDF Kitchen Sink.
- (line 9304)
+ (line 9426)
* '-B MASK_COND': ncwa netCDF Weighted Averager.
- (line 10593)
-* '-B MASK_COND' <1>: Mask condition. (line 10647)
+ (line 10716)
+* '-B MASK_COND' <1>: Mask condition. (line 10770)
* '-C': Subsetting Coordinate Variables.
- (line 2614)
+ (line 2644)
* '-c': Subsetting Coordinate Variables.
- (line 2614)
-* '-C' <1>: CF Conventions. (line 5397)
-* '-c' <1>: CF Conventions. (line 5397)
-* '-C' <2>: Examples ncap2. (line 7916)
+ (line 2644)
+* '-C' <1>: CF Conventions. (line 5472)
+* '-c' <1>: CF Conventions. (line 5472)
+* '-C' <2>: Examples ncap2. (line 8030)
* '-D': Help Requests and Bug Reports.
- (line 849)
+ (line 854)
* '-D DEBUG-LEVEL': Help Requests and Bug Reports.
- (line 864)
-* '-D DEBUG-LEVEL' <1>: Large Datasets. (line 1323)
+ (line 869)
+* '-D DEBUG-LEVEL' <1>: Large Datasets. (line 1328)
* '-D DEBUG-LEVEL' <2>: Command Line Options.
- (line 1606)
-* '-d DIM,[MIN],[MAX],STRIDE': Stride. (line 3202)
-* '-d DIM,[MIN],[MAX],[STRIDE],[SUBCYCLE]': Subcycle. (line 3314)
-* '-d DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3098)
-* '-d DIM,[MIN][,[MAX][,[STRIDE]]]' <1>: Multislabs. (line 3390)
+ (line 1614)
+* '-d DIM,[MIN],[MAX],STRIDE': Stride. (line 3246)
+* '-d DIM,[MIN],[MAX],[STRIDE],[SUBCYCLE]': Subcycle. (line 3358)
+* '-d DIM,[MIN][,[MAX][,[STRIDE]]]': Hyperslabs. (line 3142)
+* '-d DIM,[MIN][,[MAX][,[STRIDE]]]' <1>: Multislabs. (line 3434)
* '-d DIM,[MIN][,[MAX][,[STRIDE]]]' <2>: Wrapped Coordinates.
- (line 3534)
-* '-d DIM,[MIN][,[MAX][,[STRIDE]]]' <3>: UDUnits Support. (line 3694)
+ (line 3578)
+* '-d DIM,[MIN][,[MAX][,[STRIDE]]]' <3>: UDUnits Support. (line 3738)
* '-d DIM,[MIN][,[MAX]]': ncwa netCDF Weighted Averager.
- (line 10585)
+ (line 10708)
* '-F': C and Fortran Index Conventions.
- (line 3061)
+ (line 3105)
* '-f': Intrinsic mathematical methods.
- (line 8033)
+ (line 8147)
* '-G GPE_DSC': Group Path Editing.
- (line 2639)
-* '-g GRP': Subsetting Files. (line 2371)
-* '-h': History Attribute. (line 5272)
+ (line 2671)
+* '-g GRP': Subsetting Files. (line 2386)
+* '-h': History Attribute. (line 5335)
* '-H': File List Attributes.
- (line 5300)
+ (line 5363)
* '-h' <1>: ncatted netCDF Attribute Editor.
- (line 8180)
+ (line 8294)
* '-H' <1>: ncks netCDF Kitchen Sink.
- (line 9405)
+ (line 9527)
* '-I': ncwa netCDF Weighted Averager.
- (line 10621)
-* '-L': Deflation. (line 4248)
-* '-l OUTPUT-PATH': Remote storage. (line 1797)
-* '-l OUTPUT-PATH' <1>: Remote storage. (line 1858)
+ (line 10744)
+* '-L': Deflation. (line 4311)
+* '-l OUTPUT-PATH': Remote storage. (line 1810)
+* '-l OUTPUT-PATH' <1>: Remote storage. (line 1873)
* '-M': Determining File Format.
- (line 2175)
+ (line 2190)
* '-M' <1>: ncecat netCDF Ensemble Concatenator.
- (line 8957)
+ (line 9079)
* '-M' <2>: ncks netCDF Kitchen Sink.
- (line 9450)
+ (line 9572)
* '-m': ncks netCDF Kitchen Sink.
- (line 9493)
-* '-M CNK_MAP': Chunking. (line 4129)
+ (line 9615)
+* '-M CNK_MAP': Chunking. (line 4183)
* '-m MASK_VAR': ncwa netCDF Weighted Averager.
- (line 10593)
+ (line 10716)
* '-M PCK_MAP': ncpdq netCDF Permute Dimensions Quickly.
- (line 9953)
+ (line 10076)
* '-N': Normalization and Integration.
- (line 10676)
+ (line 10799)
* '-n LOOP': Large Numbers of Files.
- (line 1193)
+ (line 1198)
* '-n LOOP' <1>: Large Numbers of Files.
- (line 1263)
+ (line 1268)
* '-n LOOP' <2>: Specifying Input Files.
- (line 1662)
+ (line 1670)
* '-O': Temporary Output Files.
- (line 991)
-* '-O' <1>: Batch Mode. (line 5252)
+ (line 996)
+* '-O' <1>: Batch Mode. (line 5315)
* '-o FL_OUT': Large Numbers of Files.
- (line 1247)
+ (line 1252)
* '-o FL_OUT' <1>: Specifying Output Files.
- (line 1765)
+ (line 1778)
* '-P': ncks netCDF Kitchen Sink.
- (line 9514)
+ (line 9636)
* '-p INPUT-PATH': Specifying Input Files.
- (line 1662)
-* '-p INPUT-PATH' <1>: Remote storage. (line 1858)
+ (line 1670)
+* '-p INPUT-PATH' <1>: Remote storage. (line 1873)
* '-P PCK_PLC': ncpdq netCDF Permute Dimensions Quickly.
- (line 9886)
+ (line 10009)
* '-Q': ncks netCDF Kitchen Sink.
- (line 9520)
+ (line 9642)
* '-q': ncks netCDF Kitchen Sink.
- (line 9526)
+ (line 9648)
* '-r': Help Requests and Bug Reports.
- (line 849)
+ (line 854)
* '-r' <1>: Help Requests and Bug Reports.
- (line 864)
+ (line 869)
* '-R': Retaining Retrieved Files.
- (line 2049)
-* '-r' <2>: Operator Version. (line 5482)
+ (line 2064)
+* '-r' <2>: Operator Version. (line 5557)
* '-s': ncks netCDF Kitchen Sink.
- (line 9545)
+ (line 9667)
* '-t THR_NBR': Single and Multi-file Operators.
- (line 1417)
-* '-t THR_NBR' <1>: OpenMP Threading. (line 1525)
+ (line 1422)
+* '-t THR_NBR' <1>: OpenMP Threading. (line 1533)
* '-u': ncks netCDF Kitchen Sink.
- (line 9549)
+ (line 9671)
* '-U': ncpdq netCDF Permute Dimensions Quickly.
- (line 9937)
+ (line 10060)
* '-u ULM_NM': ncecat netCDF Ensemble Concatenator.
- (line 8906)
+ (line 9028)
* '-v': ncpdq netCDF Permute Dimensions Quickly.
- (line 10069)
-* '-v VAR': Subsetting Files. (line 2371)
+ (line 10192)
+* '-v VAR': Subsetting Files. (line 2386)
* '-v VAR' <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* '-w WEIGHT': ncwa netCDF Weighted Averager.
- (line 10593)
+ (line 10716)
* '-w WGT1[,WGT2]': ncflint netCDF File Interpolator.
- (line 9056)
-* '-x': Subsetting Files. (line 2371)
+ (line 9178)
+* '-x': Subsetting Files. (line 2386)
* '-X': Auxiliary Coordinates.
- (line 3584)
+ (line 3628)
* '-x' <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* '-X LON_MIN,LON_MAX,LAT_MIN,LAT_MAX': Auxiliary Coordinates.
- (line 3584)
-* '-y OP_TYP': Operation Types. (line 4610)
+ (line 3628)
+* '-y OP_TYP': Operation Types. (line 4673)
* '-y OP_TYP' <1>: ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* '.': ncrename netCDF Renamer.
- (line 10390)
-* '.' (wildcard character): Subsetting Files. (line 2537)
+ (line 10513)
+* '.' (wildcard character): Subsetting Files. (line 2567)
* '.bashrc': Filters for 'ncks'.
- (line 9637)
-* '.netrc': Remote storage. (line 1797)
-* '.rhosts': Remote storage. (line 1797)
+ (line 9759)
+* '.netrc': Remote storage. (line 1810)
+* '.rhosts': Remote storage. (line 1810)
* '/': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* '/' (division): Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* '/*...*/' (comment): Syntax of ncap2 statements.
- (line 5591)
+ (line 5666)
* '//' (comment): Syntax of ncap2 statements.
- (line 5591)
+ (line 5666)
* '0' (NUL): ncatted netCDF Attribute Editor.
- (line 8353)
+ (line 8467)
* 32-bit offset file format: Determining File Format.
- (line 2175)
+ (line 2190)
* 64-bit offset file format: Determining File Format.
- (line 2175)
+ (line 2190)
* '64BIT' files: File Formats and Conversion.
- (line 2089)
-* ':' (separator character): Group Path Editing.
- (line 2677)
+ (line 2104)
+* ':' (separator character): Flattening Groups. (line 2712)
* ';' (end of statement): Syntax of ncap2 statements.
- (line 5589)
+ (line 5664)
* '<arpa/nameser.h>': Windows Operating System.
- (line 502)
+ (line 507)
* '<resolv.h>': Windows Operating System.
- (line 502)
-* '?' (filename expansion): Subsetting Files. (line 2537)
+ (line 507)
+* '?' (filename expansion): Subsetting Files. (line 2567)
* '?' (question mark): ncatted netCDF Attribute Editor.
- (line 8344)
-* '?' (wildcard character): Subsetting Files. (line 2544)
+ (line 8458)
+* '?' (wildcard character): Subsetting Files. (line 2574)
* '@' (attribute): Syntax of ncap2 statements.
- (line 5599)
-* '@' (separator character): Group Path Editing.
- (line 2677)
+ (line 5674)
+* '@' (separator character): Flattening Groups. (line 2712)
* '[]' (array delimiters): Syntax of ncap2 statements.
- (line 5583)
+ (line 5658)
* '\' (backslash): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '\"' (protected double quote): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '\'' (protected end quote): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '\?' (protected question mark): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '\a' (ASCII BEL, bell): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\b' (ASCII BS, backspace): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\f' (ASCII FF, formfeed): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\n' (ASCII LF, linefeed): ncatted netCDF Attribute Editor.
- (line 8329)
+ (line 8443)
* '\n' (linefeed): Filters for 'ncks'.
- (line 9765)
+ (line 9887)
* '\r' (ASCII CR, carriage return): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\t' (ASCII HT, horizontal tab): ncatted netCDF Attribute Editor.
- (line 8329)
+ (line 8443)
* '\t' (horizontal tab): Filters for 'ncks'.
- (line 9765)
+ (line 9887)
* '\v' (ASCII VT, vertical tab): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\\' (ASCII \, backslash): ncatted netCDF Attribute Editor.
- (line 8339)
+ (line 8453)
* '\\' (protected backslash): ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* '^' (power): Intrinsic mathematical methods.
- (line 7926)
-* '^' (wildcard character): Subsetting Files. (line 2537)
+ (line 8040)
+* '^' (wildcard character): Subsetting Files. (line 2567)
* '_ChunkSizes': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_DeflateLevel': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_Endianness': ncks netCDF Kitchen Sink.
- (line 9345)
-* '_FillValue': Missing Values. (line 3939)
-* '_FillValue' <1>: Packed data. (line 4473)
+ (line 9467)
+* '_FillValue': Missing Values. (line 3983)
+* '_FillValue' <1>: Packed data. (line 4536)
* '_FillValue' <2>: ncatted netCDF Attribute Editor.
- (line 8185)
+ (line 8299)
* '_FillValue' <3>: ncflint netCDF File Interpolator.
- (line 9105)
+ (line 9227)
* _FILLVALUE: ncpdq netCDF Permute Dimensions Quickly.
- (line 9997)
+ (line 10120)
* '_FillValue' <4>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9997)
+ (line 10120)
* '_FillValue' <5>: ncrename netCDF Renamer.
- (line 10516)
+ (line 10639)
* '_Fletcher32': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_Format': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_NOFILL': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_Shuffle': ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* '_Storage': ncks netCDF Kitchen Sink.
- (line 9345)
-* '|' (wildcard character): Subsetting Files. (line 2544)
+ (line 9467)
+* '|' (wildcard character): Subsetting Files. (line 2574)
* ABS: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* absolute value: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ACOS: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ACOSH: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* 'add': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* adding data: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* adding data <1>: ncflint netCDF File Interpolator.
- (line 9032)
+ (line 9154)
* addition: Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* addition <1>: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* addition <2>: ncflint netCDF File Interpolator.
- (line 9032)
-* ADD_OFFSET: Performance. (line 1470)
-* 'add_offset': Packed data. (line 4473)
+ (line 9154)
+* ADD_OFFSET: Performance. (line 1475)
+* 'add_offset': Packed data. (line 4536)
* 'add_offset' <1>: ncecat netCDF Ensemble Concatenator.
- (line 8979)
+ (line 9101)
* 'add_offset' <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9879)
+ (line 10002)
* 'add_offset' <3>: ncrcat netCDF Record Concatenator.
- (line 10327)
-* aggregation: Combine Files. (line 11158)
-* Aleksandar Jelenak: Contributors. (line 10885)
-* Alexander Hansen: Contributors. (line 10893)
+ (line 10450)
+* aggregation: Combine Files. (line 11322)
+* Aleksandar Jelenak: Contributors. (line 11008)
+* Alexander Hansen: Contributors. (line 11016)
* 'alias': ncbo netCDF Binary Operator.
- (line 8512)
+ (line 8633)
* alias: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'alias' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9947)
-* 'all': Chunking. (line 4085)
+ (line 10070)
+* 'all': Chunking. (line 4130)
* alphabetization: ncks netCDF Kitchen Sink.
- (line 9294)
+ (line 9416)
* alphabetize output: Filters for 'ncks'.
- (line 9732)
+ (line 9854)
* alternate invocations: ncbo netCDF Binary Operator.
- (line 8468)
-* anchor: Subsetting Files. (line 2413)
-* anchoring: Subsetting Files. (line 2413)
-* Andrea Cimatoribus: Contributors. (line 10899)
-* Andrew Wittenberg: Contributors. (line 10883)
+ (line 8589)
+* anchor: Subsetting Files. (line 2443)
+* anchoring: Subsetting Files. (line 2443)
+* ancillary variables convention: CF Conventions. (line 5462)
+* 'ancillary_variables': CF Conventions. (line 5462)
+* Andrea Cimatoribus: Contributors. (line 11022)
+* Andrew Wittenberg: Contributors. (line 11006)
* annual average: Annual Average over Regions.
- (line 11387)
+ (line 11551)
* annual average from daily data: Daily data in one file.
- (line 10955)
+ (line 11097)
* annual average from monthly data: Monthly data in one file.
- (line 10978)
+ (line 11120)
* anomalies: ncbo netCDF Binary Operator.
- (line 8550)
+ (line 8671)
* anomalies <1>: Annual Average over Regions.
- (line 11387)
-* anomalies <2>: Monthly Cycle. (line 11678)
-* ANSI: Compatability. (line 415)
+ (line 11551)
+* anomalies <2>: Monthly Cycle. (line 11842)
+* ANSI: Compatability. (line 420)
* 'ANSI C': Intrinsic mathematical methods.
- (line 8032)
-* appending data: Examples ncap2. (line 7904)
+ (line 8146)
+* appending data: Examples ncap2. (line 8018)
* appending data <1>: ncks netCDF Kitchen Sink.
- (line 9234)
+ (line 9356)
* appending to files: Temporary Output Files.
- (line 991)
-* appending to files <1>: Batch Mode. (line 5252)
+ (line 996)
+* appending to files <1>: Batch Mode. (line 5315)
* appending to files <2>: Filters for 'ncks'.
- (line 9744)
+ (line 9866)
* appending variables: Temporary Output Files.
- (line 991)
+ (line 996)
* appending variables <1>: Appending Variables.
- (line 1016)
+ (line 1021)
* appending variables <2>: ncap2 netCDF Arithmetic Processor.
- (line 5547)
+ (line 5622)
* appending variables <3>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10069)
+ (line 10192)
* AR4: nces netCDF Ensemble Statistics.
- (line 8756)
+ (line 8878)
* arccosine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* arcsine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* arctangent function: Intrinsic mathematical methods.
- (line 7929)
-* 'area': CF Conventions. (line 5331)
+ (line 8043)
+* 'area': CF Conventions. (line 5394)
* area-averaging: Annual Average over Regions.
- (line 11387)
-* arithmetic operators: Missing Values. (line 3945)
-* arithmetic operators <1>: Missing Values. (line 3998)
+ (line 11551)
+* arithmetic operators: Missing Values. (line 3989)
+* arithmetic operators <1>: Missing Values. (line 4042)
* arithmetic operators <2>: ncwa netCDF Weighted Averager.
- (line 10585)
+ (line 10708)
* arithmetic processor: ncap2 netCDF Arithmetic Processor.
- (line 5514)
-* ARM conventions: ARM Conventions. (line 5451)
+ (line 5589)
+* ARM conventions: ARM Conventions. (line 5526)
* ARM conventions <1>: ncrcat netCDF Record Concatenator.
- (line 10340)
+ (line 10463)
* array: Arrays and hyperslabs.
- (line 5877)
+ (line 5952)
* 'array' function: Arrays and hyperslabs.
- (line 5877)
+ (line 5952)
* array indexing: Syntax of ncap2 statements.
- (line 5585)
+ (line 5660)
* array storage: Syntax of ncap2 statements.
- (line 5587)
+ (line 5662)
* array syntax: Syntax of ncap2 statements.
- (line 5583)
+ (line 5658)
* arrays: Arrays and hyperslabs.
- (line 5877)
+ (line 5952)
* arrival value: ncflint netCDF File Interpolator.
- (line 9072)
+ (line 9194)
* ASCII: ncatted netCDF Attribute Editor.
- (line 8327)
+ (line 8441)
* ASCII <1>: ncatted netCDF Attribute Editor.
- (line 8344)
+ (line 8458)
* ASIN: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ASINH: Intrinsic mathematical methods.
- (line 7929)
-* 'asort': Sort methods. (line 6600)
+ (line 8043)
+* 'asort': Sort methods. (line 6714)
* assignment statement: Syntax of ncap2 statements.
- (line 5589)
-* asynchronous file access: Remote storage. (line 1797)
+ (line 5664)
+* asynchronous file access: Remote storage. (line 1810)
* ATAN: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ATANH: Intrinsic mathematical methods.
- (line 7929)
-* attribute inheritance: Attributes. (line 6052)
+ (line 8043)
+* attribute inheritance: Attributes. (line 6127)
* attribute names: ncatted netCDF Attribute Editor.
- (line 8162)
+ (line 8276)
* attribute names <1>: ncrename netCDF Renamer.
- (line 10381)
-* attribute propagation: Attributes. (line 6052)
+ (line 10504)
+* attribute propagation: Attributes. (line 6127)
* attribute syntax: Syntax of ncap2 statements.
- (line 5599)
-* attribute, 'units': UDUnits Support. (line 3694)
+ (line 5674)
+* attribute, 'units': UDUnits Support. (line 3738)
* attributes: ncatted netCDF Attribute Editor.
- (line 8162)
+ (line 8276)
* attributes, appending: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, creating: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, deleting: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, editing: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, editing <1>: Annual Average over Regions.
- (line 11387)
-* attributes, editing <2>: Regrid MODIS Data. (line 11842)
+ (line 11551)
+* attributes, editing <2>: Regrid MODIS Data. (line 12006)
* attributes, global: Large Numbers of Files.
- (line 1221)
-* attributes, global <1>: History Attribute. (line 5272)
+ (line 1226)
+* attributes, global <1>: History Attribute. (line 5335)
* attributes, global <2>: File List Attributes.
- (line 5300)
-* attributes, global <3>: ARM Conventions. (line 5475)
+ (line 5363)
+* attributes, global <3>: ARM Conventions. (line 5550)
* attributes, global <4>: ncatted netCDF Attribute Editor.
- (line 8227)
+ (line 8341)
* attributes, global <5>: ncatted netCDF Attribute Editor.
- (line 8394)
+ (line 8508)
* attributes, global <6>: ncks netCDF Kitchen Sink.
- (line 9220)
+ (line 9342)
* attributes, global <7>: ncks netCDF Kitchen Sink.
- (line 9254)
+ (line 9376)
* attributes, global <8>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* attributes, global <9>: ncrename netCDF Renamer.
- (line 10436)
+ (line 10559)
* attributes, global <10>: ncrename netCDF Renamer.
- (line 10516)
+ (line 10639)
* attributes, modifying: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, modifying <1>: Annual Average over Regions.
- (line 11387)
-* attributes, modifying <2>: Regrid MODIS Data. (line 11842)
+ (line 11551)
+* attributes, modifying <2>: Regrid MODIS Data. (line 12006)
* attributes, overwriting: ncatted netCDF Attribute Editor.
- (line 8244)
+ (line 8358)
* attributes, overwriting <1>: Annual Average over Regions.
- (line 11387)
-* attributes, overwriting <2>: Regrid MODIS Data. (line 11842)
-* attributes'ncap2': Attributes. (line 6019)
+ (line 11551)
+* attributes, overwriting <2>: Regrid MODIS Data. (line 12006)
+* attributes'ncap2': Attributes. (line 6094)
* 'autoconf': Help Requests and Bug Reports.
- (line 872)
-* autoconversion: Autoconversion. (line 2275)
-* automagic: Compatability. (line 455)
+ (line 877)
+* autoconversion: Autoconversion. (line 2290)
+* automagic: Compatability. (line 460)
* automagic <1>: Large Numbers of Files.
- (line 1194)
-* automatic type conversion: Type Conversion. (line 4763)
+ (line 1199)
+* automatic type conversion: Type Conversion. (line 4826)
* automatic type conversion <1>: Intrinsic mathematical methods.
- (line 7999)
-* auxiliary coordinates: CF Conventions. (line 5397)
-* average: Operation Types. (line 4610)
+ (line 8113)
+* auxiliary coordinates: CF Conventions. (line 5472)
+* average: Operation Types. (line 4673)
* average <1>: ncwa netCDF Weighted Averager.
- (line 10629)
+ (line 10752)
* average <2>: Daily data in one file.
- (line 10941)
+ (line 11083)
* average <3>: Daily data in one file.
- (line 10955)
+ (line 11097)
* average <4>: Monthly data in one file.
- (line 10975)
+ (line 11117)
* average <5>: Monthly data in one file.
- (line 10978)
+ (line 11120)
* average <6>: One time point one file.
- (line 11004)
+ (line 11146)
* average <7>: Global Distribution of Long-term Average.
- (line 11284)
+ (line 11448)
* average <8>: Annual Average over Regions.
- (line 11387)
-* average <9>: Monthly Cycle. (line 11678)
-* averaging data: Missing Values. (line 3939)
+ (line 11551)
+* average <9>: Monthly Cycle. (line 11842)
+* averaging data: Missing Values. (line 3983)
* averaging data <1>: nces netCDF Ensemble Statistics.
- (line 8717)
+ (line 8839)
* averaging data <2>: ncra netCDF Record Averager.
- (line 10228)
+ (line 10351)
* averaging data <3>: ncwa netCDF Weighted Averager.
- (line 10553)
-* 'avg': Operation Types. (line 4610)
+ (line 10676)
+* 'avg': Operation Types. (line 4673)
* avg(): Methods and functions.
- (line 6320)
-* 'avgsqr': Operation Types. (line 4610)
-* Barry deFreese: Contributors. (line 10885)
-* 'base_time': ARM Conventions. (line 5451)
-* 'bash': Subsetting Files. (line 2589)
+ (line 6395)
+* 'avgsqr': Operation Types. (line 4673)
+* Barry deFreese: Contributors. (line 11008)
+* 'base_time': ARM Conventions. (line 5526)
+* 'bash': Subsetting Files. (line 2619)
* 'bash' <1>: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* Bash shell: ncbo netCDF Binary Operator.
- (line 8497)
+ (line 8618)
* Bash Shell: ncbo netCDF Binary Operator.
- (line 8665)
+ (line 8787)
* Bash shell <1>: Filters for 'ncks'.
- (line 9637)
-* batch mode: Batch Mode. (line 5252)
+ (line 9759)
+* batch mode: Batch Mode. (line 5315)
* beer: Promoting Single-precision to Double.
- (line 5150)
-* benchmarks: OpenMP Threading. (line 1584)
+ (line 5213)
+* benchmarks: OpenMP Threading. (line 1592)
* Bessel function: GSL special functions.
- (line 7087)
-* bilinear interpolation: Regrid MODIS Data. (line 11842)
-* Bill Kocik: Contributors. (line 10869)
+ (line 7201)
+* bilinear interpolation: Regrid MODIS Data. (line 12006)
+* Bill Kocik: Contributors. (line 10992)
* binary format: ncks netCDF Kitchen Sink.
- (line 9304)
-* binary operations: Memory for ncap2. (line 1423)
+ (line 9426)
+* binary operations: Memory for ncap2. (line 1428)
* binary operations <1>: ncbo netCDF Binary Operator.
- (line 8450)
-* binary Operators: Expressions. (line 5686)
+ (line 8571)
+* binary Operators: Expressions. (line 5761)
* blank: ncks netCDF Kitchen Sink.
- (line 9506)
-* 'bounds': CF Conventions. (line 5386)
-* bounds convention: CF Conventions. (line 5386)
-* Bourne Shell: Stride. (line 3240)
+ (line 9628)
+* 'bounds': CF Conventions. (line 5449)
+* bounds convention: CF Conventions. (line 5449)
+* Bourne Shell: Stride. (line 3284)
* Bourne Shell <1>: ncbo netCDF Binary Operator.
- (line 8665)
-* Brian Mays: Contributors. (line 10865)
+ (line 8787)
+* Brian Mays: Contributors. (line 10988)
* broadcasting: ncbo netCDF Binary Operator.
- (line 8602)
+ (line 8724)
* broadcasting groups: netCDF2/3/4 and HDF4/5 Support.
- (line 661)
+ (line 666)
* broadcasting groups <1>: ncbo netCDF Binary Operator.
- (line 8581)
+ (line 8703)
* broadcasting groups <2>: ncbo netCDF Binary Operator.
- (line 8630)
-* broadcasting variables: Expressions. (line 5635)
+ (line 8752)
+* broadcasting variables: Expressions. (line 5710)
* broadcasting variables <1>: ncbo netCDF Binary Operator.
- (line 8539)
+ (line 8660)
* broadcasting variables <2>: ncbo netCDF Binary Operator.
- (line 8541)
+ (line 8662)
* broadcasting variables <3>: ncflint netCDF File Interpolator.
- (line 9170)
+ (line 9292)
* broadcasting variables <4>: ncwa netCDF Weighted Averager.
- (line 10553)
+ (line 10676)
* 'BSD': Command Line Options.
- (line 1603)
-* Buffer sizes: Buffer sizes. (line 4355)
-* buffering: Performance. (line 1461)
+ (line 1611)
+* Buffer sizes: Buffer sizes. (line 4418)
+* buffering: Performance. (line 1466)
* bugs, reporting: Help Requests and Bug Reports.
- (line 809)
+ (line 814)
* byte(): Methods and functions.
- (line 6412)
+ (line 6487)
* C index convention: C and Fortran Index Conventions.
- (line 3061)
-* C language: Compatability. (line 437)
-* C language <1>: Missing Values. (line 3987)
+ (line 3105)
+* C language: Compatability. (line 442)
+* C language <1>: Missing Values. (line 4031)
* C language <2>: Automatic type conversion.
- (line 4892)
+ (line 4955)
* C language <3>: Promoting Single-precision to Double.
- (line 4911)
+ (line 4974)
* C language <4>: Syntax of ncap2 statements.
- (line 5577)
-* C language <5>: Expressions. (line 5606)
+ (line 5652)
+* C language <5>: Expressions. (line 5681)
* C language <6>: ncatted netCDF Attribute Editor.
- (line 8353)
+ (line 8467)
* C language <7>: ncks netCDF Kitchen Sink.
- (line 9545)
-* C Shell: Stride. (line 3240)
+ (line 9667)
+* C Shell: Stride. (line 3284)
* C Shell <1>: ncbo netCDF Binary Operator.
- (line 8665)
-* 'c++': Compatability. (line 402)
-* C++: Compatability. (line 407)
-* C89: Compatability. (line 415)
-* C89 <1>: Compatability. (line 439)
-* C99: Compatability. (line 419)
-* C99 <1>: Compatability. (line 439)
+ (line 8787)
+* 'c++': Compatability. (line 407)
+* C++: Compatability. (line 412)
+* C89: Compatability. (line 420)
+* C89 <1>: Compatability. (line 444)
+* C99: Compatability. (line 424)
+* C99 <1>: Compatability. (line 444)
* C99 <2>: Windows Operating System.
- (line 490)
+ (line 495)
* CAM3: Promoting Single-precision to Double.
- (line 5050)
-* 'CC': Compatability. (line 402)
-* 'cc': Compatability. (line 402)
+ (line 5113)
+* 'CC': Compatability. (line 407)
+* 'cc': Compatability. (line 407)
* CCM Processor: Specifying Input Files.
- (line 1662)
+ (line 1670)
* CCM Processor <1>: ncra netCDF Record Averager.
- (line 10268)
+ (line 10391)
* CCM Processor <2>: ncrcat netCDF Record Concatenator.
- (line 10346)
+ (line 10469)
* CCSM: Proposals for Institutional Funding.
- (line 10911)
-* CCSM <1>: CCSM Example. (line 12081)
-* CCSM conventions: CF Conventions. (line 5331)
+ (line 11053)
+* CCSM <1>: CCSM Example. (line 12245)
+* CCSM conventions: CF Conventions. (line 5394)
* CDL: ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* CEIL: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ceiling function: Intrinsic mathematical methods.
- (line 7929)
-* cell methods convention: CF Conventions. (line 5408)
+ (line 8043)
+* cell methods convention: CF Conventions. (line 5483)
* cell-based grids: Auxiliary Coordinates.
- (line 3601)
-* 'cell_methods': CF Conventions. (line 5408)
-* CF compliance checker: Group Path Editing.
- (line 2902)
+ (line 3645)
+* 'cell_methods': CF Conventions. (line 5483)
+* CF compliance checker: Checking CF-compliance.
+ (line 2952)
* CF conventions: Subsetting Coordinate Variables.
- (line 2630)
+ (line 2660)
* CF conventions <1>: Auxiliary Coordinates.
- (line 3584)
-* CF conventions <2>: UDUnits Support. (line 3792)
-* CF conventions <3>: CF Conventions. (line 5331)
+ (line 3628)
+* CF conventions <2>: UDUnits Support. (line 3836)
+* CF conventions <3>: CF Conventions. (line 5394)
* CF conventions <4>: ncbo netCDF Binary Operator.
- (line 8574)
-* cfchecker: Group Path Editing.
- (line 2902)
+ (line 8696)
+* cfchecker: Checking CF-compliance.
+ (line 2952)
* 'change_miss()': Missing values ncap2.
- (line 6257)
+ (line 6332)
* char(): Methods and functions.
- (line 6414)
+ (line 6489)
* characters, special: ncatted netCDF Attribute Editor.
- (line 8329)
-* Charlie Zender: Foreword. (line 203)
-* Charlie Zender <1>: Contributors. (line 10840)
-* chocolate: Contributing. (line 10819)
-* Chris Barker: Chunking. (line 4135)
+ (line 8443)
+* Charlie Zender: Foreword. (line 208)
+* Charlie Zender <1>: Contributors. (line 10963)
+* chocolate: Contributing. (line 10942)
+* Chris Barker: Chunking. (line 4189)
* chunking: netCDF2/3/4 and HDF4/5 Support.
- (line 649)
-* chunking <1>: Chunking. (line 4052)
+ (line 654)
+* chunking <1>: Chunking. (line 4096)
* chunking <2>: ncks netCDF Kitchen Sink.
- (line 9497)
-* chunking map: Chunking. (line 4070)
-* chunking map <1>: Chunking. (line 4129)
-* chunking policy: Chunking. (line 4070)
-* chunksize: Chunking. (line 4070)
-* 'clang': Compatability. (line 402)
+ (line 9619)
+* chunking map: Chunking. (line 4114)
+* chunking map <1>: Chunking. (line 4183)
+* chunking policy: Chunking. (line 4114)
+* chunksize: Chunking. (line 4114)
+* citation: Citation. (line 11034)
+* 'clang': Compatability. (line 407)
* 'CLASSIC' files: File Formats and Conversion.
- (line 2089)
-* client-server: OPeNDAP. (line 1909)
+ (line 2104)
+* client-server: OPeNDAP. (line 1924)
* Climate and Forecast Metadata Convention: UDUnits Support.
- (line 3792)
-* climate model: Philosophy. (line 891)
+ (line 3836)
+* climate model: Philosophy. (line 896)
* climate model <1>: Climate Model Paradigm.
- (line 917)
-* climate model <2>: Concatenation. (line 1116)
+ (line 922)
+* climate model <2>: Concatenation. (line 1121)
* climate model <3>: Specifying Input Files.
- (line 1725)
+ (line 1736)
* climate model <4>: ncecat netCDF Ensemble Concatenator.
- (line 8968)
+ (line 9090)
* climate model <5>: Normalization and Integration.
- (line 10739)
+ (line 10862)
* climate model <6>: Normalization and Integration.
- (line 10750)
-* clipping operators: Expressions. (line 5758)
+ (line 10873)
+* clipping operators: Expressions. (line 5833)
* CMIP: nces netCDF Ensemble Statistics.
- (line 8756)
+ (line 8878)
* CMIP <1>: ncecat netCDF Ensemble Concatenator.
- (line 8912)
-* CMIP5: CMIP5 Example. (line 11030)
-* 'cnk_all': Chunking. (line 4085)
-* 'cnk_dmn': Chunking. (line 4135)
-* 'cnk_g2d': Chunking. (line 4085)
-* 'cnk_g3d': Chunking. (line 4085)
-* 'cnk_lfp': Chunking. (line 4135)
-* CNK_MAP: Chunking. (line 4129)
-* 'cnk_prd': Chunking. (line 4135)
-* 'cnk_rd1': Chunking. (line 4135)
-* 'cnk_scl': Chunking. (line 4135)
-* 'cnk_xpl': Chunking. (line 4085)
-* 'cnk_xst': Chunking. (line 4085)
-* 'cnk_xst' <1>: Chunking. (line 4135)
-* Comeau: Compatability. (line 384)
+ (line 9034)
+* CMIP5: CMIP5 Example. (line 11172)
+* 'cnk_all': Chunking. (line 4130)
+* 'cnk_dmn': Chunking. (line 4189)
+* 'cnk_g2d': Chunking. (line 4130)
+* 'cnk_g3d': Chunking. (line 4130)
+* 'cnk_lfp': Chunking. (line 4189)
+* CNK_MAP: Chunking. (line 4183)
+* 'cnk_prd': Chunking. (line 4189)
+* 'cnk_r1d': Chunking. (line 4130)
+* 'cnk_rd1': Chunking. (line 4189)
+* 'cnk_scl': Chunking. (line 4189)
+* 'cnk_xpl': Chunking. (line 4130)
+* 'cnk_xst': Chunking. (line 4130)
+* 'cnk_xst' <1>: Chunking. (line 4189)
+* Comeau: Compatability. (line 389)
* command line options: Command Line Options.
- (line 1589)
-* command line switches: Philosophy. (line 907)
-* command line switches <1>: Common features. (line 1487)
+ (line 1597)
+* command line switches: Philosophy. (line 912)
+* command line switches <1>: Common features. (line 1492)
* command line switches <2>: Specifying Output Files.
- (line 1765)
+ (line 1778)
* command line switches <3>: Operator Reference Manual.
- (line 5504)
+ (line 5579)
* comments: Syntax of ncap2 statements.
- (line 5591)
-* 'como': Compatability. (line 402)
-* Compaq: Compatability. (line 384)
-* comparator: Mask condition. (line 10655)
-* compatability: Compatability. (line 384)
+ (line 5666)
+* 'como': Compatability. (line 407)
+* Compaq: Compatability. (line 389)
+* comparator: Mask condition. (line 10778)
+* compatability: Compatability. (line 389)
* compilers: Specifying Output Files.
- (line 1787)
+ (line 1800)
* complementary error function: Intrinsic mathematical methods.
- (line 7929)
-* compliance checker: Group Path Editing.
- (line 2902)
-* compression: Deflation. (line 4248)
+ (line 8043)
+* compliance checker: Checking CF-compliance.
+ (line 2952)
+* compression: Deflation. (line 4311)
* compression <1>: ncks netCDF Kitchen Sink.
- (line 9497)
+ (line 9619)
* concatenation: Appending Variables.
- (line 1016)
+ (line 1021)
* concatenation <1>: ncecat netCDF Ensemble Concatenator.
- (line 8872)
+ (line 8994)
* concatenation <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10027)
+ (line 10150)
* concatenation <3>: ncrcat netCDF Record Concatenator.
- (line 10299)
-* conditional Operator: Expressions. (line 5748)
+ (line 10422)
+* conditional Operator: Expressions. (line 5823)
* 'config.guess': Help Requests and Bug Reports.
- (line 872)
+ (line 877)
* 'configure.eg': Help Requests and Bug Reports.
- (line 872)
-* constraint expressions: OPeNDAP. (line 2035)
+ (line 877)
+* constraint expressions: OPeNDAP. (line 2050)
* contents: How to Use This guide.
- (line 350)
-* contributing: Contributing. (line 10808)
-* contributors: Contributors. (line 10839)
-* coordinate limits: Hyperslabs. (line 3098)
-* coordinate variable: UDUnits Support. (line 3728)
-* coordinate variable <1>: Operation Types. (line 4634)
-* coordinate variable <2>: CF Conventions. (line 5397)
+ (line 355)
+* contributing: Contributing. (line 10931)
+* contributors: Contributors. (line 10962)
+* coordinate limits: Hyperslabs. (line 3142)
+* coordinate variable: UDUnits Support. (line 3772)
+* coordinate variable <1>: Operation Types. (line 4697)
+* coordinate variable <2>: CF Conventions. (line 5472)
* coordinate variable <3>: ncbo netCDF Binary Operator.
- (line 8571)
+ (line 8693)
* coordinate variable <4>: ncwa netCDF Weighted Averager.
- (line 10621)
+ (line 10744)
* coordinate variables: ncrename netCDF Renamer.
- (line 10489)
+ (line 10612)
* 'coordinates': Auxiliary Coordinates.
- (line 3584)
-* 'coordinates' <1>: CF Conventions. (line 5397)
+ (line 3628)
+* 'coordinates' <1>: CF Conventions. (line 5472)
* coordinates: Add Coordinates to MODIS Data.
- (line 11980)
-* coordinates convention: CF Conventions. (line 5397)
+ (line 12144)
+* coordinates convention: CF Conventions. (line 5472)
* coordinates, modifying: Permute MODIS Coordinates.
- (line 12028)
+ (line 12192)
* core dump: Help Requests and Bug Reports.
- (line 809)
-* 'core dump': Large Datasets. (line 1313)
+ (line 814)
+* 'core dump': Large Datasets. (line 1318)
* 'core dump' <1>: Filters for 'ncks'.
- (line 9809)
+ (line 9931)
* COS: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* COSH: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* cosine function: Intrinsic mathematical methods.
- (line 7929)
-* covariance: Examples ncap2. (line 7856)
-* 'cp': Subsetting Files. (line 2413)
-* Cray: Compatability. (line 384)
-* Cray <1>: Large Datasets. (line 1308)
-* 'csh': Subsetting Files. (line 2589)
+ (line 8043)
+* covariance: Examples ncap2. (line 7970)
+* 'cp': Subsetting Files. (line 2443)
+* Cray: Compatability. (line 389)
+* Cray <1>: Large Datasets. (line 1313)
+* 'csh': Subsetting Files. (line 2619)
* Csh shell: Filters for 'ncks'.
- (line 9637)
-* 'cxx': Compatability. (line 402)
+ (line 9759)
+* 'cxx': Compatability. (line 407)
* Cygwin: Windows Operating System.
- (line 498)
-* Cygwin <1>: Symbolic Links. (line 534)
-* C_FORMAT: Performance. (line 1470)
+ (line 503)
+* Cygwin <1>: Symbolic Links. (line 539)
+* C_FORMAT: Performance. (line 1475)
* daily data: Daily data in one file.
- (line 10938)
+ (line 11080)
* daily data <1>: One time point one file.
- (line 11004)
+ (line 11146)
* daily data <2>: Multiple files with multiple time points.
- (line 11022)
-* Daniel Baumann: Contributors. (line 10885)
-* Daniel Wang: Contributors. (line 10857)
-* DAP: OPeNDAP. (line 1909)
-* data access protocol: OPeNDAP. (line 1909)
+ (line 11164)
+* Daniel Baumann: Contributors. (line 11008)
+* Daniel Wang: Contributors. (line 10980)
+* DAP: OPeNDAP. (line 1924)
+* data access protocol: OPeNDAP. (line 1924)
* data safety: Temporary Output Files.
- (line 928)
+ (line 933)
* data safety <1>: ncrename netCDF Renamer.
- (line 10412)
-* data, missing: Missing Values. (line 3939)
+ (line 10535)
+* data, missing: Missing Values. (line 3983)
* data, missing <1>: ncatted netCDF Attribute Editor.
- (line 8185)
-* 'date': CF Conventions. (line 5331)
-* 'datesec': CF Conventions. (line 5331)
+ (line 8299)
+* 'date': CF Conventions. (line 5394)
+* 'datesec': CF Conventions. (line 5394)
* DBG_LVL: Help Requests and Bug Reports.
- (line 864)
-* DBG_LVL <1>: Large Datasets. (line 1323)
-* DBG_LVL <2>: OpenMP Threading. (line 1573)
+ (line 869)
+* DBG_LVL <1>: Large Datasets. (line 1328)
+* DBG_LVL <2>: OpenMP Threading. (line 1581)
* DDRA: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* Debian: netCDF2/3/4 and HDF4/5 Support.
- (line 746)
+ (line 751)
* DEBUG-LEVEL: Help Requests and Bug Reports.
- (line 864)
-* DEBUG-LEVEL <1>: Large Datasets. (line 1323)
+ (line 869)
+* DEBUG-LEVEL <1>: Large Datasets. (line 1328)
* debugging: Help Requests and Bug Reports.
- (line 849)
-* debugging <1>: Large Datasets. (line 1323)
-* debugging <2>: OpenMP Threading. (line 1573)
-* DEC: Compatability. (line 384)
-* 'defdim()': Dimensions. (line 5779)
-* defining dimensions in 'ncap2': Dimensions. (line 5779)
+ (line 854)
+* debugging <1>: Large Datasets. (line 1328)
+* debugging <2>: OpenMP Threading. (line 1581)
+* DEC: Compatability. (line 389)
+* 'defdim()': Dimensions. (line 5854)
+* defining dimensions in 'ncap2': Dimensions. (line 5854)
* deflation: netCDF2/3/4 and HDF4/5 Support.
- (line 645)
-* deflation <1>: Deflation. (line 4248)
+ (line 650)
+* deflation <1>: Deflation. (line 4311)
* deflation <2>: ncks netCDF Kitchen Sink.
- (line 9497)
-* degenerate dimension: Chunking. (line 4129)
-* degenerate dimension <1>: Operation Types. (line 4679)
-* degenerate dimension <2>: Examples ncap2. (line 7904)
+ (line 9619)
+* degenerate dimension: Chunking. (line 4183)
+* degenerate dimension <1>: Operation Types. (line 4742)
+* degenerate dimension <2>: Examples ncap2. (line 8018)
* degenerate dimension <3>: ncbo netCDF Binary Operator.
- (line 8566)
+ (line 8687)
* degenerate dimension <4>: ncecat netCDF Ensemble Concatenator.
- (line 9021)
+ (line 9143)
* degenerate dimension <5>: ncflint netCDF File Interpolator.
- (line 9083)
+ (line 9205)
* degenerate dimension <6>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10189)
+ (line 10312)
* degenerate dimension <7>: ncra netCDF Record Averager.
- (line 10241)
+ (line 10364)
* degenerate dimension <8>: ncwa netCDF Weighted Averager.
- (line 10573)
+ (line 10696)
* degenerate dimension <9>: Normalization and Integration.
- (line 10730)
-* delete (groups): Group Path Editing.
- (line 2677)
+ (line 10853)
+* delete (groups): Flattening Groups. (line 2712)
* 'delete_miss()': Missing values ncap2.
- (line 6267)
-* demotion: Type Conversion. (line 4763)
-* Dennis Heimbigner: Contributors. (line 10831)
+ (line 6342)
+* demotion: Type Conversion. (line 4826)
+* Dennis Heimbigner: Contributors. (line 10954)
* derived fields: ncap2 netCDF Arithmetic Processor.
- (line 5539)
+ (line 5614)
* derived fields <1>: ncap2 netCDF Arithmetic Processor.
- (line 5551)
-* digest: MD5 digests. (line 4285)
-* Digital: Compatability. (line 384)
-* dimension limits: Hyperslabs. (line 3098)
+ (line 5626)
+* digest: MD5 digests. (line 4348)
+* Digital: Compatability. (line 389)
+* dimension limits: Hyperslabs. (line 3142)
* dimension names: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* dimension order: Annual Average over Regions.
- (line 11387)
-* dimensions, growing: Examples ncap2. (line 7826)
-* disaggregate: Group Path Editing.
- (line 2799)
+ (line 11551)
+* dimensions, growing: Examples ncap2. (line 7940)
+* disaggregate: Dismembering Files.
+ (line 2845)
* disjoint files: Appending Variables.
- (line 1038)
-* diskless files: RAM disks. (line 4386)
-* dismember: Group Path Editing.
- (line 2799)
+ (line 1043)
+* diskless files: RAM disks. (line 4449)
+* dismember: Dismembering Files.
+ (line 2845)
* Distributed Data Reduction & Analysis: Proposals for Institutional Funding.
- (line 10911)
-* Distributed Oceanographic Data System: OPeNDAP. (line 1909)
+ (line 11053)
+* Distributed Oceanographic Data System: OPeNDAP. (line 1924)
* 'divide': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* dividing data: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* division: Intrinsic mathematical methods.
- (line 7926)
-* 'dmn': Chunking. (line 4135)
-* documentation: Availability. (line 310)
-* DODS: OPeNDAP. (line 1909)
+ (line 8040)
+* 'dmn': Chunking. (line 4189)
+* documentation: Availability. (line 315)
+* DODS: OPeNDAP. (line 1924)
* DODS <1>: Retaining Retrieved Files.
- (line 2077)
-* 'DODS_ROOT': OPeNDAP. (line 1909)
+ (line 2092)
+* 'DODS_ROOT': OPeNDAP. (line 1924)
* dot product: Normalization and Integration.
- (line 10676)
+ (line 10799)
* dot product <1>: Normalization and Integration.
- (line 10695)
+ (line 10818)
* double(): Methods and functions.
- (line 6423)
+ (line 6498)
* double-precision: Intrinsic mathematical methods.
- (line 8032)
-* 'dsort': Sort methods. (line 6600)
-* duration: Subcycle. (line 3314)
-* dynamic linking: Libraries. (line 560)
-* Ed Hartnett: Contributors. (line 10831)
-* Ed Hill: Contributors. (line 10887)
-* eddy covariance: Examples ncap2. (line 7862)
+ (line 8146)
+* 'dsort': Sort methods. (line 6714)
+* duration: Subcycle. (line 3358)
+* dynamic linking: Libraries. (line 565)
+* Ed Hartnett: Contributors. (line 10954)
+* Ed Hill: Contributors. (line 11010)
+* eddy covariance: Examples ncap2. (line 7976)
* editing attributes: ncatted netCDF Attribute Editor.
- (line 8162)
-* 'egrep': Subsetting Files. (line 2514)
+ (line 8276)
+* 'egrep': Subsetting Files. (line 2544)
* Elliptic integrals: GSL special functions.
- (line 7107)
-* ensemble: Concatenation. (line 1116)
+ (line 7221)
+* ensemble: Concatenation. (line 1121)
* ensemble <1>: nces netCDF Ensemble Statistics.
- (line 8733)
+ (line 8855)
* ensemble average: nces netCDF Ensemble Statistics.
- (line 8717)
+ (line 8839)
* ensemble concatenation: ncecat netCDF Ensemble Concatenator.
- (line 8872)
+ (line 8994)
* ERF: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* ERFC: Intrinsic mathematical methods.
- (line 7929)
-* Eric Blake: Contributors. (line 10895)
+ (line 8043)
+* Eric Blake: Contributors. (line 11018)
* error function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* error tolerance: Temporary Output Files.
- (line 928)
-* Etienne Tourigny: Contributors. (line 10901)
-* exclusion: Subsetting Files. (line 2371)
+ (line 933)
+* Etienne Tourigny: Contributors. (line 11024)
+* exclusion: Subsetting Files. (line 2386)
* exclusion <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* exclusion <2>: Filters for 'ncks'.
- (line 9812)
-* execution time: Libraries. (line 561)
+ (line 9934)
+* execution time: Libraries. (line 566)
* execution time <1>: Temporary Output Files.
- (line 943)
-* execution time <2>: Performance. (line 1462)
+ (line 948)
+* execution time <2>: Performance. (line 1467)
* execution time <3>: Metadata Optimization.
- (line 1504)
-* execution time <4>: Missing Values. (line 3998)
+ (line 1512)
+* execution time <4>: Missing Values. (line 4042)
* execution time <5>: ncrename netCDF Renamer.
- (line 10427)
+ (line 10550)
* EXP: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* exponent: Promoting Single-precision to Double.
- (line 5128)
+ (line 5191)
* exponentiation: Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* exponentiation function: Intrinsic mathematical methods.
- (line 7929)
-* expressions: Expressions. (line 5601)
+ (line 8043)
+* expressions: Expressions. (line 5676)
* extended file format: Determining File Format.
- (line 2184)
+ (line 2199)
* extended regular expressions: Large Numbers of Files.
- (line 1229)
-* extended regular expressions <1>: Subsetting Files. (line 2514)
-* extended regular expressions <2>: Examples ncap2. (line 7881)
+ (line 1234)
+* extended regular expressions <1>: Subsetting Files. (line 2544)
+* extended regular expressions <2>: Examples ncap2. (line 7995)
* extended regular expressions <3>: ncatted netCDF Attribute Editor.
- (line 8205)
+ (line 8319)
* extended regular expressions <4>: ncatted netCDF Attribute Editor.
- (line 8412)
-* extraction: Subsetting Files. (line 2371)
+ (line 8526)
+* extraction: Subsetting Files. (line 2386)
* extraction <1>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* extraction <2>: Filters for 'ncks'.
- (line 9812)
+ (line 9934)
* 'f90': Windows Operating System.
- (line 498)
+ (line 503)
* features, requesting: Help Requests and Bug Reports.
- (line 809)
-* File buffers: Buffer sizes. (line 4355)
-* file combination: Combine Files. (line 11052)
+ (line 814)
+* File buffers: Buffer sizes. (line 4418)
+* file combination: Combine Files. (line 11216)
* file deletion: Retaining Retrieved Files.
- (line 2049)
+ (line 2064)
* file multiplication: ncflint netCDF File Interpolator.
- (line 9159)
+ (line 9281)
* file removal: Retaining Retrieved Files.
- (line 2049)
+ (line 2064)
* file retention: Retaining Retrieved Files.
- (line 2049)
+ (line 2064)
* files, multiple: Specifying Input Files.
- (line 1696)
+ (line 1707)
* files, numerous input: Large Numbers of Files.
- (line 1193)
-* Filipe Fernandes: Contributors. (line 10891)
+ (line 1198)
+* Filipe Fernandes: Contributors. (line 11014)
* filters: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* findgen-equivalent: Arrays and hyperslabs.
- (line 5877)
+ (line 5952)
* fix record dimension: ncecat netCDF Ensemble Concatenator.
- (line 8916)
+ (line 9038)
* fix record dimension <1>: ncecat netCDF Ensemble Concatenator.
- (line 9016)
+ (line 9138)
* fix record dimension <2>: ncks netCDF Kitchen Sink.
- (line 9397)
+ (line 9519)
* fixed dimension: ncecat netCDF Ensemble Concatenator.
- (line 8916)
+ (line 9038)
* fixed dimension <1>: ncecat netCDF Ensemble Concatenator.
- (line 9016)
+ (line 9138)
* fixed dimension <2>: ncks netCDF Kitchen Sink.
- (line 9320)
+ (line 9442)
* fixed dimension <3>: ncks netCDF Kitchen Sink.
- (line 9397)
-* flags: Examples ncap2. (line 7840)
-* flatten (groups): Group Path Editing.
- (line 2677)
-* flattening: Autoconversion. (line 2313)
+ (line 9519)
+* flags: Examples ncap2. (line 7954)
+* flatten (groups): Flattening Groups. (line 2712)
+* flattening: Autoconversion. (line 2328)
* 'float': Intrinsic mathematical methods.
- (line 8032)
+ (line 8146)
* float(): Methods and functions.
- (line 6420)
+ (line 6495)
* FLOOR: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* floor function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* 'flt_byt': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'flt_sht': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
-* for(): Loops. (line 6545)
-* force append: Batch Mode. (line 5252)
-* force overwrite: Batch Mode. (line 5252)
-* foreword: Foreword. (line 203)
+ (line 10082)
+* for(): Loops. (line 6659)
+* force append: Batch Mode. (line 5315)
+* force overwrite: Batch Mode. (line 5315)
+* foreword: Foreword. (line 208)
* Fortran: Promoting Single-precision to Double.
- (line 4911)
+ (line 4974)
* Fortran <1>: ncra netCDF Record Averager.
- (line 10276)
+ (line 10399)
* Fortran <2>: ncrcat netCDF Record Concatenator.
- (line 10353)
+ (line 10476)
* Fortran index convention: C and Fortran Index Conventions.
- (line 3061)
-* FORTRAN_FORMAT: Performance. (line 1470)
-* Francesco Lovergine: Contributors. (line 10885)
+ (line 3105)
+* FORTRAN_FORMAT: Performance. (line 1475)
+* Francesco Lovergine: Contributors. (line 11008)
* 'ftp': Windows Operating System.
- (line 504)
-* 'ftp' <1>: Remote storage. (line 1797)
+ (line 509)
+* 'ftp' <1>: Remote storage. (line 1810)
* FTP: Retaining Retrieved Files.
- (line 2066)
+ (line 2081)
* funding: Proposals for Institutional Funding.
- (line 10911)
-* 'g++': Compatability. (line 402)
+ (line 11053)
+* 'g++': Compatability. (line 407)
* 'g++' <1>: Windows Operating System.
- (line 518)
-* 'g2d': Chunking. (line 4085)
-* 'g3d': Chunking. (line 4085)
+ (line 523)
+* 'g2d': Chunking. (line 4130)
+* 'g3d': Chunking. (line 4130)
* GAG: ncecat netCDF Ensemble Concatenator.
- (line 8924)
-* GAMMA: Compatability. (line 453)
+ (line 9046)
+* GAMMA: Compatability. (line 458)
* GAMMA <1>: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* gamma function: GSL special functions.
- (line 7073)
+ (line 7187)
* gamma function <1>: Intrinsic mathematical methods.
- (line 7929)
-* Gary Strand: Contributors. (line 10883)
+ (line 8043)
+* Gary Strand: Contributors. (line 11006)
* Gaussian weights: Normalization and Integration.
- (line 10739)
-* Gavin Burris: Contributors. (line 10897)
-* Gayathri Venkitachalam: Contributors. (line 10879)
-* 'gcc': Compatability. (line 402)
+ (line 10862)
+* Gavin Burris: Contributors. (line 11020)
+* Gayathri Venkitachalam: Contributors. (line 11002)
+* 'gcc': Compatability. (line 407)
* 'gcc' <1>: Windows Operating System.
- (line 518)
+ (line 523)
* GCM: Climate Model Paradigm.
- (line 917)
+ (line 922)
* GCM <1>: Promoting Single-precision to Double.
- (line 5050)
-* geographical weight: Monthly Cycle. (line 11678)
-* George Shapavalov: Contributors. (line 10889)
-* George Shapovalov: Contributors. (line 10867)
-* George White: Contributors. (line 10883)
+ (line 5113)
+* geographical weight: Monthly Cycle. (line 11842)
+* George Shapavalov: Contributors. (line 11012)
+* George Shapovalov: Contributors. (line 10990)
+* George White: Contributors. (line 11006)
* 'gethostname': Windows Operating System.
- (line 502)
+ (line 507)
* 'getopt': Command Line Options.
- (line 1603)
+ (line 1611)
* 'getopt.h': Command Line Options.
- (line 1603)
+ (line 1611)
* 'getopt_long': Command Line Options.
- (line 1603)
+ (line 1611)
* 'getuid': Windows Operating System.
- (line 502)
+ (line 507)
* 'get_miss()': Missing values ncap2.
- (line 6262)
-* Glenn Davis: Contributors. (line 10831)
+ (line 6337)
+* Glenn Davis: Contributors. (line 10954)
* 'global' attribute: ncatted netCDF Attribute Editor.
- (line 8394)
+ (line 8508)
* 'global' attribute <1>: ncrename netCDF Renamer.
- (line 10436)
+ (line 10559)
* global attributes: Large Numbers of Files.
- (line 1221)
-* global attributes <1>: History Attribute. (line 5272)
+ (line 1226)
+* global attributes <1>: History Attribute. (line 5335)
* global attributes <2>: File List Attributes.
- (line 5300)
-* global attributes <3>: ARM Conventions. (line 5475)
+ (line 5363)
+* global attributes <3>: ARM Conventions. (line 5550)
* global attributes <4>: ncatted netCDF Attribute Editor.
- (line 8227)
+ (line 8341)
* global attributes <5>: ncatted netCDF Attribute Editor.
- (line 8394)
+ (line 8508)
* global attributes <6>: ncks netCDF Kitchen Sink.
- (line 9220)
+ (line 9342)
* global attributes <7>: ncks netCDF Kitchen Sink.
- (line 9254)
+ (line 9376)
* global attributes <8>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* global attributes <9>: ncrename netCDF Renamer.
- (line 10436)
+ (line 10559)
* global attributes <10>: ncrename netCDF Renamer.
- (line 10516)
+ (line 10639)
* globbing: Large Numbers of Files.
- (line 1229)
+ (line 1234)
* globbing <1>: Specifying Input Files.
- (line 1662)
-* globbing <2>: Subsetting Files. (line 2589)
-* globbing <3>: Examples ncap2. (line 7881)
+ (line 1670)
+* globbing <2>: Subsetting Files. (line 2619)
+* globbing <3>: Examples ncap2. (line 7995)
* globbing <4>: ncbo netCDF Binary Operator.
- (line 8498)
+ (line 8619)
* globbing <5>: ncra netCDF Record Averager.
- (line 10268)
+ (line 10391)
* globbing <6>: ncrcat netCDF Record Concatenator.
- (line 10346)
+ (line 10469)
* GNU: Command Line Options.
- (line 1590)
-* GNU <1>: Subsetting Files. (line 2514)
+ (line 1598)
+* GNU <1>: Subsetting Files. (line 2544)
* 'gnu-win32': Windows Operating System.
- (line 498)
-* GNU/Linux: Large Datasets. (line 1313)
+ (line 503)
+* GNU/Linux: Large Datasets. (line 1318)
* 'GNUmakefile': Windows Operating System.
- (line 498)
-* God: UDUnits Support. (line 3838)
-* 'grep -E': Subsetting Files. (line 2514)
+ (line 503)
+* God: UDUnits Support. (line 3882)
+* GODAD: CMIP5 Example. (line 11172)
+* 'grep -E': Subsetting Files. (line 2544)
* group aggregation: ncecat netCDF Ensemble Concatenator.
- (line 8924)
-* group aggregation <1>: Combine Files. (line 11158)
+ (line 9046)
+* group aggregation <1>: Combine Files. (line 11322)
* group names: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* group path: Group Path Editing.
- (line 2658)
+ (line 2690)
* group, aggregation: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* group, anomaly: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* group, dimension permutation: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* group, spatial averaging: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* group, standard deviation: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* group, temporal averaging: Annual Average over Regions.
- (line 11612)
+ (line 11776)
* groups: netCDF2/3/4 and HDF4/5 Support.
- (line 654)
+ (line 659)
* groups <1>: ncatted netCDF Attribute Editor.
- (line 8418)
+ (line 8532)
* groups, averaging: Global Distribution of Long-term Average.
- (line 11365)
-* groups, creating: Combine Files. (line 11158)
-* groups, moving: Group Path Editing.
- (line 2765)
-* groups, renaming: Group Path Editing.
- (line 2765)
-* growing dimensions: Examples ncap2. (line 7826)
-* GSL: Compatability. (line 446)
+ (line 11529)
+* groups, creating: Combine Files. (line 11322)
+* groups, moving: Moving Groups. (line 2802)
+* groups, renaming: Moving Groups. (line 2802)
+* growing dimensions: Examples ncap2. (line 7940)
+* GSL: Compatability. (line 451)
* GSL <1>: GSL special functions.
- (line 7058)
-* GSL <2>: GSL interpolation. (line 7450)
+ (line 7172)
+* GSL <2>: GSL interpolation. (line 7564)
* GSL_SF_BESSEL_JN: GSL special functions.
- (line 7087)
+ (line 7201)
* GSL_SF_GAMMA: GSL special functions.
- (line 7073)
+ (line 7187)
* gsl_sf_legendre_Pl: GSL special functions.
- (line 7142)
-* 'gw': CF Conventions. (line 5331)
+ (line 7256)
+* 'gw': CF Conventions. (line 5394)
* 'gw' <1>: Normalization and Integration.
- (line 10739)
+ (line 10862)
* H4CF: netCDF2/3/4 and HDF4/5 Support.
- (line 737)
+ (line 742)
* 'h4tonccf': netCDF2/3/4 and HDF4/5 Support.
- (line 737)
-* Harry Mangalam: Contributors. (line 10860)
-* hash: MD5 digests. (line 4285)
+ (line 742)
+* Harry Mangalam: Contributors. (line 10983)
+* hash: MD5 digests. (line 4348)
* HDF: netCDF2/3/4 and HDF4/5 Support.
- (line 597)
+ (line 602)
* HDF <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* HDF <2>: ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* HDF <3>: Proposals for Institutional Funding.
- (line 10918)
-* HDF unpacking: Packed data. (line 4542)
+ (line 11060)
+* HDF unpacking: Packed data. (line 4605)
* HDF4: netCDF2/3/4 and HDF4/5 Support.
- (line 674)
+ (line 679)
* HDF4 <1>: ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* HDF5: netCDF2/3/4 and HDF4/5 Support.
- (line 611)
+ (line 616)
* HDF5 <1>: netCDF2/3/4 and HDF4/5 Support.
- (line 667)
+ (line 672)
* 'hdf_name': netCDF2/3/4 and HDF4/5 Support.
- (line 728)
+ (line 733)
* 'hdp': ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* help: Help Requests and Bug Reports.
- (line 809)
-* Henry Butowsky: Contributors. (line 10846)
+ (line 814)
+* Henry Butowsky: Contributors. (line 10969)
* 'hgh_byt': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'hgh_sht': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* hidden attributes: ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* Hierarchical Data Format: netCDF2/3/4 and HDF4/5 Support.
- (line 597)
+ (line 602)
* 'history': Large Numbers of Files.
- (line 1273)
-* 'history' <1>: Remote storage. (line 1797)
-* 'history' <2>: History Attribute. (line 5272)
-* 'history' <3>: ARM Conventions. (line 5475)
+ (line 1278)
+* 'history' <1>: Remote storage. (line 1810)
+* 'history' <2>: History Attribute. (line 5335)
+* 'history' <3>: ARM Conventions. (line 5550)
* 'history' <4>: ncatted netCDF Attribute Editor.
- (line 8180)
+ (line 8294)
* 'history' <5>: Filters for 'ncks'.
- (line 9730)
+ (line 9852)
* 'hncgen': ncks netCDF Kitchen Sink.
- (line 9357)
-* HP: Compatability. (line 384)
-* HPSS: Remote storage. (line 1835)
-* 'hsi': Remote storage. (line 1835)
-* HTML: Availability. (line 310)
-* HTTP protocol: OPeNDAP. (line 1909)
-* 'hyai': CF Conventions. (line 5331)
-* 'hyam': CF Conventions. (line 5331)
-* 'hybi': CF Conventions. (line 5331)
-* 'hybm': CF Conventions. (line 5331)
-* hybrid coordinate system: Left hand casting. (line 5831)
+ (line 9479)
+* HP: Compatability. (line 389)
+* HPSS: Remote storage. (line 1850)
+* 'hsi': Remote storage. (line 1850)
+* HTML: Availability. (line 315)
+* HTTP protocol: OPeNDAP. (line 1924)
+* 'hyai': CF Conventions. (line 5394)
+* 'hyam': CF Conventions. (line 5394)
+* 'hybi': CF Conventions. (line 5394)
+* 'hybm': CF Conventions. (line 5394)
+* hybrid coordinate system: Left hand casting. (line 5906)
* hyperbolic arccosine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* hyperbolic arcsine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* hyperbolic arctangent function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* hyperbolic cosine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* hyperbolic sine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* hyperbolic tangent: Intrinsic mathematical methods.
- (line 7929)
-* hyperslab: Hyperslabs. (line 3098)
-* hyperslab <1>: Chunking. (line 4075)
+ (line 8043)
+* hyperslab: Hyperslabs. (line 3142)
+* hyperslab <1>: Chunking. (line 4119)
* hyperslab <2>: nces netCDF Ensemble Statistics.
- (line 8751)
+ (line 8873)
* hyperslab <3>: ncecat netCDF Ensemble Concatenator.
- (line 8910)
+ (line 9032)
* hyperslab <4>: ncra netCDF Record Averager.
- (line 10252)
+ (line 10375)
* hyperslab <5>: ncrcat netCDF Record Concatenator.
- (line 10322)
+ (line 10445)
* hyperslab <6>: ncwa netCDF Weighted Averager.
- (line 10585)
+ (line 10708)
* hyperslabs: Arrays and hyperslabs.
- (line 5904)
-* I/O: OPeNDAP. (line 1981)
+ (line 5979)
+* I/O: OPeNDAP. (line 1996)
* I/O <1>: C and Fortran Index Conventions.
- (line 3065)
-* I/O <2>: Multislabs. (line 3440)
-* I/O block size: Buffer sizes. (line 4355)
+ (line 3109)
+* I/O <2>: Multislabs. (line 3484)
+* I/O block size: Buffer sizes. (line 4418)
* I18N: Internationalization.
- (line 1496)
-* IBM: Compatability. (line 384)
-* 'icc': Compatability. (line 402)
-* ID Quoting: ID Quoting. (line 8097)
-* IDL: Philosophy. (line 900)
+ (line 1501)
+* IBM: Compatability. (line 389)
+* 'icc': Compatability. (line 407)
+* ID Quoting: ID Quoting. (line 8211)
+* IDL: Philosophy. (line 905)
* IEEE: Automatic type conversion.
- (line 4869)
+ (line 4932)
* IEEE NaN: ncatted netCDF Attribute Editor.
- (line 8375)
-* if(): if statement. (line 6123)
-* 'ilimit': Large Datasets. (line 1311)
+ (line 8489)
+* if(): if statement. (line 6198)
+* 'ilimit': Large Datasets. (line 1316)
* illegal names: netCDF2/3/4 and HDF4/5 Support.
- (line 728)
+ (line 733)
* implicit conversion: Promoting Single-precision to Double.
- (line 4899)
-* 'include': Include files. (line 6585)
+ (line 4962)
+* 'include': Include files. (line 6699)
* including files: Syntax of ncap2 statements.
- (line 5594)
+ (line 5669)
* index convention: C and Fortran Index Conventions.
- (line 3061)
+ (line 3105)
* indgen-equivalent: Arrays and hyperslabs.
- (line 5877)
+ (line 5952)
* inexact conversion: Intrinsic mathematical methods.
- (line 7996)
-* Info: Availability. (line 310)
+ (line 8110)
+* Info: Availability. (line 315)
* input files: Large Numbers of Files.
- (line 1247)
+ (line 1252)
* input files <1>: Specifying Input Files.
- (line 1662)
+ (line 1670)
* input files <2>: Specifying Output Files.
- (line 1765)
+ (line 1778)
* input files <3>: Specifying Output Files.
- (line 1782)
+ (line 1795)
* INPUT-PATH: Specifying Input Files.
- (line 1662)
-* INPUT-PATH <1>: Remote storage. (line 1858)
-* installation: Compatability. (line 384)
+ (line 1670)
+* INPUT-PATH <1>: Remote storage. (line 1873)
+* installation: Compatability. (line 389)
* installation <1>: Help Requests and Bug Reports.
- (line 872)
+ (line 877)
* int(): Methods and functions.
- (line 6418)
+ (line 6493)
* int64(): Methods and functions.
- (line 6433)
+ (line 6508)
* integration: Normalization and Integration.
- (line 10676)
-* integrity: MD5 digests. (line 4285)
-* Intel: Compatability. (line 384)
+ (line 10799)
+* integrity: MD5 digests. (line 4348)
+* Intel: Compatability. (line 389)
* Internationalization: Internationalization.
- (line 1496)
-* interoperability: Packed data. (line 4542)
+ (line 1501)
+* interoperability: Packed data. (line 4605)
* interpolation: ncflint netCDF File Interpolator.
- (line 9032)
-* interpolation <1>: Regrid MODIS Data. (line 11842)
-* intersection: Subsetting Files. (line 2371)
-* intersection <1>: Subsetting Files. (line 2462)
-* introduction: Introduction. (line 299)
+ (line 9154)
+* interpolation <1>: Regrid MODIS Data. (line 12006)
+* intersection: Subsetting Files. (line 2386)
+* intersection <1>: Subsetting Files. (line 2492)
+* introduction: Introduction. (line 304)
* introduction <1>: How to Use This guide.
- (line 350)
-* 'invert_map': Sort methods. (line 6600)
+ (line 355)
+* 'invert_map': Sort methods. (line 6714)
* IPCC: nces netCDF Ensemble Statistics.
- (line 8756)
+ (line 8878)
* IPCC <1>: Proposals for Institutional Funding.
- (line 10911)
-* irregular grids: Irregular grids. (line 6845)
-* ISO: Compatability. (line 407)
-* James Gallagher: Contributors. (line 10831)
-* Jim Edwards: Contributors. (line 10873)
-* Joe Hamman: Contributors. (line 10855)
-* John Caron: Contributors. (line 10831)
-* Juliana Rew: Contributors. (line 10875)
-* Karen Schuchardt: Contributors. (line 10877)
-* Keith Lindsay: Contributors. (line 10883)
+ (line 11053)
+* irregular grids: Irregular grids. (line 6959)
+* ISO: Compatability. (line 412)
+* James Gallagher: Contributors. (line 10954)
+* Jim Edwards: Contributors. (line 10996)
+* Joe Hamman: Contributors. (line 10978)
+* John Caron: Contributors. (line 10954)
+* Juliana Rew: Contributors. (line 10998)
+* Karen Schuchardt: Contributors. (line 11000)
+* Keith Lindsay: Contributors. (line 11006)
* kitchen sink: ncks netCDF Kitchen Sink.
- (line 9185)
-* Kyle Wilcox: Contributors. (line 10897)
+ (line 9307)
+* Kyle Wilcox: Contributors. (line 11020)
* L10N: Internationalization.
- (line 1497)
-* large datasets: Large Datasets. (line 1290)
-* large datasets <1>: OpenMP Threading. (line 1551)
-* Large File Support: Large Datasets. (line 1290)
+ (line 1502)
+* large datasets: Large Datasets. (line 1295)
+* large datasets <1>: OpenMP Threading. (line 1559)
+* Large File Support: Large Datasets. (line 1295)
* Large File Support <1>: Large File Support.
- (line 2337)
-* 'lat_bnds': CF Conventions. (line 5331)
-* 'LD_LIBRARY_PATH': Libraries. (line 560)
-* left hand casting: Memory for ncap2. (line 1423)
-* left hand casting <1>: Left hand casting. (line 5831)
+ (line 2352)
+* 'lat_bnds': CF Conventions. (line 5394)
+* 'LD_LIBRARY_PATH': Libraries. (line 565)
+* left hand casting: Memory for ncap2. (line 1428)
+* left hand casting <1>: Left hand casting. (line 5906)
* Legendre polynomial: GSL special functions.
- (line 7142)
-* Lempel-Ziv deflation: Deflation. (line 4248)
-* Len Makin: Contributors. (line 10871)
+ (line 7256)
+* Lempel-Ziv deflation: Deflation. (line 4311)
+* Len Makin: Contributors. (line 10994)
* lexer: ncap2 netCDF Arithmetic Processor.
- (line 5514)
-* 'lfp': Chunking. (line 4135)
-* LFS: Large Datasets. (line 1290)
+ (line 5589)
+* 'lfp': Chunking. (line 4189)
+* LFS: Large Datasets. (line 1295)
* LFS <1>: Large File Support.
- (line 2337)
-* LHS: Left hand casting. (line 5831)
-* 'libnco': Compatability. (line 407)
-* libraries: Libraries. (line 560)
+ (line 2352)
+* LHS: Left hand casting. (line 5906)
+* 'libnco': Compatability. (line 412)
+* libraries: Libraries. (line 565)
* linkers: Specifying Output Files.
- (line 1787)
+ (line 1800)
* Linux: Intrinsic mathematical methods.
- (line 8034)
-* LLVM: Compatability. (line 405)
+ (line 8148)
+* LLVM: Compatability. (line 410)
* LN: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* 'ln -s': ncbo netCDF Binary Operator.
- (line 8512)
+ (line 8633)
* 'ln -s' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9947)
+ (line 10070)
* LOG: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* LOG10: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* logarithm, base 10: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* logarithm, natural: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* 'long double': Intrinsic mathematical methods.
- (line 8032)
+ (line 8146)
* long options: Command Line Options.
- (line 1602)
+ (line 1610)
* long options <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10121)
+ (line 10244)
* long-term average: Global Distribution of Long-term Average.
- (line 11284)
+ (line 11448)
* longitude: Wrapped Coordinates.
- (line 3534)
-* 'lon_bnds': CF Conventions. (line 5331)
-* Lori Sentman: Contributors. (line 10883)
+ (line 3578)
+* 'lon_bnds': CF Conventions. (line 5394)
+* Lori Sentman: Contributors. (line 11006)
* 'lrint()'.: Automatic type conversion.
- (line 4869)
+ (line 4932)
* 'lround()'.: Automatic type conversion.
- (line 4861)
-* Luk Claes: Contributors. (line 10885)
-* Macintosh: Compatability. (line 384)
-* 'Makefile': Compatability. (line 412)
+ (line 4924)
+* Luk Claes: Contributors. (line 11008)
+* Macintosh: Compatability. (line 389)
+* 'Makefile': Compatability. (line 417)
* 'Makefile' <1>: Windows Operating System.
- (line 498)
-* 'Makefile' <2>: OPeNDAP. (line 1921)
-* malloc(): Memory for ncap2. (line 1432)
+ (line 503)
+* 'Makefile' <2>: OPeNDAP. (line 1936)
+* malloc(): Memory for ncap2. (line 1437)
* mantissa: Promoting Single-precision to Double.
- (line 5128)
-* manual type conversion: Type Conversion. (line 4763)
-* 'map_dmn': Chunking. (line 4135)
-* 'map_lfp': Chunking. (line 4135)
-* 'map_prd': Chunking. (line 4135)
-* 'map_rd1': Chunking. (line 4135)
-* 'map_scl': Chunking. (line 4135)
-* 'map_xst': Chunking. (line 4135)
-* Mark Flanner: Contributors. (line 10883)
-* Markus Liebig: Contributors. (line 10883)
-* Martin Dix: Contributors. (line 10883)
-* Martin Otte: Contributors. (line 10901)
-* Martin Schmidt: Contributors. (line 10883)
-* Martin Schultz: Group Path Editing.
- (line 2902)
-* mask: Irregular grids. (line 6845)
-* mask <1>: Examples ncap2. (line 7849)
-* mask condition: Mask condition. (line 10647)
+ (line 5191)
+* manual type conversion: Type Conversion. (line 4826)
+* 'map_dmn': Chunking. (line 4189)
+* 'map_lfp': Chunking. (line 4189)
+* 'map_prd': Chunking. (line 4189)
+* 'map_rd1': Chunking. (line 4189)
+* 'map_scl': Chunking. (line 4189)
+* 'map_xst': Chunking. (line 4189)
+* Mark Flanner: Contributors. (line 11006)
+* Markus Liebig: Contributors. (line 11006)
+* Martin Dix: Contributors. (line 11006)
+* Martin Otte: Contributors. (line 11024)
+* Martin Schmidt: Contributors. (line 11006)
+* Martin Schultz: Checking CF-compliance.
+ (line 2952)
+* mask: Irregular grids. (line 6959)
+* mask <1>: Examples ncap2. (line 7963)
+* mask condition: Mask condition. (line 10770)
* mask condition <1>: Normalization and Integration.
- (line 10778)
+ (line 10901)
* masked average: ncwa netCDF Weighted Averager.
- (line 10553)
-* Mass Store System: Remote storage. (line 1797)
-* Matej Vela: Contributors. (line 10885)
+ (line 10676)
+* Mass Store System: Remote storage. (line 1810)
+* Matej Vela: Contributors. (line 11008)
* mathematical functions: Intrinsic mathematical methods.
- (line 7929)
-* Matlab: Philosophy. (line 900)
-* 'max': Operation Types. (line 4610)
+ (line 8043)
+* Matlab: Philosophy. (line 905)
+* 'max': Operation Types. (line 4673)
* max(): Methods and functions.
- (line 6326)
-* maximum: Operation Types. (line 4610)
-* MD5 digest: MD5 digests. (line 4285)
-* mean: Operation Types. (line 4610)
+ (line 6401)
+* maximum: Operation Types. (line 4673)
+* MD5 digest: MD5 digests. (line 4348)
+* mean: Operation Types. (line 4673)
* memory available: Memory Requirements.
- (line 1334)
-* memory available <1>: RAM disks. (line 4386)
-* memory leaks: Memory for ncap2. (line 1423)
+ (line 1339)
+* memory available <1>: RAM disks. (line 4449)
+* memory leaks: Memory for ncap2. (line 1428)
* memory requirements: Memory Requirements.
- (line 1334)
-* memory requirements <1>: Subsetting Files. (line 2495)
-* memory requirements <2>: RAM disks. (line 4386)
+ (line 1339)
+* memory requirements <1>: Subsetting Files. (line 2525)
+* memory requirements <2>: RAM disks. (line 4449)
* merging files: Appending Variables.
- (line 1016)
+ (line 1021)
* merging files <1>: ncks netCDF Kitchen Sink.
- (line 9234)
+ (line 9356)
* metadata: ncks netCDF Kitchen Sink.
- (line 9493)
+ (line 9615)
* metadata optimization: Metadata Optimization.
- (line 1504)
+ (line 1512)
* metadata, global: ncecat netCDF Ensemble Concatenator.
- (line 8957)
+ (line 9079)
* metadata, global <1>: ncks netCDF Kitchen Sink.
- (line 9450)
-* Michael Decker: Group Path Editing.
- (line 2902)
+ (line 9572)
+* Michael Decker: Checking CF-compliance.
+ (line 2952)
* Michael Prather: Promoting Single-precision to Double.
- (line 5237)
-* Michael Schulz: Contributors. (line 10883)
-* Microsoft: Compatability. (line 384)
+ (line 5300)
+* Michael Schulz: Contributors. (line 11006)
+* Microsoft: Compatability. (line 389)
* Microsoft <1>: Windows Operating System.
- (line 483)
+ (line 488)
* Microsoft Visual Studio: Windows Operating System.
- (line 483)
+ (line 488)
* Mike Folk: netCDF2/3/4 and HDF4/5 Support.
- (line 597)
-* Mike Page: Contributors. (line 10883)
-* 'min': Operation Types. (line 4610)
+ (line 602)
+* Mike Page: Contributors. (line 11006)
+* 'min': Operation Types. (line 4673)
* min(): Methods and functions.
- (line 6328)
-* minimum: Operation Types. (line 4610)
-* missing values: Missing Values. (line 3939)
+ (line 6403)
+* minimum: Operation Types. (line 4673)
+* missing values: Missing Values. (line 3983)
* missing values <1>: ncatted netCDF Attribute Editor.
- (line 8185)
+ (line 8299)
* missing values <2>: ncflint netCDF File Interpolator.
- (line 9105)
+ (line 9227)
* missing values <3>: ncks netCDF Kitchen Sink.
- (line 9506)
+ (line 9628)
* missing values ncap2: Missing values ncap2.
- (line 6219)
-* 'missing_value': Missing Values. (line 3939)
-* 'missing_value' <1>: Packed data. (line 4473)
+ (line 6294)
+* 'missing_value': Missing Values. (line 3983)
+* 'missing_value' <1>: Packed data. (line 4536)
* 'missing_value' <2>: ncrename netCDF Renamer.
- (line 10516)
-* MKS units: UDUnits Support. (line 3708)
-* MKS units <1>: UDUnits Support. (line 3838)
-* MODIS: Regrid MODIS Data. (line 11842)
+ (line 10639)
+* MKS units: UDUnits Support. (line 3752)
+* MKS units <1>: UDUnits Support. (line 3882)
+* MODIS: Regrid MODIS Data. (line 12006)
* MODIS <1>: Add Coordinates to MODIS Data.
- (line 11980)
+ (line 12144)
* modulus: Intrinsic mathematical methods.
- (line 7926)
-* monotonic coordinates: Performance. (line 1465)
+ (line 8040)
+* monotonic coordinates: Performance. (line 1470)
* monthly average: Daily data in one file.
- (line 10941)
-* monthly average <1>: Monthly Cycle. (line 11678)
+ (line 11083)
+* monthly average <1>: Monthly Cycle. (line 11842)
* monthly data: Monthly data in one file.
- (line 10972)
+ (line 11114)
* monthly data <1>: One time point one file.
- (line 11004)
+ (line 11146)
* monthly data <2>: Multiple files with multiple time points.
- (line 11022)
-* move groups: Group Path Editing.
- (line 2765)
-* MRO: Subcycle. (line 3314)
-* MSA: Multislabs. (line 3390)
-* 'msk_*': CF Conventions. (line 5331)
-* 'msrcp': Remote storage. (line 1835)
+ (line 11164)
+* move groups: Moving Groups. (line 2802)
+* MRO: Subcycle. (line 3358)
+* MSA: Multislabs. (line 3434)
+* 'msk_*': CF Conventions. (line 5394)
+* 'msrcp': Remote storage. (line 1850)
* msrcp: Retaining Retrieved Files.
- (line 2066)
-* 'msread': Remote storage. (line 1835)
-* MSS: Remote storage. (line 1797)
+ (line 2081)
+* 'msread': Remote storage. (line 1850)
+* MSS: Remote storage. (line 1810)
* multi-file operators: Single and Multi-file Operators.
- (line 1352)
+ (line 1357)
* multi-file operators <1>: Specifying Input Files.
- (line 1696)
+ (line 1707)
* multi-file operators <2>: Specifying Output Files.
- (line 1777)
+ (line 1790)
* multi-file operators <3>: nces netCDF Ensemble Statistics.
- (line 8786)
+ (line 8908)
* multi-file operators <4>: ncecat netCDF Ensemble Concatenator.
- (line 8952)
+ (line 9074)
* multi-file operators <5>: ncra netCDF Record Averager.
- (line 10245)
+ (line 10368)
* multi-file operators <6>: ncrcat netCDF Record Concatenator.
- (line 10315)
-* multi-hyperslab: Multislabs. (line 3390)
-* Multi-Record Operator: Subcycle. (line 3314)
+ (line 10438)
+* multi-hyperslab: Multislabs. (line 3434)
+* Multi-Record Operator: Subcycle. (line 3358)
* multiplication: Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* multiplication <1>: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* multiplication <2>: ncflint netCDF File Interpolator.
- (line 9159)
+ (line 9281)
* 'multiply': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* multiplying data: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* multiplying data <1>: ncflint netCDF File Interpolator.
- (line 9032)
-* multislab: Multislabs. (line 3390)
-* 'mv': Subsetting Files. (line 2413)
-* 'MVS': Compatability. (line 402)
+ (line 9154)
+* multislab: Multislabs. (line 3434)
+* 'mv': Subsetting Files. (line 2443)
+* 'MVS': Compatability. (line 407)
* MVS: Windows Operating System.
- (line 483)
+ (line 488)
* naked characters: ncbo netCDF Binary Operator.
- (line 8497)
+ (line 8618)
* NaN: ncatted netCDF Attribute Editor.
- (line 8375)
+ (line 8489)
+* NARR (North American Regional Reanalysis)a: Where statement.
+ (line 6620)
* NASA: Proposals for Institutional Funding.
- (line 10918)
+ (line 11060)
* NASA EOSDIS: Large Numbers of Files.
- (line 1194)
-* National Virtual Ocean Data System: OPeNDAP. (line 2011)
+ (line 1199)
+* National Virtual Ocean Data System: OPeNDAP. (line 2026)
* ncadd: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* ncap: ncap2 netCDF Arithmetic Processor.
- (line 5514)
-* ncap2: Compatability. (line 446)
+ (line 5589)
+* ncap2: Compatability. (line 451)
* ncap2 <1>: ncap2 netCDF Arithmetic Processor.
- (line 5514)
-* 'ncap2': Memory for ncap2. (line 1423)
-* 'ncap2' <1>: OpenMP Threading. (line 1551)
+ (line 5589)
+* 'ncap2': Memory for ncap2. (line 1428)
+* 'ncap2' <1>: OpenMP Threading. (line 1559)
* 'ncap2' <2>: Manual type conversion.
- (line 5242)
+ (line 5305)
* 'ncap2' <3>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9879)
+ (line 10002)
* NCAR: Climate Model Paradigm.
- (line 917)
-* NCAR MSS: Remote storage. (line 1797)
-* ncatted: Missing Values. (line 3966)
+ (line 922)
+* NCAR MSS: Remote storage. (line 1810)
+* ncatted: Missing Values. (line 4010)
* ncatted <1>: ncatted netCDF Attribute Editor.
- (line 8162)
-* 'ncatted': Subsetting Files. (line 2514)
-* 'ncatted' <1>: Missing Values. (line 3991)
-* 'ncatted' <2>: History Attribute. (line 5290)
+ (line 8276)
+* 'ncatted': Subsetting Files. (line 2544)
+* 'ncatted' <1>: Missing Values. (line 4035)
+* 'ncatted' <2>: History Attribute. (line 5353)
* 'ncattget': ncatted netCDF Attribute Editor.
- (line 8169)
+ (line 8283)
* 'ncattget' <1>: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'ncavg': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* ncbo: ncbo netCDF Binary Operator.
- (line 8450)
-* 'ncbo': Missing Values. (line 4014)
+ (line 8571)
+* 'ncbo': Missing Values. (line 4058)
* ncdiff: ncbo netCDF Binary Operator.
- (line 8450)
-* ncdismember: Group Path Editing.
- (line 2799)
-* ncdismember <1>: Group Path Editing.
- (line 2902)
+ (line 8571)
+* ncdismember: Dismembering Files.
+ (line 2845)
+* ncdismember <1>: Checking CF-compliance.
+ (line 2952)
* ncdivide: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* 'ncdmnsz': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'ncdump': Determining File Format.
- (line 2206)
+ (line 2221)
* 'ncdump' <1>: ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* 'ncdump' <2>: ncks netCDF Kitchen Sink.
- (line 9493)
+ (line 9615)
* 'ncdump' <3>: ncks netCDF Kitchen Sink.
- (line 9553)
+ (line 9675)
* ncecat: ncecat netCDF Ensemble Concatenator.
- (line 8872)
-* 'ncecat': Concatenation. (line 1103)
+ (line 8994)
+* 'ncecat': Concatenation. (line 1108)
* nces: nces netCDF Ensemble Statistics.
- (line 8717)
-* 'nces': Averaging. (line 1161)
-* 'nces' <1>: Missing Values. (line 4014)
+ (line 8839)
+* 'nces': Averaging. (line 1166)
+* 'nces' <1>: Missing Values. (line 4058)
* 'ncextr': ncks netCDF Kitchen Sink.
- (line 9198)
+ (line 9320)
* ncflint: ncflint netCDF File Interpolator.
- (line 9032)
-* 'ncflint': Interpolating. (line 1183)
-* 'ncflint' <1>: Missing Values. (line 4014)
+ (line 9154)
+* 'ncflint': Interpolating. (line 1188)
+* 'ncflint' <1>: Missing Values. (line 4058)
* 'ncgen': ncks netCDF Kitchen Sink.
- (line 9357)
+ (line 9479)
* 'ncgen-hdf': ncks netCDF Kitchen Sink.
- (line 9357)
-* ncks: Deflation. (line 4279)
-* ncks <1>: Examples ncap2. (line 7904)
+ (line 9479)
+* ncks: Deflation. (line 4342)
+* ncks <1>: Examples ncap2. (line 8018)
* ncks <2>: ncks netCDF Kitchen Sink.
- (line 9185)
+ (line 9307)
* 'ncks': Determining File Format.
- (line 2175)
-* NCL: Philosophy. (line 900)
+ (line 2190)
+* NCL: Philosophy. (line 905)
* NCL <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10075)
+ (line 10198)
* 'nclist': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'ncl_convert2nc': netCDF2/3/4 and HDF4/5 Support.
- (line 714)
+ (line 719)
* 'ncl_convert2nc' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10075)
+ (line 10198)
* 'ncmax': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'ncmdn': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* 'ncmin': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* NcML: ncks netCDF Kitchen Sink.
- (line 9553)
+ (line 9675)
* ncmult: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* ncmultiply: ncbo netCDF Binary Operator.
- (line 8450)
-* NCO availability: Availability. (line 302)
-* NCO homepage: Availability. (line 326)
+ (line 8571)
+* NCO availability: Availability. (line 307)
+* NCO homepage: Availability. (line 331)
* nco script file: Annual Average over Regions.
- (line 11387)
-* 'NCO User Guide': Availability. (line 310)
+ (line 11551)
+* 'NCO User Guide': Availability. (line 315)
* 'nco.config.log.${GNU_TRP}.foo': Help Requests and Bug Reports.
- (line 872)
+ (line 877)
* 'nco.configure.${GNU_TRP}.foo': Help Requests and Bug Reports.
- (line 872)
+ (line 877)
* 'nco.make.${GNU_TRP}.foo': Help Requests and Bug Reports.
- (line 872)
+ (line 877)
* 'nco_input_file_list': Large Numbers of Files.
- (line 1221)
+ (line 1226)
* 'nco_input_file_list' <1>: File List Attributes.
- (line 5300)
+ (line 5363)
* 'nco_input_file_number': Large Numbers of Files.
- (line 1221)
+ (line 1226)
* 'nco_input_file_number' <1>: File List Attributes.
- (line 5300)
-* 'nco_openmp_thread_number': OpenMP Threading. (line 1525)
+ (line 5363)
+* 'nco_openmp_thread_number': OpenMP Threading. (line 1533)
* ncpack: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
-* ncpdq: Chunking. (line 4075)
+ (line 9984)
+* ncpdq: Chunking. (line 4119)
* ncpdq <1>: ncecat netCDF Ensemble Concatenator.
- (line 8979)
+ (line 9101)
* ncpdq <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* ncpdq <3>: ncrcat netCDF Record Concatenator.
- (line 10327)
-* 'ncpdq': Concatenation. (line 1136)
-* 'ncpdq' <1>: OpenMP Threading. (line 1551)
-* ncra: Examples ncap2. (line 7904)
+ (line 10450)
+* 'ncpdq': Concatenation. (line 1141)
+* 'ncpdq' <1>: OpenMP Threading. (line 1559)
+* ncra: Examples ncap2. (line 8018)
* ncra <1>: ncra netCDF Record Averager.
- (line 10228)
-* 'ncra': Averaging. (line 1161)
-* 'ncra' <1>: Missing Values. (line 4014)
+ (line 10351)
+* 'ncra': Averaging. (line 1166)
+* 'ncra' <1>: Missing Values. (line 4058)
* ncrcat: ncrcat netCDF Record Concatenator.
- (line 10299)
-* 'ncrcat': Concatenation. (line 1103)
-* 'ncrcat' <1>: OpenMP Threading. (line 1551)
+ (line 10422)
+* 'ncrcat': Concatenation. (line 1108)
+* 'ncrcat' <1>: OpenMP Threading. (line 1559)
* 'ncrecsz': Filters for 'ncks'.
- (line 9637)
-* ncrename: Missing Values. (line 3966)
+ (line 9759)
+* ncrename: Missing Values. (line 4010)
* ncrename <1>: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* 'ncrng': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* NCSA: netCDF2/3/4 and HDF4/5 Support.
- (line 611)
+ (line 616)
* ncsub: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* ncsubtract: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* 'ncunits': Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* ncunpack: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
-* ncwa: Examples ncap2. (line 7904)
+ (line 9984)
+* ncwa: Examples ncap2. (line 8018)
* ncwa <1>: ncwa netCDF Weighted Averager.
- (line 10553)
-* 'ncwa': Averaging. (line 1161)
-* 'ncwa' <1>: OpenMP Threading. (line 1551)
-* 'ncwa' <2>: Missing Values. (line 4014)
+ (line 10676)
+* 'ncwa': Averaging. (line 1166)
+* 'ncwa' <1>: OpenMP Threading. (line 1559)
+* 'ncwa' <2>: Missing Values. (line 4058)
* 'NC_BYTE': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
-* 'NC_CHAR': Hyperslabs. (line 3169)
+ (line 10082)
+* 'NC_CHAR': Hyperslabs. (line 3213)
* 'NC_CHAR' <1>: ncbo netCDF Binary Operator.
- (line 8571)
+ (line 8693)
* 'NC_CHAR' <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
-* 'NC_DISKLESS': RAM disks. (line 4386)
+ (line 10082)
+* 'NC_DISKLESS': RAM disks. (line 4449)
* 'NC_DOUBLE': Intrinsic mathematical methods.
- (line 8032)
+ (line 8146)
* 'NC_DOUBLE' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_FLOAT': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_FORMAT_DAP2': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_FORMAT_DAP4': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_FORMAT_NC3': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_FORMAT_NC_HDF4': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_FORMAT_NC_HDF5': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_FORMAT_PNETCDF': Determining File Format.
- (line 2184)
+ (line 2199)
* 'NC_INT': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_INT64': netCDF2/3/4 and HDF4/5 Support.
- (line 636)
+ (line 641)
* 'NC_INT64' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_SHORT': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_UBYTE': netCDF2/3/4 and HDF4/5 Support.
- (line 636)
+ (line 641)
* 'NC_UBYTE' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_UINT': netCDF2/3/4 and HDF4/5 Support.
- (line 636)
+ (line 641)
* 'NC_UINT' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_UINT64': netCDF2/3/4 and HDF4/5 Support.
- (line 636)
+ (line 641)
* 'NC_UINT64' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'NC_USHORT': netCDF2/3/4 and HDF4/5 Support.
- (line 636)
+ (line 641)
* 'NC_USHORT' <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
+ (line 10082)
* 'nc__enddef()': Metadata Optimization.
- (line 1504)
+ (line 1512)
* ndims(): Methods and functions.
- (line 6362)
+ (line 6437)
* NEARBYINT: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* nearest integer function (exact): Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* nearest integer function (inexact): Intrinsic mathematical methods.
- (line 7929)
-* NEC: Compatability. (line 384)
+ (line 8043)
+* NEC: Compatability. (line 389)
* Neil Davis: Automatic type conversion.
- (line 4855)
+ (line 4918)
* nesting: Syntax of ncap2 statements.
- (line 5594)
-* netCDF: Availability. (line 330)
+ (line 5669)
+* netCDF: Availability. (line 335)
* netCDF2: netCDF2/3/4 and HDF4/5 Support.
- (line 585)
+ (line 590)
* netCDF2 <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* 'NETCDF2_ONLY': netCDF2/3/4 and HDF4/5 Support.
- (line 606)
+ (line 611)
* netCDF3: netCDF2/3/4 and HDF4/5 Support.
- (line 585)
+ (line 590)
* netCDF3 <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* netCDF3 classic file format: Determining File Format.
- (line 2175)
+ (line 2190)
* netCDF4: netCDF2/3/4 and HDF4/5 Support.
- (line 611)
+ (line 616)
* netCDF4 <1>: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* netCDF4 <2>: Multiple Record Dimensions.
- (line 3901)
+ (line 3945)
* netCDF4 classic file format: Determining File Format.
- (line 2175)
+ (line 2190)
* netCDF4 file format: Determining File Format.
- (line 2175)
+ (line 2190)
* 'NETCDF4' files: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* 'NETCDF4_CLASSIC' files: File Formats and Conversion.
- (line 2089)
+ (line 2104)
* 'NETCDF4_ROOT': netCDF2/3/4 and HDF4/5 Support.
- (line 751)
-* Nick Bower: Contributors. (line 10885)
+ (line 756)
+* Nick Bower: Contributors. (line 11008)
* 'NINTAP': Specifying Input Files.
- (line 1662)
+ (line 1670)
* 'NINTAP' <1>: ncra netCDF Record Averager.
- (line 10268)
+ (line 10391)
* 'NINTAP' <2>: ncrcat netCDF Record Concatenator.
- (line 10346)
-* non-coordinate grid properties: CF Conventions. (line 5362)
-* non-rectangular grids: Irregular grids. (line 6845)
-* non-standard grids: Irregular grids. (line 6845)
+ (line 10469)
+* non-coordinate grid properties: CF Conventions. (line 5425)
+* non-rectangular grids: Irregular grids. (line 6959)
+* non-standard grids: Irregular grids. (line 6959)
* normalization: Normalization and Integration.
- (line 10676)
+ (line 10799)
+* North American Regional Reanalysis (NARR): Where statement.
+ (line 6620)
* Not-a-Number: ncatted netCDF Attribute Editor.
- (line 8375)
+ (line 8489)
* 'NO_NETCDF_2': netCDF2/3/4 and HDF4/5 Support.
- (line 595)
+ (line 600)
* NRA: Proposals for Institutional Funding.
- (line 10918)
-* 'nrnet': Remote storage. (line 1835)
+ (line 11060)
+* 'nrnet': Remote storage. (line 1850)
* NSF: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* NSF <1>: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* NT (Microsoft operating system): Windows Operating System.
- (line 483)
+ (line 488)
* NUL: ncatted netCDF Attribute Editor.
- (line 8353)
+ (line 8467)
* 'NUL': ncpdq netCDF Permute Dimensions Quickly.
- (line 9997)
+ (line 10120)
* NUL-termination: ncatted netCDF Attribute Editor.
- (line 8353)
+ (line 8467)
* null operation: ncflint netCDF File Interpolator.
- (line 9156)
-* number literals 'ncap2': Number literals. (line 6073)
+ (line 9278)
+* number literals 'ncap2': Number literals. (line 6148)
* 'number_miss()': Missing values ncap2.
- (line 6269)
+ (line 6344)
* 'numerator': Normalization and Integration.
- (line 10676)
-* NVODS: OPeNDAP. (line 2011)
+ (line 10799)
+* NVODS: OPeNDAP. (line 2026)
* 'nxt_lsr': ncpdq netCDF Permute Dimensions Quickly.
- (line 9959)
-* oceanography: OPeNDAP. (line 1909)
+ (line 10082)
+* oceanography: OPeNDAP. (line 1924)
* octal dump: Determining File Format.
- (line 2218)
+ (line 2233)
* 'od': Determining File Format.
- (line 2218)
-* 'OMP_NUM_THREADS': OpenMP Threading. (line 1551)
-* on-line documentation: Availability. (line 310)
-* open source: Foreword. (line 222)
-* open source <1>: OPeNDAP. (line 2011)
+ (line 2233)
+* 'OMP_NUM_THREADS': OpenMP Threading. (line 1559)
+* on-line documentation: Availability. (line 315)
+* open source: Foreword. (line 227)
+* open source <1>: OPeNDAP. (line 2026)
* Open-source Project for a Network Data Access Protocol: OPeNDAP.
- (line 1909)
-* OPeNDAP.: OPeNDAP. (line 1909)
+ (line 1924)
+* OPeNDAP.: OPeNDAP. (line 1924)
* OpenMP: Memory Requirements.
- (line 1341)
+ (line 1346)
* OpenMP <1>: Single and Multi-file Operators.
- (line 1416)
-* OpenMP <2>: OpenMP Threading. (line 1525)
-* operation types: Operation Types. (line 4610)
+ (line 1421)
+* OpenMP <2>: OpenMP Threading. (line 1533)
+* operation types: Operation Types. (line 4673)
* operation types <1>: ncra netCDF Record Averager.
- (line 10261)
+ (line 10384)
* operation types <2>: ncwa netCDF Weighted Averager.
- (line 10629)
-* operator speed: Libraries. (line 561)
+ (line 10752)
+* operator speed: Libraries. (line 566)
* operator speed <1>: Temporary Output Files.
- (line 943)
-* operator speed <2>: Performance. (line 1462)
+ (line 948)
+* operator speed <2>: Performance. (line 1467)
* operator speed <3>: Metadata Optimization.
- (line 1504)
-* operator speed <4>: Missing Values. (line 3998)
+ (line 1512)
+* operator speed <4>: Missing Values. (line 4042)
* operator speed <5>: ncrename netCDF Renamer.
- (line 10427)
-* operators: Summary. (line 285)
+ (line 10550)
+* operators: Summary. (line 290)
* OptIPuter: Proposals for Institutional Funding.
- (line 10911)
-* Orion Powlawski: Contributors. (line 10887)
-* 'ORO': CF Conventions. (line 5331)
+ (line 11053)
+* Orion Powlawski: Contributors. (line 11010)
+* 'ORO': CF Conventions. (line 5394)
* 'ORO' <1>: Normalization and Integration.
- (line 10750)
+ (line 10873)
* orphan dimensions: ncks netCDF Kitchen Sink.
- (line 9534)
-* OS: Compatability. (line 384)
+ (line 9656)
+* OS: Compatability. (line 389)
* output file: Large Numbers of Files.
- (line 1247)
+ (line 1252)
* output file <1>: Specifying Output Files.
- (line 1765)
-* OUTPUT-PATH: Remote storage. (line 1858)
-* overview: Performance. (line 1447)
+ (line 1778)
+* OUTPUT-PATH: Remote storage. (line 1873)
+* overview: Performance. (line 1452)
* overwriting files: Temporary Output Files.
- (line 991)
-* overwriting files <1>: Batch Mode. (line 5252)
+ (line 996)
+* overwriting files <1>: Batch Mode. (line 5315)
* pack(): Methods and functions.
- (line 6344)
-* 'pack(x)': Packed data. (line 4473)
-* packing: OPeNDAP. (line 1973)
-* packing <1>: Chunking. (line 4075)
-* packing <2>: Packed data. (line 4473)
+ (line 6419)
+* 'pack(x)': Packed data. (line 4536)
+* packing: OPeNDAP. (line 1988)
+* packing <1>: Chunking. (line 4119)
+* packing <2>: Packed data. (line 4536)
* packing <3>: ncecat netCDF Ensemble Concatenator.
- (line 8979)
+ (line 9101)
* packing <4>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* packing <5>: ncrcat netCDF Record Concatenator.
- (line 10327)
+ (line 10450)
* packing map: ncpdq netCDF Permute Dimensions Quickly.
- (line 9953)
+ (line 10076)
* packing policy: ncpdq netCDF Permute Dimensions Quickly.
- (line 9878)
+ (line 10001)
* pack_byte(): Methods and functions.
- (line 6347)
+ (line 6422)
* pack_int(): Methods and functions.
- (line 6351)
+ (line 6426)
* pack_short(): Methods and functions.
- (line 6349)
-* papers: Performance. (line 1447)
-* 'parallel': Parallel. (line 12074)
-* parallelism: OpenMP Threading. (line 1525)
+ (line 6424)
+* papers: Performance. (line 1452)
+* 'parallel': Parallel. (line 12238)
+* parallelism: OpenMP Threading. (line 1533)
* parallelism <1>: Proposals for Institutional Funding.
- (line 10913)
+ (line 11055)
* parser: ncap2 netCDF Arithmetic Processor.
- (line 5514)
+ (line 5589)
* pasting variables: Appending Variables.
- (line 1016)
-* 'pathcc': Compatability. (line 402)
-* 'pathCC': Compatability. (line 402)
-* PathScale: Compatability. (line 384)
-* Patrice Dumas: Contributors. (line 10887)
-* Patrick Kursawe: Contributors. (line 10889)
+ (line 1021)
+* 'pathcc': Compatability. (line 407)
+* 'pathCC': Compatability. (line 407)
+* PathScale: Compatability. (line 389)
+* Patrice Dumas: Contributors. (line 11010)
+* Patrick Kursawe: Contributors. (line 11012)
* pattern matching: Large Numbers of Files.
- (line 1229)
-* pattern matching <1>: Subsetting Files. (line 2514)
+ (line 1234)
+* pattern matching <1>: Subsetting Files. (line 2544)
* pattern matching <2>: ncatted netCDF Attribute Editor.
- (line 8205)
+ (line 8319)
* pattern matching <3>: ncatted netCDF Attribute Editor.
- (line 8412)
-* PayPal: Contributing. (line 10812)
+ (line 8526)
+* PayPal: Contributing. (line 10935)
* PCK_MAP: ncpdq netCDF Permute Dimensions Quickly.
- (line 9953)
+ (line 10076)
* PCK_PLC: ncpdq netCDF Permute Dimensions Quickly.
- (line 9886)
+ (line 10009)
* peak memory usage: Memory Requirements.
- (line 1334)
-* peak memory usage <1>: RAM disks. (line 4386)
-* Pedro Vicente: Contributors. (line 10861)
-* performance: Libraries. (line 561)
+ (line 1339)
+* peak memory usage <1>: RAM disks. (line 4449)
+* Pedro Vicente: Contributors. (line 10984)
+* performance: Libraries. (line 566)
* performance <1>: Temporary Output Files.
- (line 943)
-* performance <2>: Performance. (line 1453)
-* performance <3>: Performance. (line 1462)
+ (line 948)
+* performance <2>: Performance. (line 1458)
+* performance <3>: Performance. (line 1467)
* performance <4>: Metadata Optimization.
- (line 1504)
-* performance <5>: Missing Values. (line 3998)
+ (line 1512)
+* performance <5>: Missing Values. (line 4042)
* performance <6>: ncrename netCDF Renamer.
- (line 10427)
-* Perl: Philosophy. (line 900)
+ (line 10550)
+* Perl: Philosophy. (line 905)
* Perl <1>: Large Numbers of Files.
- (line 1260)
+ (line 1265)
* Perl <2>: ncatted netCDF Attribute Editor.
- (line 8327)
+ (line 8441)
* permute dimensions: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* permute(): Arrays and hyperslabs.
- (line 5996)
-* Peter Campbell: Contributors. (line 10883)
-* 'pgcc': Compatability. (line 402)
-* 'pgCC': Compatability. (line 402)
-* PGI: Compatability. (line 384)
-* philosophy: Philosophy. (line 891)
+ (line 6071)
+* Peter Campbell: Contributors. (line 11006)
+* 'pgcc': Compatability. (line 407)
+* 'pgCC': Compatability. (line 407)
+* PGI: Compatability. (line 389)
+* philosophy: Philosophy. (line 896)
* pipes: Large Numbers of Files.
- (line 1242)
-* 'plc_all': Chunking. (line 4085)
-* 'plc_g2d': Chunking. (line 4085)
-* 'plc_g3d': Chunking. (line 4085)
-* 'plc_xpl': Chunking. (line 4085)
-* 'plc_xst': Chunking. (line 4085)
-* portability: Compatability. (line 384)
+ (line 1247)
+* 'plc_all': Chunking. (line 4130)
+* 'plc_g2d': Chunking. (line 4130)
+* 'plc_g3d': Chunking. (line 4130)
+* 'plc_r1d': Chunking. (line 4130)
+* 'plc_xpl': Chunking. (line 4130)
+* 'plc_xst': Chunking. (line 4130)
+* portability: Compatability. (line 389)
* positional arguments: Specifying Output Files.
- (line 1765)
+ (line 1778)
* POSIX: Command Line Options.
- (line 1590)
-* POSIX <1>: Subsetting Files. (line 2532)
+ (line 1598)
+* POSIX <1>: Subsetting Files. (line 2562)
* POW: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* power: Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* power function: Intrinsic mathematical methods.
- (line 7929)
-* 'prd': Chunking. (line 4135)
+ (line 8043)
+* 'prd': Chunking. (line 4189)
* precision: Intrinsic mathematical methods.
- (line 8032)
+ (line 8146)
* preprocessor tokens: Windows Operating System.
- (line 498)
-* presentations: Availability. (line 320)
-* print() 'ncap2': print statement. (line 6190)
-* 'printf': Compatability. (line 415)
+ (line 503)
+* presentations: Availability. (line 325)
+* print() 'ncap2': print statement. (line 6265)
+* 'printf': Compatability. (line 420)
* 'printf()': ncatted netCDF Attribute Editor.
- (line 8329)
+ (line 8443)
* 'printf()' <1>: ncks netCDF Kitchen Sink.
- (line 9545)
+ (line 9667)
* 'printf()' <2>: Filters for 'ncks'.
- (line 9765)
+ (line 9887)
* printing files contents: ncks netCDF Kitchen Sink.
- (line 9185)
+ (line 9307)
* printing variables: ncks netCDF Kitchen Sink.
- (line 9185)
+ (line 9307)
* Processor: ncra netCDF Record Averager.
- (line 10268)
+ (line 10391)
* Processor <1>: ncrcat netCDF Record Concatenator.
- (line 10346)
+ (line 10469)
* Processor, CCM: Specifying Input Files.
- (line 1662)
-* promotion: Type Conversion. (line 4763)
+ (line 1670)
+* promotion: Type Conversion. (line 4826)
* promotion <1>: Promoting Single-precision to Double.
- (line 4899)
+ (line 4962)
* promotion <2>: Intrinsic mathematical methods.
- (line 7999)
+ (line 8113)
* proposals: Proposals for Institutional Funding.
- (line 10911)
-* pseudonym: Symbolic Links. (line 534)
-* publications: Availability. (line 320)
-* QLogic: Compatability. (line 384)
+ (line 11053)
+* pseudonym: Symbolic Links. (line 539)
+* publications: Availability. (line 325)
+* QLogic: Compatability. (line 389)
* Qt: Windows Operating System.
- (line 490)
+ (line 495)
* quadruple-precision: Intrinsic mathematical methods.
- (line 8032)
-* Quick Start: Quick Start. (line 10931)
+ (line 8146)
+* Quick Start: Quick Start. (line 11073)
* quiet: ncks netCDF Kitchen Sink.
- (line 9526)
-* quotes: Subsetting Files. (line 2589)
-* quotes <1>: Examples ncap2. (line 7881)
+ (line 9648)
+* quotes: Subsetting Files. (line 2619)
+* quotes <1>: Examples ncap2. (line 7995)
* quotes <2>: ncbo netCDF Binary Operator.
- (line 8498)
+ (line 8619)
* quotes <3>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10121)
+ (line 10244)
+* 'r1d': Chunking. (line 4130)
* RAG: ncecat netCDF Ensemble Concatenator.
- (line 8896)
+ (line 9018)
* RAM: Memory Requirements.
- (line 1334)
-* RAM <1>: RAM disks. (line 4386)
+ (line 1339)
+* RAM <1>: RAM disks. (line 4449)
* RAM disks: Temporary Output Files.
- (line 949)
-* RAM disks <1>: RAM disks. (line 4386)
+ (line 954)
+* RAM disks <1>: RAM disks. (line 4449)
* RAM files: Temporary Output Files.
- (line 949)
-* RAM files <1>: RAM disks. (line 4386)
-* RAM variables: RAM disks. (line 4426)
+ (line 954)
+* RAM files <1>: RAM disks. (line 4449)
+* RAM variables: RAM disks. (line 4489)
* RAM variables <1>: Methods and functions.
- (line 6450)
-* ram_delete(): RAM variables. (line 6462)
-* ram_write(): RAM variables. (line 6462)
+ (line 6525)
+* ram_delete(): RAM variables. (line 6537)
+* ram_write(): RAM variables. (line 6537)
* random walk: Promoting Single-precision to Double.
- (line 5116)
-* rank: Expressions. (line 5635)
+ (line 5179)
+* rank: Expressions. (line 5710)
* rank <1>: ncbo netCDF Binary Operator.
- (line 8539)
+ (line 8660)
* rank <2>: ncbo netCDF Binary Operator.
- (line 8552)
+ (line 8673)
* rank <3>: ncbo netCDF Binary Operator.
- (line 8602)
+ (line 8724)
* rank <4>: ncwa netCDF Weighted Averager.
- (line 10594)
+ (line 10717)
* 'rcp': Windows Operating System.
- (line 504)
-* 'rcp' <1>: Remote storage. (line 1797)
-* RCS: Operator Version. (line 5482)
-* 'rd1': Chunking. (line 4135)
+ (line 509)
+* 'rcp' <1>: Remote storage. (line 1810)
+* RCS: Operator Version. (line 5557)
+* 'rd1': Chunking. (line 4189)
* re-dimension: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* re-order dimensions: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* record aggregation: ncecat netCDF Ensemble Concatenator.
- (line 8896)
-* record append: Record Appending. (line 3263)
+ (line 9018)
+* record append: Record Appending. (line 3307)
* record average: ncra netCDF Record Averager.
- (line 10228)
+ (line 10351)
* record concatenation: ncrcat netCDF Record Concatenator.
- (line 10299)
+ (line 10422)
* record dimension: Appending Variables.
- (line 1019)
+ (line 1024)
* record dimension <1>: C and Fortran Index Conventions.
- (line 3079)
-* record dimension <2>: Chunking. (line 4232)
+ (line 3123)
+* record dimension <2>: Chunking. (line 4295)
* record dimension <3>: nces netCDF Ensemble Statistics.
- (line 8751)
+ (line 8873)
* record dimension <4>: ncecat netCDF Ensemble Concatenator.
- (line 8906)
+ (line 9028)
* record dimension <5>: ncecat netCDF Ensemble Concatenator.
- (line 8910)
+ (line 9032)
* record dimension <6>: ncecat netCDF Ensemble Concatenator.
- (line 9016)
+ (line 9138)
* record dimension <7>: ncks netCDF Kitchen Sink.
- (line 9320)
+ (line 9442)
* record dimension <8>: ncks netCDF Kitchen Sink.
- (line 9397)
+ (line 9519)
* record dimension <9>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10025)
+ (line 10148)
* record dimension <10>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10027)
+ (line 10150)
* record dimension <11>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10176)
+ (line 10299)
* record dimension <12>: ncra netCDF Record Averager.
- (line 10228)
+ (line 10351)
* record dimension <13>: ncra netCDF Record Averager.
- (line 10241)
+ (line 10364)
* record dimension <14>: ncrcat netCDF Record Concatenator.
- (line 10312)
+ (line 10435)
* record variable: C and Fortran Index Conventions.
- (line 3074)
+ (line 3118)
* record variable <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10029)
-* rectangular grids: Irregular grids. (line 6845)
-* recursion: Subsetting Files. (line 2413)
-* recursive: Subsetting Files. (line 2413)
-* 'regex': Subsetting Files. (line 2532)
+ (line 10152)
+* rectangular grids: Irregular grids. (line 6959)
+* recursion: Subsetting Files. (line 2443)
+* recursive: Subsetting Files. (line 2443)
+* 'regex': Subsetting Files. (line 2562)
* regression: Annual Average over Regions.
- (line 11387)
+ (line 11551)
* regressions archive: Help Requests and Bug Reports.
- (line 879)
-* regrid: Regrid MODIS Data. (line 11842)
+ (line 884)
+* regrid: Regrid MODIS Data. (line 12006)
* regular expressions: Large Numbers of Files.
- (line 1229)
+ (line 1234)
* regular expressions <1>: Specifying Input Files.
- (line 1662)
-* regular expressions <2>: Subsetting Files. (line 2514)
-* regular expressions <3>: Examples ncap2. (line 7881)
+ (line 1670)
+* regular expressions <2>: Subsetting Files. (line 2544)
+* regular expressions <3>: Examples ncap2. (line 7995)
* regular expressions <4>: ncatted netCDF Attribute Editor.
- (line 8205)
+ (line 8319)
* regular expressions <5>: ncatted netCDF Attribute Editor.
- (line 8412)
-* 'remap': Sort methods. (line 6600)
-* Remik Ziemlinski: Contributors. (line 10883)
+ (line 8526)
+* 'remap': Sort methods. (line 6714)
+* Remik Ziemlinski: Contributors. (line 11006)
* remote files: Windows Operating System.
- (line 504)
-* remote files <1>: Remote storage. (line 1797)
-* rename groups: Group Path Editing.
- (line 2765)
+ (line 509)
+* remote files <1>: Remote storage. (line 1810)
+* rename groups: Moving Groups. (line 2802)
* renaming attributes: ncrename netCDF Renamer.
- (line 10381)
-* renaming attributes <1>: Regrid MODIS Data. (line 11842)
+ (line 10504)
+* renaming attributes <1>: Regrid MODIS Data. (line 12006)
* renaming dimensions: ncrename netCDF Renamer.
- (line 10381)
-* renaming dimensions <1>: Regrid MODIS Data. (line 11842)
+ (line 10504)
+* renaming dimensions <1>: Regrid MODIS Data. (line 12006)
* renaming groups: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* renaming variables: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* renaming variables <1>: Annual Average over Regions.
- (line 11387)
-* renaming variables <2>: Regrid MODIS Data. (line 11842)
+ (line 11551)
+* renaming variables <2>: Regrid MODIS Data. (line 12006)
* reporting bugs: Help Requests and Bug Reports.
- (line 809)
+ (line 814)
* reshape variables: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
-* 'restrict': Compatability. (line 439)
+ (line 9984)
+* 'restrict': Compatability. (line 444)
* reverse data: ncpdq netCDF Permute Dimensions Quickly.
- (line 10151)
+ (line 10274)
* reverse dimensions: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* reverse dimensions <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10108)
+ (line 10231)
* reverse dimensions <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10130)
+ (line 10253)
* reverse(): Arrays and hyperslabs.
- (line 5989)
-* 'rew': Chunking. (line 4135)
+ (line 6064)
+* 'rew': Chunking. (line 4189)
+* Rich Signell: Contributors. (line 11006)
* RINT: Intrinsic mathematical methods.
- (line 7929)
-* 'rms': Operation Types. (line 4610)
-* 'rmssdn': Operation Types. (line 4610)
+ (line 8043)
+* 'rms': Operation Types. (line 4673)
+* 'rmssdn': Operation Types. (line 4673)
* rmssdn(): Methods and functions.
- (line 6332)
-* root-mean-square: Operation Types. (line 4610)
-* Rorik Peterson: Contributors. (line 10852)
+ (line 6407)
+* root-mean-square: Operation Types. (line 4673)
+* Rorik Peterson: Contributors. (line 10975)
* ROUND: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* rounding: Promoting Single-precision to Double.
- (line 5116)
+ (line 5179)
* rounding functions: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* RPM: netCDF2/3/4 and HDF4/5 Support.
- (line 746)
+ (line 751)
* running average: ncra netCDF Record Averager.
- (line 10228)
-* Russ Rew: Contributors. (line 10831)
-* Russ Rew <1>: Contributors. (line 10863)
+ (line 10351)
+* Russ Rew: Contributors. (line 10954)
+* Russ Rew <1>: Contributors. (line 10986)
* safeguards: Temporary Output Files.
- (line 928)
+ (line 933)
* safeguards <1>: ncrename netCDF Renamer.
- (line 10412)
-* 'scale_factor': Packed data. (line 4473)
+ (line 10535)
+* 'scale_factor': Packed data. (line 4536)
* 'scale_factor' <1>: ncecat netCDF Ensemble Concatenator.
- (line 8979)
+ (line 9101)
* 'scale_factor' <2>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9879)
+ (line 10002)
* 'scale_factor' <3>: ncrcat netCDF Record Concatenator.
- (line 10327)
-* SCALE_FORMAT: Performance. (line 1470)
-* scaling: Performance. (line 1453)
+ (line 10450)
+* SCALE_FORMAT: Performance. (line 1475)
+* scaling: Performance. (line 1458)
* scaling <1>: ncflint netCDF File Interpolator.
- (line 9159)
+ (line 9281)
* Scientific Data Operators: Proposals for Institutional Funding.
- (line 10911)
-* 'scl': Chunking. (line 4135)
-* Scott Capps: Contributors. (line 10881)
+ (line 11053)
+* 'scl': Chunking. (line 4189)
+* Scott Capps: Contributors. (line 11004)
* 'scp': Windows Operating System.
- (line 504)
-* 'scp' <1>: Remote storage. (line 1797)
+ (line 509)
+* 'scp' <1>: Remote storage. (line 1810)
* script file: ncap2 netCDF Arithmetic Processor.
- (line 5532)
+ (line 5607)
* SDO: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* seasonal average: Monthly data in one file.
- (line 10975)
-* security: MD5 digests. (line 4285)
+ (line 11117)
+* security: MD5 digests. (line 4348)
* SEIII: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* semi-colon: Syntax of ncap2 statements.
- (line 5589)
+ (line 5664)
* separator: ncks netCDF Kitchen Sink.
- (line 9583)
-* server: Large Datasets. (line 1308)
-* server <1>: OPeNDAP. (line 1909)
+ (line 9705)
+* server: Large Datasets. (line 1313)
+* server <1>: OPeNDAP. (line 1924)
* server <2>: Retaining Retrieved Files.
- (line 2069)
+ (line 2084)
* server <3>: Retaining Retrieved Files.
- (line 2077)
+ (line 2092)
* Server-Side Distributed Data Reduction & Analysis: Proposals for Institutional Funding.
- (line 10911)
-* server-side processing: OPeNDAP. (line 2035)
+ (line 11053)
+* server-side processing: OPeNDAP. (line 2050)
* server-side processing <1>: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* 'set_miss()': Missing values ncap2.
- (line 6247)
+ (line 6322)
* 'sftp': Windows Operating System.
- (line 504)
-* 'sftp' <1>: Remote storage. (line 1797)
-* SGI: Compatability. (line 384)
+ (line 509)
+* 'sftp' <1>: Remote storage. (line 1810)
+* SGI: Compatability. (line 389)
* Sh shell: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* shared memory machines: Memory Requirements.
- (line 1341)
-* shared memory parallelism: OpenMP Threading. (line 1525)
+ (line 1346)
+* shared memory parallelism: OpenMP Threading. (line 1533)
* shell: Large Numbers of Files.
- (line 1229)
-* shell <1>: Subsetting Files. (line 2589)
-* shell <2>: UDUnits Support. (line 3765)
-* shell <3>: Examples ncap2. (line 7881)
+ (line 1234)
+* shell <1>: Subsetting Files. (line 2619)
+* shell <2>: UDUnits Support. (line 3809)
+* shell <3>: Examples ncap2. (line 7995)
* shell <4>: ncbo netCDF Binary Operator.
- (line 8498)
+ (line 8619)
* shell <5>: Filters for 'ncks'.
- (line 9637)
-* SIGNEDNESS: Performance. (line 1470)
+ (line 9759)
+* SIGNEDNESS: Performance. (line 1475)
* SIN: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* sine function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* single-precision: Intrinsic mathematical methods.
- (line 8032)
+ (line 8146)
* SINH: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* size(): Methods and functions.
- (line 6360)
-* SMP: OpenMP Threading. (line 1525)
-* 'sort': Sort methods. (line 6600)
+ (line 6435)
+* SLD (Swath-like Data): Where statement. (line 6603)
+* SMP: OpenMP Threading. (line 1533)
+* 'sort': Sort methods. (line 6714)
* sort alphabetically: ncks netCDF Kitchen Sink.
- (line 9294)
+ (line 9416)
* sort alphabetically <1>: Filters for 'ncks'.
- (line 9732)
-* source code: Availability. (line 302)
+ (line 9854)
+* source code: Availability. (line 307)
* spatial distribution: Global Distribution of Long-term Average.
- (line 11284)
+ (line 11448)
* special attributes: ncks netCDF Kitchen Sink.
- (line 9345)
+ (line 9467)
* special characters: ncatted netCDF Attribute Editor.
- (line 8344)
-* speed: Libraries. (line 561)
+ (line 8458)
+* speed: Libraries. (line 566)
* speed <1>: Temporary Output Files.
- (line 943)
-* speed <2>: Large Datasets. (line 1317)
-* speed <3>: Performance. (line 1462)
+ (line 948)
+* speed <2>: Large Datasets. (line 1322)
+* speed <3>: Performance. (line 1467)
* speed <4>: Metadata Optimization.
- (line 1504)
-* speed <5>: Missing Values. (line 3998)
+ (line 1512)
+* speed <5>: Missing Values. (line 4042)
* speed <6>: ncrename netCDF Renamer.
- (line 10427)
-* 'sqravg': Operation Types. (line 4610)
+ (line 10550)
+* 'sqravg': Operation Types. (line 4673)
* sqravg(): Methods and functions.
- (line 6322)
-* 'sqrt': Operation Types. (line 4610)
+ (line 6397)
+* 'sqrt': Operation Types. (line 4673)
* SQRT: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* square root function: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* SSDDRA: Proposals for Institutional Funding.
- (line 10911)
+ (line 11053)
* SSH: Windows Operating System.
- (line 504)
+ (line 509)
* SSH <1>: Retaining Retrieved Files.
- (line 2066)
+ (line 2081)
* sshort(): Methods and functions.
- (line 6416)
-* standard deviation: Operation Types. (line 4610)
-* standard deviation <1>: Operation Types. (line 4690)
+ (line 6491)
+* standard deviation: Operation Types. (line 4673)
+* standard deviation <1>: Operation Types. (line 4753)
* standard deviation <2>: Annual Average over Regions.
- (line 11387)
+ (line 11551)
* standard input: Large Numbers of Files.
- (line 1212)
+ (line 1217)
* standard input <1>: nces netCDF Ensemble Statistics.
- (line 8786)
+ (line 8908)
* standard input <2>: ncecat netCDF Ensemble Concatenator.
- (line 8952)
+ (line 9074)
* standard input <3>: ncra netCDF Record Averager.
- (line 10245)
+ (line 10368)
* standard input <4>: ncrcat netCDF Record Concatenator.
- (line 10315)
+ (line 10438)
* 'standard_name': Auxiliary Coordinates.
- (line 3584)
-* 'stat() system call': Buffer sizes. (line 4355)
+ (line 3628)
+* 'stat() system call': Buffer sizes. (line 4418)
* statement: Syntax of ncap2 statements.
- (line 5575)
-* static linking: Libraries. (line 560)
+ (line 5650)
+* static linking: Libraries. (line 565)
* 'stdin': Large Numbers of Files.
- (line 1212)
+ (line 1217)
* 'stdin' <1>: File List Attributes.
- (line 5300)
+ (line 5363)
* 'stdin' <2>: nces netCDF Ensemble Statistics.
- (line 8786)
+ (line 8908)
* 'stdin' <3>: ncecat netCDF Ensemble Concatenator.
- (line 8952)
+ (line 9074)
* 'stdin' <4>: ncra netCDF Record Averager.
- (line 10245)
+ (line 10368)
* 'stdin' <5>: ncrcat netCDF Record Concatenator.
- (line 10315)
-* Steve Emmerson: Contributors. (line 10831)
-* stride: Hyperslabs. (line 3123)
-* stride <1>: Stride. (line 3202)
-* stride <2>: Multislabs. (line 3429)
-* stride <3>: UDUnits Support. (line 3756)
+ (line 10438)
+* Steve Emmerson: Contributors. (line 10954)
+* stride: Hyperslabs. (line 3167)
+* stride <1>: Stride. (line 3246)
+* stride <2>: Multislabs. (line 3473)
+* stride <3>: UDUnits Support. (line 3800)
* stride <4>: ncra netCDF Record Averager.
- (line 10253)
+ (line 10376)
* stride <5>: ncra netCDF Record Averager.
- (line 10284)
+ (line 10407)
* stride <6>: ncrcat netCDF Record Concatenator.
- (line 10323)
+ (line 10446)
* stride <7>: ncrcat netCDF Record Concatenator.
- (line 10364)
+ (line 10487)
* strings: ncatted netCDF Attribute Editor.
- (line 8353)
-* Stu Muller: Contributors. (line 10883)
-* stub: Remote storage. (line 1867)
-* sub-cycle: Subcycle. (line 3314)
-* subcycle: Subcycle. (line 3314)
-* subsetting: Subsetting Files. (line 2371)
+ (line 8467)
+* Stu Muller: Contributors. (line 11006)
+* stub: Remote storage. (line 1882)
+* sub-cycle: Subcycle. (line 3358)
+* subcycle: Subcycle. (line 3358)
+* subsetting: Subsetting Files. (line 2386)
* subsetting <1>: Subsetting Coordinate Variables.
- (line 2614)
-* subsetting <2>: CF Conventions. (line 5397)
+ (line 2644)
+* subsetting <2>: CF Conventions. (line 5472)
* subsetting <3>: Filters for 'ncks'.
- (line 9738)
+ (line 9860)
* subsetting <4>: Filters for 'ncks'.
- (line 9812)
+ (line 9934)
* 'subtract': ncbo netCDF Binary Operator.
- (line 8468)
+ (line 8589)
* subtracting data: ncbo netCDF Binary Operator.
- (line 8450)
+ (line 8571)
* subtraction: Intrinsic mathematical methods.
- (line 7926)
+ (line 8040)
* subtraction <1>: ncbo netCDF Binary Operator.
- (line 8450)
-* summary: Summary. (line 285)
-* Sun: Compatability. (line 384)
-* swap space: Large Datasets. (line 1295)
+ (line 8571)
+* summary: Summary. (line 290)
+* Sun: Compatability. (line 389)
+* swap space: Large Datasets. (line 1300)
* swap space <1>: Memory Requirements.
- (line 1334)
-* swap space <2>: RAM disks. (line 4386)
+ (line 1339)
+* swap space <2>: RAM disks. (line 4449)
+* Swath-like Data (SLD): Where statement. (line 6603)
* switches: Command Line Options.
- (line 1590)
-* symbolic links: Symbolic Links. (line 524)
+ (line 1598)
+* symbolic links: Symbolic Links. (line 529)
* symbolic links <1>: Statistics vs. Concatenation.
- (line 1072)
+ (line 1077)
* symbolic links <2>: Large Numbers of Files.
- (line 1254)
+ (line 1259)
* symbolic links <3>: ncbo netCDF Binary Operator.
- (line 8512)
+ (line 8633)
* symbolic links <4>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9947)
-* synchronous file access: Remote storage. (line 1797)
-* synonym: Symbolic Links. (line 534)
+ (line 10070)
+* synchronous file access: Remote storage. (line 1810)
+* synonym: Symbolic Links. (line 539)
* syntax: Syntax of ncap2 statements.
- (line 5575)
-* System calls: Buffer sizes. (line 4355)
-* Takeshi Enomoto: Contributors. (line 10893)
+ (line 5650)
+* System calls: Buffer sizes. (line 4418)
+* Takeshi Enomoto: Contributors. (line 11016)
* TAN: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* TANH: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* temporary files: Temporary Output Files.
- (line 928)
-* temporary files <1>: RAM disks. (line 4466)
+ (line 933)
+* temporary files <1>: RAM disks. (line 4529)
* temporary output files: Temporary Output Files.
- (line 928)
-* temporary output files <1>: RAM disks. (line 4466)
+ (line 933)
+* temporary output files <1>: RAM disks. (line 4529)
* temporary output files <2>: ncrename netCDF Renamer.
- (line 10412)
-* TeXinfo: Availability. (line 310)
+ (line 10535)
+* TeXinfo: Availability. (line 315)
* threads: Memory Requirements.
- (line 1341)
+ (line 1346)
* threads <1>: Single and Multi-file Operators.
- (line 1416)
-* threads <2>: OpenMP Threading. (line 1525)
-* THR_NBR: OpenMP Threading. (line 1551)
-* 'time': UDUnits Support. (line 3747)
-* 'time' <1>: ARM Conventions. (line 5451)
-* time-averaging: Examples ncap2. (line 7904)
+ (line 1421)
+* threads <2>: OpenMP Threading. (line 1533)
+* THR_NBR: OpenMP Threading. (line 1559)
+* 'time': UDUnits Support. (line 3791)
+* 'time' <1>: ARM Conventions. (line 5526)
+* time-averaging: Examples ncap2. (line 8018)
* time-averaging <1>: Daily data in one file.
- (line 10941)
+ (line 11083)
* time-averaging <2>: Daily data in one file.
- (line 10955)
+ (line 11097)
* time-averaging <3>: Monthly data in one file.
- (line 10975)
+ (line 11117)
* time-averaging <4>: Monthly data in one file.
- (line 10978)
+ (line 11120)
* time-averaging <5>: One time point one file.
- (line 11004)
+ (line 11146)
* time-averaging <6>: Global Distribution of Long-term Average.
- (line 11284)
+ (line 11448)
* time-averaging <7>: Annual Average over Regions.
- (line 11387)
-* time-averaging <8>: Monthly Cycle. (line 11678)
-* timestamp: History Attribute. (line 5272)
-* 'time_offset': ARM Conventions. (line 5451)
-* total: Operation Types. (line 4610)
+ (line 11551)
+* time-averaging <8>: Monthly Cycle. (line 11842)
+* timestamp: History Attribute. (line 5335)
+* 'time_offset': ARM Conventions. (line 5526)
+* total: Operation Types. (line 4673)
* transpose: C and Fortran Index Conventions.
- (line 3072)
+ (line 3116)
* transpose <1>: ncpdq netCDF Permute Dimensions Quickly.
- (line 10039)
+ (line 10162)
* TREFHT: Promoting Single-precision to Double.
- (line 5050)
+ (line 5113)
* TRUNC: Intrinsic mathematical methods.
- (line 7929)
+ (line 8043)
* 'trunc()': Automatic type conversion.
- (line 4842)
-* truncate (groups): Group Path Editing.
- (line 2677)
+ (line 4905)
+* truncate (groups): Flattening Groups. (line 2712)
* truncation function: Intrinsic mathematical methods.
- (line 7929)
-* truth condition: Mask condition. (line 10647)
+ (line 8043)
+* truth condition: Mask condition. (line 10770)
* truth condition <1>: Normalization and Integration.
- (line 10778)
-* 'ttl': Operation Types. (line 4610)
+ (line 10901)
+* 'ttl': Operation Types. (line 4673)
* ttl(): Methods and functions.
- (line 6334)
-* type conversion: Type Conversion. (line 4757)
+ (line 6409)
+* type conversion: Type Conversion. (line 4820)
* type(): Methods and functions.
- (line 6364)
+ (line 6439)
* ubyte(): Methods and functions.
- (line 6427)
-* UDUnits: Compatability. (line 393)
-* UDUnits <1>: UDUnits Support. (line 3694)
-* UDUnits <2>: CF Conventions. (line 5331)
+ (line 6502)
+* UDUnits: Compatability. (line 398)
+* UDUnits <1>: UDUnits Support. (line 3738)
+* UDUnits <2>: CF Conventions. (line 5394)
* uint(): Methods and functions.
- (line 6431)
-* 'ulimit': Large Datasets. (line 1313)
-* unary operations: Memory for ncap2. (line 1423)
+ (line 6506)
+* 'ulimit': Large Datasets. (line 1318)
+* unary operations: Memory for ncap2. (line 1428)
* underlying file format: Determining File Format.
- (line 2184)
-* UNICOS: Large Datasets. (line 1308)
-* Unidata: Compatability. (line 393)
+ (line 2199)
+* UNICOS: Large Datasets. (line 1313)
+* Unidata: Compatability. (line 398)
* Unidata <1>: netCDF2/3/4 and HDF4/5 Support.
- (line 611)
-* Unidata <2>: UDUnits Support. (line 3694)
-* union: Subsetting Files. (line 2371)
-* union <1>: Subsetting Files. (line 2462)
+ (line 616)
+* Unidata <2>: UDUnits Support. (line 3738)
+* union: Subsetting Files. (line 2386)
+* union <1>: Subsetting Files. (line 2492)
* union of files: Appending Variables.
- (line 1038)
+ (line 1043)
* unit64(): Methods and functions.
- (line 6435)
-* 'units': UDUnits Support. (line 3694)
-* 'units' <1>: UDUnits Support. (line 3715)
-* 'units' <2>: UDUnits Support. (line 3747)
+ (line 6510)
+* 'units': UDUnits Support. (line 3738)
+* 'units' <1>: UDUnits Support. (line 3759)
+* 'units' <2>: UDUnits Support. (line 3791)
* 'units' <3>: ncatted netCDF Attribute Editor.
- (line 8401)
+ (line 8515)
* 'units' <4>: ncatted netCDF Attribute Editor.
- (line 8404)
+ (line 8518)
* 'units' <5>: ncflint netCDF File Interpolator.
- (line 9177)
-* UNIX: Compatability. (line 393)
+ (line 9299)
+* UNIX: Compatability. (line 398)
* UNIX <1>: Windows Operating System.
- (line 502)
+ (line 507)
* UNIX <2>: Large Numbers of Files.
- (line 1229)
+ (line 1234)
* UNIX <3>: Command Line Options.
- (line 1590)
+ (line 1598)
* UNIX <4>: Specifying Input Files.
- (line 1668)
+ (line 1676)
* UNIX <5>: Filters for 'ncks'.
- (line 9637)
+ (line 9759)
* unlimited dimension: ncecat netCDF Ensemble Concatenator.
- (line 8906)
-* 'unmap': Sort methods. (line 6600)
+ (line 9028)
+* 'unmap': Sort methods. (line 6714)
* unpack(): Methods and functions.
- (line 6353)
-* 'unpack(x)': Packed data. (line 4473)
-* unpacking: OPeNDAP. (line 1973)
-* unpacking <1>: Packed data. (line 4473)
+ (line 6428)
+* 'unpack(x)': Packed data. (line 4536)
+* unpacking: OPeNDAP. (line 1988)
+* unpacking <1>: Packed data. (line 4536)
* unpacking <2>: ncecat netCDF Ensemble Concatenator.
- (line 8979)
+ (line 9101)
* unpacking <3>: ncpdq netCDF Permute Dimensions Quickly.
- (line 9861)
+ (line 9984)
* unpacking <4>: ncrcat netCDF Record Concatenator.
- (line 10327)
-* URL: Remote storage. (line 1797)
-* 'User Guide': Availability. (line 310)
+ (line 10450)
+* URL: Remote storage. (line 1810)
+* 'User Guide': Availability. (line 315)
* ushort(): Methods and functions.
- (line 6429)
-* value list: Attributes. (line 6031)
+ (line 6504)
+* value list: Attributes. (line 6106)
* variable names: ncrename netCDF Renamer.
- (line 10381)
+ (line 10504)
* variables, appending: Annual Average over Regions.
- (line 11387)
-* variance: Operation Types. (line 4610)
-* version: Operator Version. (line 5482)
+ (line 11551)
+* variance: Operation Types. (line 4673)
+* version: Operator Version. (line 5557)
* Vista (Microsoft operating system): Windows Operating System.
- (line 483)
+ (line 488)
+* Weather and Research Forecast (WRF) Model: Where statement.
+ (line 6603)
* weighted average: ncwa netCDF Weighted Averager.
- (line 10553)
-* weighted average <1>: Monthly Cycle. (line 11678)
-* Wenshan Wang: Contributors. (line 10903)
-* 'wget': Remote storage. (line 1797)
-* where(): Where statement. (line 6477)
-* while(): Loops. (line 6545)
-* whitespace: UDUnits Support. (line 3756)
+ (line 10676)
+* weighted average <1>: Monthly Cycle. (line 11842)
+* Wenshan Wang: Contributors. (line 11026)
+* 'wget': Remote storage. (line 1810)
+* where(): Where statement. (line 6552)
+* while(): Loops. (line 6659)
+* whitespace: UDUnits Support. (line 3800)
* wildcards: Specifying Input Files.
- (line 1662)
-* wildcards <1>: Subsetting Files. (line 2514)
+ (line 1670)
+* wildcards <1>: Subsetting Files. (line 2544)
* wildcards <2>: ncatted netCDF Attribute Editor.
- (line 8205)
+ (line 8319)
* wildcards <3>: ncatted netCDF Attribute Editor.
- (line 8412)
+ (line 8526)
* 'WIN32': Windows Operating System.
- (line 498)
-* Windows: Compatability. (line 384)
+ (line 503)
+* Windows: Compatability. (line 389)
* Windows <1>: Windows Operating System.
- (line 483)
-* wrapped coordinates: Hyperslabs. (line 3174)
+ (line 488)
+* wrapped coordinates: Hyperslabs. (line 3218)
* wrapped coordinates <1>: Wrapped Coordinates.
- (line 3534)
-* wrapped coordinates <2>: Irregular grids. (line 6874)
+ (line 3578)
+* wrapped coordinates <2>: Irregular grids. (line 6988)
* wrapped coordinates <3>: Filters for 'ncks'.
- (line 9850)
+ (line 9973)
* wrapped filenames: Specifying Input Files.
- (line 1725)
-* WRF: Irregular grids. (line 6932)
-* WWW documentation: Availability. (line 310)
+ (line 1736)
+* WRF: Irregular grids. (line 7046)
+* WRF (Weather and Research Forecast Model): Where statement.
+ (line 6603)
+* WWW documentation: Availability. (line 315)
* 'xargs': Large Numbers of Files.
- (line 1229)
+ (line 1234)
* 'xargs' <1>: Specifying Output Files.
- (line 1782)
-* 'xlC': Compatability. (line 402)
-* 'xlc': Compatability. (line 402)
+ (line 1795)
+* 'xlC': Compatability. (line 407)
+* 'xlc': Compatability. (line 407)
* XML: ncks netCDF Kitchen Sink.
- (line 9553)
+ (line 9675)
* XP (Microsoft operating system): Windows Operating System.
- (line 483)
-* 'xpl': Chunking. (line 4085)
-* 'xst': Chunking. (line 4085)
-* 'xst' <1>: Chunking. (line 4135)
-* Yorick: Philosophy. (line 900)
-* Yorick <1>: Performance. (line 1473)
+ (line 488)
+* 'xpl': Chunking. (line 4130)
+* 'xst': Chunking. (line 4130)
+* 'xst' <1>: Chunking. (line 4189)
+* Yorick: Philosophy. (line 905)
+* Yorick <1>: Performance. (line 1478)
diff --git a/doc/nco.xml b/doc/nco.xml
index 51f45c4..00c3163 100644
--- a/doc/nco.xml
+++ b/doc/nco.xml
@@ -85,6 +85,7 @@ Legend (defined in "highlighting" section of TeXInfo manual):
@command{}: Commands, e.g., @command{ncra}
@dfn{}: Define use of term, e.g., @dfn{supercalifragilisticexpialidocious}
@email{}: E-mail address, e.g., @email{surname at uci dot edu}
+ at emph{}: Emphasize text, e.g., @emph{important}
@env{}: Environment variable, e.g., @env{HOME}
@file{}: Filename, e.g., @file{in.nc}
@html: Text until @end html passed without translation
@@ -97,6 +98,7 @@ Legend (defined in "highlighting" section of TeXInfo manual):
@url{}: URL, synonym for @uref
@var{}: Metasyntactic variable, e.g., @var{}
@verbatim: Anything goes inside environment (no @'s needed to protect special characters like braces)
+ at verbatiminclude: Insert contents of file here, e.g., @verbatiminclude{nco.sh}
@example: Quoted environment (@'s needed to protect special characters like braces)
@w{}: Unbreakable text, e.g., @w{of 1}
@@ -116,14 +118,14 @@ Octave TeXInfo manual shows clean TeXInfo structure
<setfilename file="nco.info" spaces=" ">nco.info</setfilename>
<!-- c Define edition, date, ... -->
-<set name="nco-edition" line=" nco-edition 4.4.4">4.4.4</set>
-<set name="doc-edition" line=" doc-edition 4.4.4">4.4.4</set>
+<set name="nco-edition" line=" nco-edition 4.4.5">4.4.5</set>
+<set name="doc-edition" line=" doc-edition 4.4.5">4.4.5</set>
<set name="copyright-years" line=" copyright-years 1995--2014">1995--2014</set>
<set name="update-year" line=" update-year 2014">2014</set>
-<set name="update-date" line=" update-date 20 May 2014">20 May 2014</set>
-<set name="update-month" line=" update-month May 2014">May 2014</set>
+<set name="update-date" line=" update-date 8 July 2014">8 July 2014</set>
+<set name="update-month" line=" update-month July 2014">July 2014</set>
-<settitle spaces=" "><acronym><acronymword>NCO</acronymword></acronym> 4.4.4 User Guide</settitle>
+<settitle spaces=" "><acronym><acronymword>NCO</acronymword></acronym> 4.4.5 User Guide</settitle>
<!-- c Uncomment following line to produce guide in smallbook format -->
<!-- c @smallbook -->
@@ -507,8 +509,8 @@ ncflint, ncks, ncra, ncrcat, ncrename, ncwa">
</ignore>
<title spaces=" ">NCO User Guide</title>
<subtitle spaces=" ">A suite of netCDF operators</subtitle>
-<subtitle spaces=" ">Edition 4.4.4, for <acronym><acronymword>NCO</acronymword></acronym> Version 4.4.4</subtitle>
-<subtitle spaces=" ">May 2014</subtitle>
+<subtitle spaces=" ">Edition 4.4.5, for <acronym><acronymword>NCO</acronymword></acronym> Version 4.4.5</subtitle>
+<subtitle spaces=" ">July 2014</subtitle>
<author spaces=" ">by Charlie Zender</author>
<author spaces=" ">Department of Earth System Science</author>
@@ -584,8 +586,8 @@ examples from the field of climate modeling and analysis.
The <acronym><acronymword>NCO</acronymword></acronym> homepage is <uref><urefurl>http://nco.sf.net</urefurl></uref>, and
there is a mirror at <uref><urefurl>http://dust.ess.uci.edu/nco</urefurl></uref>.
</para>
-<para>This documentation is for <acronym><acronymword>NCO</acronymword></acronym> version 4.4.4.
-It was last updated 20 May 2014.
+<para>This documentation is for <acronym><acronymword>NCO</acronymword></acronym> version 4.4.5.
+It was last updated 8 July 2014.
Corrections, additions, and rewrites of this documentation are very
welcome.
</para>
@@ -683,32 +685,54 @@ March 2008&linebreak;
Grenoble, France&linebreak;
</para>
<sp value="2" line=" 2"></sp>
-<para>The end of the <acronym><acronymword>NSF</acronymword></acronym> SEI grant in August, 2008 curtailed <acronym><acronymword>NCO</acronymword></acronym>
-development.
-Fortunately we could justify supporting Henry Butowsky on other research
+<para>The end of the <acronym><acronymword>NSF</acronymword></acronym> <acronym><acronymword>SEI</acronymword></acronym> grant in August, 2008 curtailed
+<acronym><acronymword>NCO</acronymword></acronym> development.
+Fortunately we could justify supporting Henry Butowsky on other research
grants until May, 2010 while he developed the key <command>ncap2</command>
features used in our climate research.
-And recentely the NASA ACCESS program commenced funding NCO support for
-netCDF4 group functionality.&linebreak;
-Thus <acronym><acronymword>NCO</acronymword></acronym> will grow and evade bit-rot for the foreseeable future.
-</para>
-<para>On a personal level, I continue to receive with gratitude the thanks of
-<acronym><acronymword>NCO</acronymword></acronym> users at nearly every scientific meeting I attend.
-People introduce themselves, shake my hand and extol, sometimes rather
-effusively, these time-saving tools.
+And recently the <acronym><acronymword>NASA</acronymword></acronym> <acronym><acronymword>ACCESS</acronymword></acronym> program commenced
+funding us to support netCDF4 group functionality.
+Thus <acronym><acronymword>NCO</acronymword></acronym> will grow and evade bit-rot for the foreseeable
+future.
+</para>
+<para>I continue to receive with gratitude the thanks of <acronym><acronymword>NCO</acronymword></acronym> users
+at nearly every scientific meeting I attend.
+People introduce themselves, shake my hand and extol <acronym><acronymword>NCO</acronymword></acronym>,
+often effusively, while I grin in stupid embarassment.
These exchanges lighten me like anti-gravity.
Sometimes I daydream how many hours <acronym><acronymword>NCO</acronymword></acronym> has turned from grunt
work to productive research for researchers world-wide, or from research
-into early happy hours.
+into early happy-hours.
It&textrsquo;s a cool feeling.
</para>
-<!-- c @uref{http://www.nasa.gov/mission_pages/IPY/main/PolarExploration.html,NNX07AR23G}.@* -->
<sp value="1" line=" 1"></sp>
<noindent></noindent>
<para>Charlie Zender&linebreak;
April, 2012&linebreak;
Irvine, California&linebreak;
</para>
+<ignore>
+ at sp 2
+The @acronym{NASA} @acronym{ACCESS} 2011 program generously supported
+(Cooperative Agreement NNX12AF48A) @acronym{NCO} from 2012--2014.
+We accomplished our goals and produced the first iteration of a
+Group-oriented Data Analysis and Distribution (@acronym{GODAD}) software
+ecosystem.
+Shifting geoscience data analysis to @acronym{GODAD}, no small task,
+drives our plans.
+Partly due to this success, the @acronym{NASA} @acronym{ACCESS} 2013
+program agreed to support (Cooperative Agreement NNX14AH55A)
+ at acronym{NCO} from 2014--2016.
+This support will allow us to implement support for Swath-like Data
+(@acronym{SLD}) and re-gridding.
+
+ at sp 1
+ at noindent
+Charlie Zender@*
+June, 2014@*
+Irvine, California@*
+</ignore>
+
<html endspaces=" ">
<a name="smr"></a> <!&textndash; http://nco.sf.net/nco.html#smr &textndash;>
</html>
@@ -845,7 +869,7 @@ descriptions of <uref><urefurl>http://nco.sf.net/#bug</urefurl><urefdesc spaces=
are on our homepage
(<uref><urefurl>http://nco.sf.net/</urefurl></uref>).
</para>
-<para>There are twelve operators in the current version (4.4.4).
+<para>There are twelve operators in the current version (4.4.5).
The function of each is explained in <ref label="Operator-Reference-Manual"><xrefnodename>Operator Reference Manual</xrefnodename><xrefinfoname spaces=" ">Operator Reference Manual</xrefinfoname></ref>.
Many of the tasks that <acronym><acronymword>NCO</acronymword></acronym> can accomplish are described during
the explanation of common <acronym><acronymword>NCO</acronymword></acronym> Features (<pxref label="Common-features"><xrefnodename>Common features</xrefnodename></pxref>).
@@ -1213,7 +1237,7 @@ following <acronym><acronymword>UNIX</acronymword></acronym> commands in the dir
<acronym><acronymword>NCO</acronymword></acronym> executables are installed.
</para><example endspaces=" ">
<pre xml:space="preserve">ln -s -f ncbo ncdiff # ncbo --op_typ='+'
-ln -s -f ncra ncecat # ncra --pseudonym='ncecat'
+ln -s -f ncra nces # ncra --pseudonym='nces'
ln -s -f ncra ncrcat # ncra --pseudonym='ncrcat'
ln -s -f ncbo ncadd # ncbo --op_typ='+'
ln -s -f ncbo ncsubtract # ncbo --op_typ='-'
@@ -1221,7 +1245,7 @@ ln -s -f ncbo ncmultiply # ncbo --op_typ='*'
ln -s -f ncbo ncdivide # ncbo --op_typ='/'
ln -s -f ncpdq ncpack # ncpdq
ln -s -f ncpdq ncunpack # ncpdq --unpack
-# NB: Cygwin executable (and link) names have an '.exe' suffix, e.g.,
+# NB: Windows/Cygwin executable/link names have '.exe' suffix, e.g.,
ln -s -f ncbo.exe ncdiff.exe
...
</pre></example>
@@ -2122,12 +2146,14 @@ Initially the record dimension is <code>time</code>.
Our goal is to create a single file that contains joins all the
spatially adjacent regions into one single time-evolving dataset.
</para><example endspaces=" ">
-<pre xml:space="preserve">for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
- ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
+<verbatim xml:space="preserve">
+for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell
+ ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension
done
ncrcat foo_??.nc out.nc # Concatenate along x
ncpdq -a time,x out.nc out.nc # Revert to time as record dimension
-</pre></example>
+</verbatim>
+</example>
<para>Note that <command>ncrcat</command> will not concatenate fixed-length variables,
whereas <command>ncecat</command> concatenates both fixed-length and record
@@ -2237,9 +2263,11 @@ more, typically) of input filenames to the multi-file operators is
to pass the filenames with the <acronym><acronymword>UNIX</acronymword></acronym> <dfn>standard input</dfn>
feature, aka <code>stdin</code>:
</para><example endspaces=" ">
-<pre xml:space="preserve"># Pipe large numbers of filenames to stdin
-/bin/ls | grep ${CASEID}_'......'.nc | ncecat -o foo.nc
-</pre></example>
+<verbatim xml:space="preserve">
+# Pipe large numbers of filenames to stdin
+/bin/ls | grep ${CASEID}_'......'.nc | ncecat -o foo.nc
+</verbatim>
+</example>
<para>This method avoids all constraints on command line size imposed by
the operating system.
A drawback to this method is that the <code>history</code> attribute
@@ -2280,9 +2308,11 @@ and to pipe the results to <command>xargs</command> which, in turn, passes the
matching filenames to an <acronym><acronymword>NCO</acronymword></acronym> multi-file operator, e.g.,
<command>ncecat</command>.
</para><example endspaces=" ">
-<pre xml:space="preserve"># Use xargs to transfer filenames on the command line
-/bin/ls | grep ${CASEID}_'......'.nc | xargs -x ncecat -o foo.nc
-</pre></example>
+<verbatim xml:space="preserve">
+# Use xargs to transfer filenames on the command line
+/bin/ls | grep ${CASEID}_'......'.nc | xargs -x ncecat -o foo.nc
+</verbatim>
+</example>
<cindex index="cp" spaces=" "><indexterm index="cp" number="247">pipes</indexterm></cindex>
<para>The single quotes protect the only sensitive parts of the extended
regular expression (the <command>grep</command> argument), and allow shell
@@ -2319,13 +2349,15 @@ directory. If there are 999,999 netCDF files present, the links are
named <file>000001.nc</file> to <file>999999.nc</file>:
<cindex index="cp" spaces=" "><indexterm index="cp" number="253"><code>-n <var>loop</var></code></indexterm></cindex>
</para><example endspaces=" ">
-<pre xml:space="preserve"># Create enumerated symbolic links
+<verbatim xml:space="preserve">
+# Create enumerated symbolic links
/bin/ls | grep \.nc | perl -e \
-'$idx=1;while(<STDIN>){chop;symlink $_,sprintf("%06d.nc",$idx++);}'
+'$idx=1;while(<STDIN>){chop;symlink $_,sprintf("%06d.nc",$idx++);}'
ncecat -n 999999,6,1 000001.nc foo.nc
# Remove symbolic links when finished
/bin/rm ??????.nc
-</pre></example>
+</verbatim>
+</example>
<para>The <samp>-n <var>loop</var></samp> option tells the <acronym><acronymword>NCO</acronymword></acronym> operator to
automatically generate the filnames of the symbolic links.
This circumvents any <acronym><acronymword>OS</acronymword></acronym> and shell limits on command line size.
@@ -2729,7 +2761,11 @@ feature is automatic and cannot be controlled by the user.
<cindex index="cp" spaces=" "><indexterm index="cp" number="312">L10N</indexterm></cindex>
<para><acronym><acronymword>NCO</acronymword></acronym> support for <dfn>internationalization</dfn> of textual input
and output (e.g., Warning messages) is nascent.
-We hope to produce foreign language string catalogues in 2004.
+We introduced the first foreign language string catalogues (French and
+Spanish) in 2004, yet did not activate these in distributions because
+the catalogues were nearly empty.
+We seek volunteers to populate our templates with translations for their
+favorite languages.
<!-- c fxm: Work on this section -->
</para>
<html endspaces=" ">
@@ -3043,12 +3079,15 @@ ncra -n 5,2,1 85.nc 8589.nc
force.
The second method relies on the operating system shell to <dfn>glob</dfn>
(expand) the <dfn>regular expression</dfn> <code>8[56789].nc</code>.
-The shell passes valid filenames which match the expansion to
-<command>ncra</command>.
-The third method uses the <samp>-p <var>input-path</var></samp> argument to specify
+The shell then passes the valid filenames (those which match the
+regular expansion) to <command>ncra</command>.
+In this case <command>ncra</command> never knows that a regular expression was
+used, because the shell intercepts and expands and matches the regular
+expression before <command>ncra</command> is actually invoked.
+The third method uses the <samp>-p <var>input-path</var></samp> argument to specify
the directory where all the input files reside.
<acronym><acronymword>NCO</acronymword></acronym> prepends <var>input-path</var> (e.g.,
-<file>/data/usrname/model</file>) to all <var>input-files</var> (though not to
+<file>/data/username/model</file>) to all <var>input-files</var> (though not to
<var>output-file</var>).
Thus, using <samp>-p</samp>, the path to any number of input files need only
be specified once.
@@ -3057,8 +3096,13 @@ automatically generated if necessary.
</para>
<para>The last method passes (with <samp>-n</samp>) syntax concisely describing
the entire set of filenames
-<footnote><para>The <samp>-n</samp> option is a backward compatible superset of the
-<code>NINTAP</code> option from the <acronym><acronymword>NCAR</acronymword></acronym> <acronym><acronymword>CCM</acronymword></acronym> Processor.</para></footnote>.
+<footnote><para>The <samp>-n</samp> option is a backward-compatible superset of the
+<code>NINTAP</code> option from the <acronym><acronymword>NCAR</acronymword></acronym> <acronym><acronymword>CCM</acronymword></acronym> Processor.
+The <acronym><acronymword>CCM</acronymword></acronym> Processor was custom-written Fortran code maintained
+for many years by Lawrence Buja at <acronym><acronymword>NCAR</acronymword></acronym>, and phased-out in
+the late 1990s.
+<acronym><acronymword>NCO</acronymword></acronym> stole some ideas, like <code>NINTAP</code>-functionality,
+from the <acronym><acronymword>CCM</acronymword></acronym> Processor capabilities.</para></footnote>.
<cindex index="cp" spaces=" "><indexterm index="cp" number="367">multi-file operators</indexterm></cindex>
<cindex index="cp" spaces=" "><indexterm index="cp" number="368">files, multiple</indexterm></cindex>
This option is only available with the <dfn>multi-file operators</dfn>:
@@ -3075,8 +3119,8 @@ For example, in the file <file>ccm3_h0001.nc</file>, we have
<var>alphanumeric_prefix</var> = <file>ccm3_h</file>, <var>numeric_suffix</var> =
<file>0001</file>, and <var>filetype</var> = <file>nc</file>.
</para>
-<para><acronym><acronymword>NCO</acronymword></acronym> is able to decode lists of such filenames encoded using the
-<samp>-n</samp> option.
+<para><acronym><acronymword>NCO</acronymword></acronym> decodes lists of such filenames encoded using the
+<samp>-n</samp> syntax.
The simpler (3-argument) <samp>-n</samp> usage takes the form
<code>-n <var>file_number</var>,<var>digit_number</var>,<var>numeric_increment</var></code>
where <var>file_number</var> is the number of files, <var>digit_number</var> is
@@ -3125,12 +3169,12 @@ ncra -n 3,2,1,12,1 85_12.nc 85_1202.nc
suffice to specify consecutive months (<code>06, 07, 08</code>) which do not
&textldquo;wrap&textrdquo; back to a minimum value.
The second example shows how to use the optional fourth and fifth
-elements of the <samp>-n</samp> option to specify a wrap value to <acronym><acronymword>NCO</acronymword></acronym>.
-The fourth argument to <samp>-n</samp>, if present, specifies the maximum
+elements of the <samp>-n</samp> option to specify a wrap value.
+The fourth argument to <samp>-n</samp>, when present, specifies the maximum
integer value of <var>numeric_suffix</var>.
-In this case the maximum value <w>is 12,</w> and will be formatted as
+In the example the maximum value <w>is 12,</w> and will be formatted as
<file>12</file> in the filename string.
-The fifth argument to <samp>-n</samp>, if present, specifies the minimum
+The fifth argument to <samp>-n</samp>, when present, specifies the minimum
integer value of <var>numeric_suffix</var>.
The default minimum filename suffix <w>is 1,</w> which is formatted as
<file>01</file> in this case.
@@ -3237,16 +3281,18 @@ particular access protocol.
<html endspaces=" ">
<a name="ftp"></a> <!&textndash; http://nco.sf.net/nco.html#ftp &textndash;>
</html>
-<para>To access a file via an anonymous <acronym><acronymword>FTP</acronymword></acronym> server, supply the
-remote file&textrsquo;s <acronym><acronymword>URL</acronymword></acronym>.
+<para>To access a file via an anonymous <acronym><acronymword>FTP</acronymword></acronym> server, simply supply
+the remote file&textrsquo;s <acronym><acronymword>URL</acronymword></acronym>.
+Anonymous <acronym><acronymword>FTP</acronymword></acronym> usually requires no further credentials,
+e.g., no <file>.netrc</file> file is necessary.
<acronym><acronymword>FTP</acronymword></acronym> is an intrinsically insecure protocol because it transfers
-passwords in plain text format.
+passwords in plain text format.
Users should access sites using anonymous <acronym><acronymword>FTP</acronymword></acronym>, or better yet,
-secure <acronym><acronymword>FTP</acronymword></acronym> when possible.
+secure <acronym><acronymword>FTP</acronymword></acronym> (<acronym><acronymword>SFTP</acronymword></acronym>, see below) when possible.
Some <acronym><acronymword>FTP</acronymword></acronym> servers require a login/password combination for a
valid user account.
-<acronym><acronymword>NCO</acronymword></acronym> allows these transactions so long as the required
-information is stored in the <file>.netrc</file> file.
+<acronym><acronymword>NCO</acronymword></acronym> allows transactions that require additional credentials
+so long as the required information is stored in the <file>.netrc</file> file.
Usually this information is the remote machine name, login, and
password, in plain text, separated by those very keywords, e.g.,
</para><example endspaces=" ">
@@ -3273,7 +3319,7 @@ specified with a homebrew syntax of the form
<pre xml:space="preserve">sftp://machine.domain.tld:/path/to/filename
</pre></example>
<para>Note the second colon following the top-level-domain, <code>tld</code>.
-This syntax is a hybrid between an <acronym><acronymword>FTP URL</acronymword></acronym> and a standard
+This syntax is a hybrid between an <acronym><acronymword>FTP URL</acronymword></acronym> and standard
remote file syntax.
</para>
<html endspaces=" ">
@@ -3527,7 +3573,7 @@ input and output file format:
one = 1
</pre></example>
<para>And, of course, <acronym><acronymword>OPeNDAP</acronymword></acronym>-enabled <acronym><acronymword>NCO</acronymword></acronym> clients continue
-to support other, orthogonal features such as UDUnits
+to support orthogonal features such as UDUnits
(<pxref label="UDUnits-Support"><xrefnodename>UDUnits Support</xrefnodename></pxref>):
</para><example endspaces=" ">
<pre xml:space="preserve">% ncks -u -C -H -v wvl -d wvl,'0.4 micron','0.7 micron' \
@@ -3552,9 +3598,9 @@ http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/su
<cindex index="cp" spaces=" "><indexterm index="cp" number="431">unpacking</indexterm></cindex>
<para>All with one command!
The data in this particular input file also happen to be packed
-(<pxref label="Methods-and-functions"><xrefnodename>Methods and functions</xrefnodename></pxref>), although this is completely transparent
-to the user since <acronym><acronymword>NCO</acronymword></acronym> automatically unpacks data before
-attempting arithmetic.
+(<pxref label="Methods-and-functions"><xrefnodename>Methods and functions</xrefnodename></pxref>), although this complication is
+transparent to the user since <acronym><acronymword>NCO</acronymword></acronym> automatically unpacks data
+before attempting arithmetic.
</para>
<para><acronym><acronymword>NCO</acronymword></acronym> obtains remote files from the <acronym><acronymword>OPeNDAP</acronymword></acronym> server
(e.g., <file>www.cdc.noaa.gov</file>) rather than the local machine.
@@ -4107,14 +4153,10 @@ build time.
<cindex index="cp" spaces=" "><indexterm index="cp" number="500"><code>--xcl</code></indexterm></cindex>
<cindex index="cp" spaces=" "><indexterm index="cp" number="501"><code>--unn</code></indexterm></cindex>
<cindex index="cp" spaces=" "><indexterm index="cp" number="502"><code>--union</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="503"><code>--gxvx</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="504"><code>--grp_xtr_var_xcl</code></indexterm></cindex>
<cartouche endspaces=" ">
-<para>Options <code>--unn</code>&linebreak;
-Availability: <command>ncbo</command>, <command>nces</command>,
-<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
-<command>ncra</command>, <command>ncrcat</command>, <command>ncwa</command>&linebreak;
-Short options: &linebreak;
-Long options: <samp>--unn</samp> and <samp>--union</samp>&linebreak;
-Options <code>-g <var>grp</var></code>&linebreak;
+<para>Options <code>-g <var>grp</var></code>&linebreak;
Availability: <command>ncbo</command>, <command>nces</command>,
<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
<command>ncra</command>, <command>ncrcat</command>, <command>ncwa</command>&linebreak;
@@ -4126,6 +4168,16 @@ Availability: (<command>ncap2</command>), <command>ncbo</command>, <command>nces
<command>ncra</command>, <command>ncrcat</command>, <command>ncwa</command>&linebreak;
Short options: <samp>-v</samp>, <samp>-x</samp>&linebreak;
Long options: <samp>--variable</samp>, <samp>--exclude</samp> or <samp>--xcl</samp>&linebreak;
+Options <code>--unn</code>&linebreak;
+Availability: <command>ncbo</command>, <command>nces</command>,
+<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
+<command>ncra</command>, <command>ncrcat</command>, <command>ncwa</command>&linebreak;
+Short options: &linebreak;
+Long options: <samp>--unn</samp> and <samp>--union</samp>&linebreak;
+Options <code>--grp_xtr_var_xcl</code>&linebreak;
+Availability: <command>ncks</command>&linebreak;
+Short options: &linebreak;
+Long options: <samp>--gxvx</samp> and <samp>--grp_xtr_var_xcl</samp>&linebreak;
</para></cartouche>
<para>Subsetting variables refers to explicitly specifying variables and
groups to be included or excluded from operator actions.
@@ -4162,12 +4214,31 @@ distinctions.
When learning this syntax it is helpful to keep in mind the similarity
between group hierarchies and directory structures.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="503"><command>mv</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="504"><command>cp</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="505">recursion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="506">recursive</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="507">anchor</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="508">anchoring</indexterm></cindex>
+<html endspaces=" ">
+<a name="gxvx"></a> <!&textndash; http://nco.sf.net/nco.html#gxvx &textndash;>
+<a name="grp_xtr_var_xcl"></a> <!&textndash; http://nco.sf.net/nco.html#grp_xtr_var_xcl &textndash;>
+</html>
+<para>As of <acronym><acronymword>NCO</acronymword></acronym> 4.4.4 (June, 2014), <command>ncks</command> (alone) supports
+an option to include specified groups yet exclude specified variables.
+The <samp>--grp_xtr_var_xcl</samp> switch (with long option equivalent
+<samp>--gxvx</samp>) extracts all contents of groups given as arguments to
+<samp>-g <var>grp</var>[,&dots;]</samp>, except for variables given as arguments
+to <samp>-v <var>var</var>[,&dots;]</samp>.
+Use this when one or a few variables in hierarchical files are not to be
+extracted, and all other variables are.
+This is useful when coercing netCDF4 files into netCDF3 files such as
+with converting, flattening, or dismembering files
+(see <ref label="Flattening-Groups"><xrefnodename>Flattening Groups</xrefnodename></ref>).
+</para><example endspaces=" ">
+<pre xml:space="preserve">ncks --grp_xtr_var_xcl -g g1 -v v1 # Extract all of group g1 except v1
+</pre></example>
+
+<cindex index="cp" spaces=" "><indexterm index="cp" number="505"><command>mv</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="506"><command>cp</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="507">recursion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="508">recursive</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="509">anchor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="510">anchoring</indexterm></cindex>
<html endspaces=" ">
<a name="rcr"></a> <!&textndash; http://nco.sf.net/nco.html#rcr &textndash;>
<a name="recursion"></a> <!&textndash; http://nco.sf.net/nco.html#recursion &textndash;>
@@ -4244,12 +4315,12 @@ The fifth command is a special case of the fourth command.
<a name="union"></a> <!&textndash; http://nco.sf.net/nco.html#union &textndash;>
<a name="intersection"></a> <!&textndash; http://nco.sf.net/nco.html#intersection &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="509">union</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="510">intersection</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="511"><code>--unn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="512"><code>--union</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="513"><code>--nsx</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="514"><code>--intersection</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="511">union</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="512">intersection</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="513"><code>--unn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="514"><code>--union</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="515"><code>--nsx</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="516"><code>--intersection</code></indexterm></cindex>
<para>As mentioned above, both <samp>-v</samp> and <samp>-g</samp> options may be
specified simultaneously and <acronym><acronymword>NCO</acronymword></acronym> will, by default, extract the
intersection of the lists, i.e., the specified variables found in the
@@ -4296,7 +4367,7 @@ As discussed below, the group and variable specifications may be comma
separated lists of regular expressions for added control over
subsetting.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="515">memory requirements</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="517">memory requirements</indexterm></cindex>
<para>Remember, if averaging or concatenating large files stresses your
systems memory or disk resources, then the easiest solution is often to
subset (with <samp>-g</samp> and/or <samp>-v</samp>) to retain only the most
@@ -4326,14 +4397,14 @@ indicates that <emph>only</emph> user-defined variables should be output.
<a name="rx"></a> <!&textndash; http://nco.sf.net/nco.html#rx &textndash;>
<a name="wildcarding"></a> <!&textndash; http://nco.sf.net/nco.html#wildcarding &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="516">extended regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="517">regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="518">pattern matching</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="519">wildcards</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="520"><command>grep -E</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="521"><command>egrep</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="522"><command>ncatted</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="523"><acronym><acronymword>GNU</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="518">extended regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="519">regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="520">pattern matching</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="521">wildcards</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="522"><command>grep -E</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="523"><command>egrep</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="524"><command>ncatted</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="525"><acronym><acronymword>GNU</acronymword></acronym></indexterm></cindex>
<para>Regular expressions the syntax that <acronym><acronymword>NCO</acronymword></acronym> use pattern-match
object names in netCDF file against user requests.
The user can select all variables beginning with the string <samp>DST</samp>
@@ -4355,8 +4426,8 @@ to <command>ncatted</command> may contain <dfn>extended regular expressions</dfn
As of <acronym><acronymword>NCO</acronymword></acronym> 4.2.4 (November, 2012), group name arguments
to the <samp>-g</samp> switch may contain <dfn>extended regular expressions</dfn>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="524"><acronym><acronymword>POSIX</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="525"><code>regex</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="526"><acronym><acronymword>POSIX</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="527"><code>regex</code></indexterm></cindex>
<para>Because of its wide availability, <acronym><acronymword>NCO</acronymword></acronym> uses the <acronym><acronymword>POSIX</acronymword></acronym>
regular expression library <code>regex</code>.
Regular expressions of arbitary complexity may be used.
@@ -4364,11 +4435,11 @@ Since netCDF variable names are relatively simple constructs, only a
few varieties of variable wildcards are likely to be useful.
For convenience, we define the most useful pattern matching operators
here:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="526"><code>.</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="527"><code>$</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="528"><code>^</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="529"><code>?</code> (filename expansion)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="530"><code>*</code> (filename expansion)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="528"><code>.</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="529"><code>$</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="530"><code>^</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="531"><code>?</code> (filename expansion)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="532"><code>*</code> (filename expansion)</indexterm></cindex>
</para><table commandarg="samp" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="samp">^</itemformat></item>
</tableterm><tableitem><para>Matches the beginning of a string
@@ -4379,10 +4450,10 @@ here:
</para></tableitem></tableentry></table>
<noindent></noindent>
<para>The most useful repetition and combination operators are
-<cindex index="cp" spaces=" "><indexterm index="cp" number="531"><code>?</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="532"><code>*</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="533"><code>+</code> (wildcard character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="534"><code>|</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="533"><code>?</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="534"><code>*</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="535"><code>+</code> (wildcard character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="536"><code>|</code> (wildcard character)</indexterm></cindex>
</para><table commandarg="samp" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="samp">?</itemformat></item>
</tableterm><tableitem><para>The preceding regular expression is optional and matched at most once
@@ -4405,23 +4476,25 @@ those groups, and file <file>in.nc</file> with variables <code>Q</code>,
<code>Q01</code>&textndash;<code>Q99</code>, <code>Q100</code>, <code>QAA</code>&textndash;<code>QZZ</code>,
<code>Q_H2O</code>, <code>X_H2O</code>, <code>Q_CO2</code>, <code>X_CO2</code>.
</para><example endspaces=" ">
-<pre xml:space="preserve">ncks -v '.+' in.nc # All variables (default)
+<verbatim xml:space="preserve">
+ncks -v '.+' in.nc # All variables (default)
ncks -v 'Q.?' in.nc # Variables that contain Q
ncks -v '^Q.?' in.nc # Variables that start with Q
ncks -v '^Q+.?.' in.nc # Q, Q0--Q9, Q01--Q99, QAA--QZZ, etc.
ncks -v '^Q..' in.nc # Q01--Q99, QAA--QZZ, etc.
ncks -v '^Q[0-9][0-9]' in.nc # Q01--Q99, Q100
-ncks -v '^Q[[:digit:]]{2}' in.nc # Q01--Q99
+ncks -v '^Q[[:digit:]]{2}' in.nc # Q01--Q99
ncks -v 'H2O$' in.nc # Q_H2O, X_H2O
ncks -v 'H2O$|CO2$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
ncks -v '^Q[0-9][0-9]$' in.nc # Q01--Q99
ncks -v '^Q[0-6][0-9]|7[0-3]' in.nc # Q01--Q73, Q100
ncks -v '(Q[0-6][0-9]|7[0-3])$' in.nc # Q01--Q73
-ncks -v '^[a-z]_[a-z]{3}$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
+ncks -v '^[a-z]_[a-z]{3}$' in.nc # Q_H2O, X_H2O, Q_CO2, X_CO2
ncks -g 'g.' in_grp.nc # 10 Groups g0-g9
ncks -g 's.' in_grp.nc # 100 sub-groups g0/s0, g0/s1, ... g9/s9
ncks -g 'g.' -v 'v.' in_grp.nc # All variables 'v.' in groups 'g.'
-</pre></example>
+</verbatim>
+</example>
<para>Beware&textmdash;two of the most frequently used repetition pattern matching
operators, <samp>*</samp> and <samp>?</samp>, are also valid pattern matching
operators for filename expansion (globbing) at the shell-level.
@@ -4441,11 +4514,11 @@ extended regular expressions which <acronym><acronymword>NCO</acronymword></acro
<a name="globbing"></a> <!&textndash; http://nco.sf.net/nco.html#globbing &textndash;>
<a name="glb"></a> <!&textndash; http://nco.sf.net/nco.html#glb &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="535">globbing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="536">shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="537"><command>bash</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="538"><command>csh</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="539">quotes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="537">globbing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="538">shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="539"><command>bash</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="540"><command>csh</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="541">quotes</indexterm></cindex>
<para>One must be careful to protect any special characters in the regular
expression specification from being interpreted (globbed) by the shell.
This is accomplish by enclosing special characters within single or
@@ -4472,13 +4545,13 @@ filename expansion (globbing).
</section>
<node name="Subsetting-Coordinate-Variables" spaces=" "><nodename>Subsetting Coordinate Variables</nodename><nodenext spaces=" ">Group Path Editing</nodenext><nodeprev spaces=" ">Subsetting Files</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Subsetting Coordinate Variables</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="540">subsetting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="541"><code>-C</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="542"><code>-c</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="543"><code>--no-coords</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="544"><code>--no-crd</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="545"><code>--coords</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="546"><code>--crd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="542">subsetting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="543"><code>-C</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="544"><code>-c</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="545"><code>--no-coords</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="546"><code>--no-crd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="547"><code>--coords</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="548"><code>--crd</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
@@ -4502,13 +4575,16 @@ automatically specifying that <emph>all</emph> coordinate variables in the
<var>input-files</var> should appear in the <var>output-file</var>.
Thus <samp>-c</samp> allows the user to select all the coordinate variables
without having to know their names.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="547"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
-As of <acronym><acronymword>NCO</acronymword></acronym> version 3.9.6 (January, 2009)
-both <samp>-c</samp> and <samp>-C</samp> honor the <acronym><acronymword>CF</acronymword></acronym> <code>coordinates</code>
-convention described in <ref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></ref>.
+<cindex index="cp" spaces=" "><indexterm index="cp" number="549"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
+As of <acronym><acronymword>NCO</acronymword></acronym> version 4.4.5 (July, 2014)
+both <samp>-c</samp> and <samp>-C</samp> honor the <acronym><acronymword>CF</acronymword></acronym> <code>ancillary_variables</code>
+convention described in <ref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></ref>.
As of <acronym><acronymword>NCO</acronymword></acronym> version 4.0.8 (April, 2011)
both <samp>-c</samp> and <samp>-C</samp> honor the <acronym><acronymword>CF</acronymword></acronym> <code>bounds</code>
convention described in <ref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></ref>.
+As of <acronym><acronymword>NCO</acronymword></acronym> version 3.9.6 (January, 2009)
+both <samp>-c</samp> and <samp>-C</samp> honor the <acronym><acronymword>CF</acronymword></acronym> <code>coordinates</code>
+convention described in <ref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></ref>.
</para>
<html endspaces=" ">
<a name="gpe"></a> <!&textndash; http://nco.sf.net/nco.html#gpe &textndash;>
@@ -4516,8 +4592,8 @@ convention described in <ref label="CF-Conventions"><xrefnodename>CF Conventions
</section>
<node name="Group-Path-Editing" spaces=" "><nodename>Group Path Editing</nodename><nodenext spaces=" ">C and Fortran Index Conventions</nodenext><nodeprev spaces=" ">Subsetting Coordinate Variables</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Group Path Editing</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="548"><code>-G <var>gpe_dsc</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="549"><code>--gpe <var>gpe_dsc</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="550"><code>-G <var>gpe_dsc</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="551"><code>--gpe <var>gpe_dsc</var></code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Options <code>-G <var>gpe_dsc</var></code>&linebreak;
Availability: <command>ncbo</command>, <command>ncecat</command>, <command>nces</command>,
@@ -4544,7 +4620,7 @@ the following order:&linebreak;
<table commandarg="var" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="var">grp_pth</itemformat></item>
</tableterm><tableitem><para>Group Path.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="550">group path</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="552">group path</indexterm></cindex>
This (optional) component specifies the output group path that should be
appended after any editing (i.e., deletion or truncation) of the input
path is performed.
@@ -4568,16 +4644,24 @@ Hence, <samp>-G :-1</samp> is the same as <samp>-G &arobase;1</samp>.
This is simply a way of making the <var>lvl_nbr</var> argument
positive-definite.
</para>
+<menu endspaces=" ">
+<menuentry leadingtext="* "><menunode separator="::">Flattening Groups</menunode><menudescription><pre xml:space="preserve">
+</pre></menudescription></menuentry><menuentry leadingtext="* "><menunode separator="::">Moving Groups</menunode><menudescription><pre xml:space="preserve">
+</pre></menudescription></menuentry><menuentry leadingtext="* "><menunode separator="::">Dismembering Files</menunode><menudescription><pre xml:space="preserve">
+</pre></menudescription></menuentry><menuentry leadingtext="* "><menunode separator="::">Checking CF-compliance</menunode><menudescription><pre xml:space="preserve">
+</pre></menudescription></menuentry></menu>
+<node name="Flattening-Groups" spaces=" "><nodename>Flattening Groups</nodename><nodenext spaces=" ">Moving Groups</nodenext><nodeprev spaces=" ">Group Path Editing</nodeprev><nodeup spaces=" ">Group Path Editing</nodeup></node>
+<subsection spaces=" "><sectiontitle>Deletion, Truncation, and Flattening of Groups</sectiontitle>
<html endspaces=" ">
<a name="flatten"></a> <!&textndash; http://nco.sf.net/nco.html#flatten &textndash;>
<a name="delete"></a> <!&textndash; http://nco.sf.net/nco.html#delete &textndash;>
<a name="truncate"></a> <!&textndash; http://nco.sf.net/nco.html#truncate &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="551"><code>&arobase;</code> (separator character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="552"><code>:</code> (separator character)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="553">delete (groups)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="554">truncate (groups)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="555">flatten (groups)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="553"><code>&arobase;</code> (separator character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="554"><code>:</code> (separator character)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="555">delete (groups)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="556">truncate (groups)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="557">flatten (groups)</indexterm></cindex>
<para><acronym><acronymword>GPE</acronymword></acronym> has three editing modes: Delete, Truncate, and
Flatten.
Select one of <acronym><acronymword>GPE</acronymword></acronym>&textrsquo;s three editing modes by supplying a
@@ -4638,7 +4722,8 @@ groups and their placement in the output file as shown by the following
commands.
All commands below may be assumed to end with <samp>in.nc out.nc</samp>.
</para><example endspaces=" ">
-<pre xml:space="preserve"># Prepending paths without editing:
+<verbatim xml:space="preserve">
+# Prepending paths without editing:
ncks # /g?/v? -> /g?/v?
ncks -v v1 # /g?/v1 -> /g?/v1
ncks -g g1 # /g1/v? -> /g1/v?
@@ -4670,7 +4755,7 @@ ncks -G g2: # /g?/v? -> /g2/v?
ncks -G g2: -g g1/g1 -v v1 # /g1/g1/v1 -> /g2/v1
# Truncate-mode: Truncate from and Append to path tail
# Syntax: -G [apn]:-lvl_nbr = # of levels to truncate
-# NB: -G [apn]:-lvl_nbr is equivalent to -G [apn]&arobase;lvl_nbr
+# NB: -G [apn]:-lvl_nbr is equivalent to -G [apn]@lvl_nbr
ncks -G :-1 -g g1 -v v1 # /g1/v1 -> /v1
ncks -G :-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/v1
ncks -G :-2 -g g1/g2 -v v1 # /g1/g2/v1 -> /v1
@@ -4678,16 +4763,20 @@ ncks -G :-2 -g g1 -v v1 # /g1/v1 -> /v1
ncks -G g2:-1 -v v1 # /g?/v1 -> /g2/v1
ncks -G g2:-1 -g g1 -v v1 # /g1/v1 -> /g2/v1
ncks -G g1:-1 -g g1/g2 -v v1 # /g1/g2/v1 -> /g1/g1/v1
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="mv"></a> <!&textndash; http://nco.sf.net/nco.html#mv &textndash;>
<a name="move"></a> <!&textndash; http://nco.sf.net/nco.html#move &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="556">move groups</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="557">groups, moving</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="558">rename groups</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="559">groups, renaming</indexterm></cindex>
+</subsection>
+<node name="Moving-Groups" spaces=" "><nodename>Moving Groups</nodename><nodenext spaces=" ">Dismembering Files</nodenext><nodeprev spaces=" ">Flattening Groups</nodeprev><nodeup spaces=" ">Group Path Editing</nodeup></node>
+<subsection spaces=" "><sectiontitle>Moving Groups</sectiontitle>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="558">move groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="559">groups, moving</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="560">rename groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="561">groups, renaming</indexterm></cindex>
<para>Until fall 2013 (netCDF version 4.3.1-pre1), netCDF contained no library
function for renaming groups, and therefore <command>ncrename</command> cannot
rename groups.
@@ -4741,8 +4830,11 @@ all other groups (e.g., <code>ecmwf</code>, <code>giss</code>).
<a name="disaggregate"></a> <!&textndash; http://nco.sf.net/nco.html#disaggregate &textndash;>
<a name="ncdismember"></a> <!&textndash; http://nco.sf.net/nco.html#ncdismember &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="560">disaggregate</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="561">dismember</indexterm></cindex>
+</subsection>
+<node name="Dismembering-Files" spaces=" "><nodename>Dismembering Files</nodename><nodenext spaces=" ">Checking CF-compliance</nodenext><nodeprev spaces=" ">Moving Groups</nodeprev><nodeup spaces=" ">Group Path Editing</nodeup></node>
+<subsection spaces=" "><sectiontitle>Dismembering Files</sectiontitle>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="562">disaggregate</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="563">dismember</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="5" mergedindex="cp">ncdismember</indexterm></findex>
<para>Let us show how to completely disaggregate (or, more memorably)
<emph>dismember</emph> a hierarchical dataset.
@@ -4814,7 +4906,8 @@ for grp_in in ${grp_lst} ; do
eval ${cmd}
if [ ${flg_cf} = 'cf' ]; then
# cfchecker needs Conventions <= 1.5
- ncatted -h -a Conventions,global,o,c,"CF-${cf_vrs}" ${drc_out}/${grp_out}.nc
+ no_bck_sls=`echo ${drc_out}/${grp_out} | sed 's/\\\ / /g'`
+ ncatted -h -a Conventions,global,o,c,CF-${cf_vrs} ${no_bck_sls}.nc
else # !flg_cf
echo ${drc_out}/${grp_out}.nc
fi # !flg_cf
@@ -4856,12 +4949,15 @@ as <code>NC_STRING</code> and <code>NC_UBYTE</code>) to corresponding netCDF3
atomic types (<code>NC_CHAR</code> and <code>NC_SHORT</code>) when the output format
is netCDF3.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="562"><acronym><acronymword>CF</acronymword></acronym> compliance checker</indexterm></cindex>
+</subsection>
+<node name="Checking-CF_002dcompliance" spaces=" "><nodename>Checking CF-compliance</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Dismembering Files</nodeprev><nodeup spaces=" ">Group Path Editing</nodeup></node>
+<subsection spaces=" "><sectiontitle>Checking CF-compliance</sectiontitle>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="564"><acronym><acronymword>CF</acronymword></acronym> compliance checker</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="6" mergedindex="cp">cfchecker</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="7" mergedindex="cp">ncdismember</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="563">compliance checker</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="564">Martin Schultz</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="565">Michael Decker</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="565">compliance checker</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="566">Martin Schultz</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="567">Michael Decker</indexterm></cindex>
<para>One application of dismembering is to check the <acronym><acronymword>CF</acronymword></acronym>-compliance of each
group in a file.
When invoked with the optional third argumnt <samp>cf</samp>,
@@ -4924,15 +5020,15 @@ of the procedure necessary to check <acronym><acronymword>HDF</acronymword></acr
</para><example endspaces=" ">
<verbatim xml:space="preserve">
cat > ~/ncdismember.txt << 'EOF'
- Preparing an RPM-based OS to Test Hierarchical Files for CF-Compliance
+ Preparing an RPM-based OS to Test HDF & netCDF Files for CF-Compliance
By Charlie Zender, UCI & NASA Dataset Interoperability Working Group (DIWG)
Installation Summary:
-1. HDF4 [with netCDF support _disabled_]
+1. HDF4 [with internal netCDF support _disabled_]
2. HDF5
-3. netCDF version 4.3.1 (or later) [with HDF4 support _enabled_]
-4. NCO version 4.4.0 (or later)
+3. netCDF [with external HDF4 support _enabled_]
+4. NCO
5. numpy
6. netcdf4-python
7. python-lxml
@@ -4963,20 +5059,19 @@ cd hdf5-1.8.11
./configure --enable-shared --prefix=${H5DIR}
make && make check && make install
-# 3. netCDF version 4.3.1. Build in non-default manner with HDF4. No RPM.
+# 3. netCDF version 4.3.1 or later. Build in non-default manner with HDF4.
# Per http://www.unidata.ucar.edu/software/netcdf/docs/build_hdf4.html
# Earlier versions of netCDF may fail checking some HDF4 files
-wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.1.tar.gz
-tar xvzf netcdf-4.3.1.tar.gz
-cd netcdf-4.3.1
+wget -c ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.2.tar.gz
+tar xvzf netcdf-4.3.2.tar.gz
+cd netcdf-4.3.2
CPPFLAGS="-I${H5DIR}/include -I${H4DIR}/include" \
LDFLAGS="-L${H5DIR}/lib -L${H4DIR}/lib" \
./configure --enable-hdf4 --enable-hdf4-file-tests
-make && make check && make installas
+make && make check && make install
-# 4. NCO version 4.4.4. No RPM for this version. Must install by hand.
-# Earlier versions of NCO are relatively useless for ncdismember
-cd ${DATA}/tmp
+# 4. NCO version 4.4.0 or later. Some RPMs available. Or install by hand.
+# Later versions of NCO have much better support for ncdismember
wget http://nco.sourceforge.net/src/nco-4.4.4.tar.gz .
tar xvzf nco-4.4.4.tar.gz
cd nco-4.4.4
@@ -4994,14 +5089,13 @@ sudo yum install python-lxml -y
# 8. CFunits-python. No RPM available. Must install by hand.
# http://code.google.com/p/cfunits-python/
-cd ${DATA}/tmp
wget http://cfunits-python.googlecode.com/files/cfunits-0.9.6.tar.gz .
+tar xvzf cfunits-0.9.6.tar.gz
cd cfunits-0.9.6
sudo python setup.py install
# 9. CFChecker. No RPM available. Must install by hand.
# https://bitbucket.org/mde_/cfchecker
-cd ${DATA}/tmp
wget https://bitbucket.org/mde_/cfchecker/downloads/CFchecker-1.5.15.tar.bz2 .
tar xvjf CFchecker-1.5.15.tar.bz2
cd CFchecker
@@ -5033,14 +5127,15 @@ EOF
<a name="ftn"></a> <!&textndash; http://nco.sf.net/nco.html#ftn &textndash;>
<a name="-F"></a> <!&textndash; http://nco.sf.net/nco.html#-F &textndash;>
</html>
+</subsection>
</section>
<node name="C-and-Fortran-Index-Conventions" spaces=" "><nodename>C and Fortran Index Conventions</nodename><nodenext spaces=" ">Hyperslabs</nodenext><nodeprev spaces=" ">Group Path Editing</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>C and Fortran Index conventions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="566">index convention</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="567">Fortran index convention</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="568">C index convention</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="569"><code>-F</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="570"><code>--fortran</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="568">index convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="569">Fortran index convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="570">C index convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="571"><code>-F</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="572"><code>--fortran</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5048,7 +5143,7 @@ EOF
Short options: <samp>-F</samp>&linebreak;
Long options: <samp>--fortran</samp>&linebreak;
</para></cartouche>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="571">I/O</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="573">I/O</indexterm></cindex>
<para>The <samp>-F</samp> switch changes <acronym><acronymword>NCO</acronymword></acronym> to read and write with
the Fortran index convention.
By default, <acronym><acronymword>NCO</acronymword></acronym> uses C-style (0-based) indices for all I/O.
@@ -5058,17 +5153,17 @@ dimensions are ordered from slowest (inner-most) to fastest
In Fortran, indices count <w>from 1</w> (rather <w>than 0</w>), and
dimensions are ordered from fastest (inner-most) to slowest
(outer-most) varying.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="572">transpose</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="574">transpose</indexterm></cindex>
Hence <w>C and</w> Fortran data storage conventions represent mathematical
transposes of eachother.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="573">record variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="575">record variable</indexterm></cindex>
Note that record variables contain the record dimension as the most
slowly varying dimension.
See <ref label="ncpdq-netCDF-Permute-Dimensions-Quickly"><xrefnodename>ncpdq netCDF Permute Dimensions Quickly</xrefnodename></ref> for techniques
to re-order (including transpose) dimensions and to reverse data
storage order.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="574">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="576">record dimension</indexterm></cindex>
<para>Consider a file <file>85.nc</file> containing <w>12 months</w> of data in the
record dimension <code>time</code>.
The following hyperslab operations produce identical results, a
@@ -5099,12 +5194,12 @@ lon(1)=0 lev(1)=100 lat(1)=-90 three_dmn_var(1)=0
</section>
<node name="Hyperslabs" spaces=" "><nodename>Hyperslabs</nodename><nodenext spaces=" ">Stride</nodenext><nodeprev spaces=" ">C and Fortran Index Conventions</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Hyperslabs </sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="575">hyperslab</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="576">dimension limits</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="577">coordinate limits</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="578"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="579"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="580"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="577">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="578">dimension limits</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="579">coordinate limits</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="580"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="581"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="582"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5141,7 +5236,7 @@ ncks -F -d lon,1,2 in.nc out.nc
ncks -d lon,1,2 in.nc out.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="581">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="583">stride</indexterm></cindex>
<para>Coordinate values should be specified using real notation with a decimal
point required in the value, whereas dimension indices are specified
using integer notation without a decimal point.
@@ -5198,13 +5293,13 @@ ncks -F -d lon,-3, in.nc out.nc
instead of simply <code>.</code> in order to make obvious the selection of
hyperslab elements based on coordinate value rather than index.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="582"><code>NC_CHAR</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="584"><code>NC_CHAR</code></indexterm></cindex>
<para>User-specified coordinate limits are promoted to double-precision values
while searching for the indices which bracket the range.
Thus, hyperslabs on coordinates of type <code>NC_CHAR</code> are computed
numerically rather than lexically, so the results are unpredictable.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="583">wrapped coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="585">wrapped coordinates</indexterm></cindex>
<para>The relative magnitude of <var>min</var> and <var>max</var> indicate to the
operator whether to expect a <dfn>wrapped coordinate</dfn>
(<pxref label="Wrapped-Coordinates"><xrefnodename>Wrapped Coordinates</xrefnodename></pxref>), such as longitude.
@@ -5242,10 +5337,10 @@ This option may be specified more than once in a single command
</section>
<node name="Stride" spaces=" "><nodename>Stride</nodename><nodenext spaces=" ">Record Appending</nodenext><nodeprev spaces=" ">Hyperslabs</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Stride </sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="584">stride</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="585"><code>-d <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="586"><code>--dimension <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="587"><code>--dmn <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="586">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="587"><code>-d <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="588"><code>--dimension <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="589"><code>--dmn <var>dim</var>,[<var>min</var>],[<var>max</var>],<var>stride</var></code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5298,18 +5393,20 @@ data are stored in records <w>2, 14, &dots; 50</w> so the desired
Without the <var>stride</var> option, the procedure is very awkward.
One could use <command>ncks</command> five times and then use <command>ncrcat</command> to
concatenate the resulting files together:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="588">Bourne Shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="589">C Shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="590">Bourne Shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="591">C Shell</indexterm></cindex>
</para><example endspaces=" ">
-<pre xml:space="preserve">for idx in 02 14 26 38 50; do # Bourne Shell
- ncks -d time,${idx} 8501_8912.nc foo.${idx}
+<verbatim xml:space="preserve">
+for idx in 02 14 26 38 50; do # Bourne Shell
+ ncks -d time,${idx} 8501_8912.nc foo.${idx}
done
foreach idx (02 14 26 38 50) # C Shell
- ncks -d time,${idx} 8501_8912.nc foo.${idx}
+ ncks -d time,${idx} 8501_8912.nc foo.${idx}
end
ncrcat foo.?? 8589_03.nc
rm foo.??
-</pre></example>
+</verbatim>
+</example>
<para>With the <var>stride</var> option, <command>ncks</command> performs this hyperslab
extraction in one operation:
</para><example endspaces=" ">
@@ -5333,9 +5430,9 @@ ncrcat -F -d time,3,,12 85.nc 86.nc 87.nc 88.nc 89.nc 8503_8903.nc
</section>
<node name="Record-Appending" spaces=" "><nodename>Record Appending</nodename><nodenext spaces=" ">Subcycle</nodenext><nodeprev spaces=" ">Stride</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Record Appending</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="590">record append</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="591"><code>--rec_apn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="592"><code>--record_append</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="592">record append</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="593"><code>--rec_apn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="594"><code>--record_append</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncra</command>, <command>ncrcat</command>&linebreak;
Short options: None&linebreak;
@@ -5411,15 +5508,15 @@ We recommend users try to understand the safety trade-offs involved.
</section>
<node name="Subcycle" spaces=" "><nodename>Subcycle</nodename><nodenext spaces=" ">Multislabs</nodenext><nodeprev spaces=" ">Record Appending</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Subcycle</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="593">duration</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="594">sub-cycle</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="595">subcycle</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="596">MRO</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="597">Multi-Record Operator</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="598"><code>--mro</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="599"><code>-d <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],[<var>subcycle</var>]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="600"><code>--dimension <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],[<var>subcycle</var>]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="601"><code>--dmn <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],<var>subcycle</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="595">duration</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="596">sub-cycle</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="597">subcycle</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="598">MRO</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="599">Multi-Record Operator</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="600"><code>--mro</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="601"><code>-d <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],[<var>subcycle</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="602"><code>--dimension <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],[<var>subcycle</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="603"><code>--dmn <var>dim</var>,[<var>min</var>],[<var>max</var>],[<var>stride</var>],<var>subcycle</var>]</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncra</command>, <command>ncrcat</command>&linebreak;
Short options: <samp>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>][,[<var>subcycle</var>]]]]</samp>&linebreak;
@@ -5456,14 +5553,16 @@ Traditionally, we would first compute the climatological monthly
mean for each month of summer.
Each of these is a 150-year mean, i.e.,
</para><example endspaces=" ">
-<pre xml:space="preserve"># Step 1: Create climatological monthly files clm06.nc..clm08.nc
-for mth in {6..8}; do
+<verbatim xml:space="preserve">
+# Step 1: Create climatological monthly files clm06.nc..clm08.nc
+for mth in {6..8}; do
mm=`printf "%02d" $mth`
- ncra -O -F -d time,${mm},,12 -n 150,4,1 1850.nc clm${mm}.nc
+ ncra -O -F -d time,${mm},,12 -n 150,4,1 1850.nc clm${mm}.nc
done
# Step 2: Average climatological monthly files into summertime mean
ncra -O clm06 clm07.nc clm08.nc clm_JJA.nc
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent>
<para>So far, nothing is unusual and this task can be performed by any
<acronym><acronymword>NCO</acronymword></acronym> version.
@@ -5517,15 +5616,15 @@ records.
</section>
<node name="Multislabs" spaces=" "><nodename>Multislabs</nodename><nodenext spaces=" ">Wrapped Coordinates</nodenext><nodeprev spaces=" ">Subcycle</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Multislabs </sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="602">multislab</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="603">multi-hyperslab</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="604"><acronym><acronymword>MSA</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="605"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="606"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="607"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="608"><code>--msa</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="609"><code>--msa_usr_rdr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="610"><code>--msa_user_order</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="604">multislab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="605">multi-hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="606"><acronym><acronymword>MSA</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="607"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="608"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="609"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="610"><code>--msa</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="611"><code>--msa_usr_rdr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="612"><code>--msa_user_order</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5578,7 +5677,7 @@ to specify the multislab.
the sizes of the multislabs.
This can be used to extend and or pad coordinate grids.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="611">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="613">stride</indexterm></cindex>
<para>Users may specify redundant ranges of indices in a multislab, e.g.,
</para><example endspaces=" ">
<pre xml:space="preserve">ncks -d lon,0,4 -d lon,2,9,2 in.nc out.nc
@@ -5595,7 +5694,7 @@ the <var>stride</var> option only supports index-based hyper-slabbing.
</para>
<para>Multislabs are more efficient than the alternative of sequentially
performing hyperslab operations and concatenating the results.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="612">I/O</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="614">I/O</indexterm></cindex>
This is because <acronym><acronymword>NCO</acronymword></acronym> employs a novel multislab algorithm to
minimize the number of I/O operations when retrieving irregularly spaced
data from disk.
@@ -5715,11 +5814,11 @@ hyperslabs makes this clearer.
</section>
<node name="Wrapped-Coordinates" spaces=" "><nodename>Wrapped Coordinates</nodename><nodenext spaces=" ">Auxiliary Coordinates</nodenext><nodeprev spaces=" ">Multislabs</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Wrapped Coordinates</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="613">wrapped coordinates</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="614">longitude</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="615"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="616"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="617"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="615">wrapped coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="616">longitude</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="617"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="618"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="619"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncks</command>&linebreak;
Short options: <samp>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</samp>&linebreak;
@@ -5792,13 +5891,13 @@ values (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref
</section>
<node name="Auxiliary-Coordinates" spaces=" "><nodename>Auxiliary Coordinates</nodename><nodenext spaces=" ">UDUnits Support</nodenext><nodeprev spaces=" ">Wrapped Coordinates</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Auxiliary Coordinates</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="618"><code>-X</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="619"><code>--auxiliary</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="620"><code>standard_name</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="621"><code>coordinates</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="622"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="623"><code>-X <var>lon_min</var>,<var>lon_max</var>,<var>lat_min</var>,<var>lat_max</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="624"><code>--auxiliary <var>lon_min</var>,<var>lon_max</var>,<var>lat_min</var>,<var>lat_max</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="620"><code>-X</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="621"><code>--auxiliary</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="622"><code>standard_name</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="623"><code>coordinates</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="624"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="625"><code>-X <var>lon_min</var>,<var>lon_max</var>,<var>lat_min</var>,<var>lat_max</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="626"><code>--auxiliary <var>lon_min</var>,<var>lon_max</var>,<var>lat_min</var>,<var>lat_max</var></code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5816,7 +5915,7 @@ ranges.
This works on datasets that associate coordinate variables to
grid-mappings using the <acronym><acronymword>CF</acronymword></acronym>-convention (<pxref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></pxref>)
<code>coordinates</code> and <code>standard_name</code> attributes described
-<uref><urefurl>http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
+<uref><urefurl>http://cfconventions.org/1.6.html#coordinate-system</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
Currently, <acronym><acronymword>NCO</acronymword></acronym> understands auxiliary coordinate variables
pointed to by the <code>standard_name</code> attributes for <var>latitude</var> and
<var>longitude</var>.
@@ -5824,7 +5923,7 @@ Cells that contain a value within the user-specified range
[<var>lon_min</var>,<var>lon_max</var>,<var>lat_min</var>,<var>lat_max</var>] are
included in the output hyperslab.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="625">cell-based grids</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="627">cell-based grids</indexterm></cindex>
<para>A cell-based grid collapses the horizontal spatial information
(latitude and longitude) and stores it along a one-dimensional
coordinate that has a one-to-one mapping to both latitude and longitude
@@ -5936,13 +6035,13 @@ to avoid confusion.
</section>
<node name="UDUnits-Support" spaces=" "><nodename>UDUnits Support</nodename><nodenext spaces=" ">Rebasing Time Coordinate</nodenext><nodeprev spaces=" ">Auxiliary Coordinates</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>UDUnits Support </sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="626">UDUnits</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="627">Unidata</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="628"><code>units</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="629">attribute, <code>units</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="630"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="631"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="632"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="628">UDUnits</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="629">Unidata</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="630"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="631">attribute, <code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="632"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="633"><code>--dimension <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="634"><code>--dmn <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]]</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>, <command>ncra</command>,
@@ -5964,7 +6063,7 @@ may become required in a future version of <acronym><acronymword>NCO</acronymwor
</para>
<para>Two examples suffice to demonstrate the power and convenience of UDUnits
support.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="633">MKS units</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="635">MKS units</indexterm></cindex>
First, consider extraction of a variable containing non-record
coordinates with physical dimensions stored in MKS units.
In the following example, the user extracts all wavelengths
@@ -5975,7 +6074,7 @@ very frequently used in visible spectroscopy, microns:
wvl[0]=5e-07 meter
</pre></example>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="634"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="636"><code>units</code></indexterm></cindex>
<para>The hyperslab returns the correct values because the <var>wvl</var> variable
is stored on disk with a length dimension that UDUnits recognizes in the
<code>units</code> attribute.
@@ -5995,7 +6094,7 @@ because each hyperslab argument contains text characters and non-initial
spaces.
Third, <acronym><acronymword>NCO</acronymword></acronym> determines whether the <var>wvl</var> is dimensioned
with a coordinate variable that has a <code>units</code> attribute.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="635">coordinate variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="637">coordinate variable</indexterm></cindex>
In this case, <var>wvl</var> itself is a coordinate variable.
The value of its <code>units</code> attribute is <code>meter</code>.
Thus <var>wvl</var> passes this test so UDUnits conversion is attempted.
@@ -6017,8 +6116,8 @@ At this point, <acronym><acronymword>NCO</acronymword></acronym> can perform a c
the same algorithm as if the user had specified the hyperslab without
requesting units conversion.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="636"><code>units</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="637"><code>time</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="638"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="639"><code>time</code></indexterm></cindex>
<para>The translation and dimensional innterpretation of time coordinates
shows a more powerful, and probably more common, UDUnits application.
In this example, the user prints all data between <w>4 PM</w> and <w>7 PM</w>
@@ -6030,8 +6129,8 @@ since the year 1900:
time_udunits[1]=876018 hours since 1900-01-01 00:00:0.0
</pre></example>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="638">stride</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="639">whitespace</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="640">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="641">whitespace</indexterm></cindex>
<para>Here, the user invokes the stride (<pxref label="Stride"><xrefnodename>Stride</xrefnodename></pxref>) capability to obtain
every other timeslice.
This is possible because the UDUnits feature is additive, not
@@ -6047,7 +6146,7 @@ time period spread across multiple input files
<noindent></noindent>
<para>Note that there is no excess whitespace before or after the individual
elements of the <samp>-d</samp> argument.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="640">shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="642">shell</indexterm></cindex>
This is important since, as far as the shell knows, <samp>-d</samp> takes
only <emph>one</emph> command-line argument.
Parsing this argument into its component
@@ -6081,8 +6180,8 @@ export UDUNITS2_XML_PATH='/unusual/location/share/udunits/udunits2.xml'
<para>This run-time flexibility can enable the full functionality of
pre-built binaries on machines with libraries in different locations.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="641">Climate and Forecast Metadata Convention</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="642"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="643">Climate and Forecast Metadata Convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="644"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
<para>The <uref><urefurl>http://www.unidata.ucar.edu/packages/udunits</urefurl><urefdesc spaces=" ">UDUnits</urefdesc></uref>
package documentation describes the supported formats of time
dimensions.
@@ -6142,8 +6241,8 @@ data:
<para><samp>ncks -v lon_cal -d lon_cal,'1964-3-1 0:00:0.0','1964-3-4 00:00:0.0'</samp>
results in <code>lon_cal=1,2,3,4</code>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="643">MKS units</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="644">God</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="645">MKS units</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="646">God</indexterm></cindex>
<para>netCDF variables should always be stored with MKS (i.e., God&textrsquo;s) units,
so that application programs may assume MKS dimensions apply to all
input variables.
@@ -6226,9 +6325,9 @@ but also any bounds associated with the record coordinate (e.g.,
</section>
<node name="Multiple-Record-Dimensions" spaces=" "><nodename>Multiple Record Dimensions</nodename><nodenext spaces=" ">Missing Values</nodenext><nodeprev spaces=" ">Rebasing Time Coordinate</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Multiple Record Dimensions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="645">netCDF4</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="646"><code>--mrd</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="647"><code>--multiple_record_dimensions</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="647">netCDF4</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="648"><code>--mrd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="649"><code>--multiple_record_dimensions</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability:
<command>ncecat</command>, <command>ncpdq</command>
@@ -6285,11 +6384,11 @@ Use <samp>--mrd</samp> to override this.
</section>
<node name="Missing-Values" spaces=" "><nodename>Missing Values</nodename><nodenext spaces=" ">Chunking</nodenext><nodeprev spaces=" ">Multiple Record Dimensions</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Missing values</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="648">missing values</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="649">data, missing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="650">averaging data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="651"><code>missing_value</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="652"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="650">missing values</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="651">data, missing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="652">averaging data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="653"><code>missing_value</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="654"><code>_FillValue</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncflint</command>, <command>ncpdq</command>, <command>ncra</command>, <command>ncwa</command>&linebreak;
@@ -6299,7 +6398,7 @@ Short options: None&linebreak;
<para>The phrase <dfn>missing data</dfn> refers to data points that are missing,
invalid, or for any reason not intended to be arithmetically processed
in the same fashion as valid data.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="653">arithmetic operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="655">arithmetic operators</indexterm></cindex>
The <acronym><acronymword>NCO</acronymword></acronym> arithmetic operators attempt to handle missing data in
an intelligent fashion.
There are four steps in the <acronym><acronymword>NCO</acronymword></acronym> treatment of missing data:
@@ -6364,7 +6463,7 @@ If <var>var_type</var> equals <var>att_type</var> then <acronym><acronymword>NCO
straightforwardly compares each value of <var>var</var> to
<var>_FillValue</var> to determine which elements of <var>var</var> are to be
treated as missing data.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="654">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="656">C language</indexterm></cindex>
If not, then <acronym><acronymword>NCO</acronymword></acronym> converts <var>_FillValue</var> from
<var>att_type</var> to <var>var_type</var> by using the implicit conversion rules
<w>of C</w>, or, if <var>att_type</var> is <code>NC_CHAR</code>
@@ -6373,7 +6472,7 @@ uses <var>att_type</var> = <code>NC_CHAR</code> and <var>_FillValue</var> =
<samp>-99999.</samp>.
</para></footnote>, by typecasting the results of the <w>C function</w>
<code>strtod(<var>_FillValue</var>)</code>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="655"><command>ncatted</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="657"><command>ncatted</command></indexterm></cindex>
You may use the <acronym><acronymword>NCO</acronymword></acronym> operator <command>ncatted</command> to change the
<code>_FillValue</code> attribute and all data whose data is
<var>_FillValue</var> to a new value
@@ -6382,11 +6481,11 @@ You may use the <acronym><acronymword>NCO</acronymword></acronym> operator <comm
</listitem><listitem>
<para>Identifying missing data during arithmetic operations.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="656">performance</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="657">operator speed</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="658">speed</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="659">execution time</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="660">arithmetic operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="658">performance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="659">operator speed</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="660">speed</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="661">execution time</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="662">arithmetic operators</indexterm></cindex>
<para>When an <acronym><acronymword>NCO</acronymword></acronym> arithmetic operator processes a variable <var>var</var>
with a <code>_FillValue</code> attribute, it compares each value of
<var>var</var> to <var>_FillValue</var> before performing an operation.
@@ -6406,11 +6505,11 @@ valid or not.
</listitem><listitem>
<para>Treatment of any data identified as missing in arithmetic operators.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="661"><command>nces</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="662"><command>ncra</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="663"><command>ncwa</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="664"><command>ncbo</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="665"><command>ncflint</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="663"><command>nces</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="664"><command>ncra</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="665"><command>ncwa</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="666"><command>ncbo</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="667"><command>ncflint</command></indexterm></cindex>
<para><acronym><acronymword>NCO</acronymword></acronym> averagers (<command>ncra</command>, <command>nces</command>, <command>ncwa</command>)
do not count any element with the value <var>_FillValue</var> towards the
average.
@@ -6454,17 +6553,17 @@ important information from being lost.
</section>
<node name="Chunking" spaces=" "><nodename>Chunking</nodename><nodenext spaces=" ">Deflation</nodenext><nodeprev spaces=" ">Missing Values</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Chunking</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="666"><code>--cnk_byt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="667"><code>--cnk_dmn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="668"><code>--cnk_map</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="669"><code>--cnk_plc</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="670"><code>--cnk_scl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="671"><code>--chunk_byte</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="672"><code>--chunk_dimension</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="673"><code>--chunk_map</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="674"><code>--chunk_policy</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="675"><code>--chunk_scalar</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="676">chunking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="668"><code>--cnk_byt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="669"><code>--cnk_dmn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="670"><code>--cnk_map</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="671"><code>--cnk_plc</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="672"><code>--cnk_scl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="673"><code>--chunk_byte</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="674"><code>--chunk_dimension</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="675"><code>--chunk_map</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="676"><code>--chunk_policy</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="677"><code>--chunk_scalar</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="678">chunking</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
@@ -6489,9 +6588,9 @@ Dataset chunking issues are described in detail
and
<uref><urefurl>http://www.unidata.ucar.edu/blogs/developer/en/entry/chunking_data_choosing_shapes</urefurl><urefdesc>here</urefdesc></uref>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="677">chunking policy</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="678">chunking map</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="679">chunksize</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="679">chunking policy</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="680">chunking map</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="681">chunksize</indexterm></cindex>
<para>The <acronym><acronymword>NCO</acronymword></acronym> chunking implementation is designed to be flexible.
Users control three aspects of the chunking implementation.
These are known as the <dfn>chunking policy</dfn>, <dfn>chunking map</dfn>,
@@ -6499,9 +6598,9 @@ and <dfn>chunksize</dfn>.
The first two are high-level mechanisms that apply to an entire file
and all variables and dimensions, while the third allows per-dimension
specification of parameters.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="680">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="682">hyperslab</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="10" mergedindex="cp">ncpdq</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="681">packing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="683">packing</indexterm></cindex>
The implementation is a hybrid of the <command>ncpdq</command> packing policies
(<pxref label="ncpdq-netCDF-Permute-Dimensions-Quickly"><xrefnodename>ncpdq netCDF Permute Dimensions Quickly</xrefnodename></pxref>), and the hyperslab
specifications (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>).
@@ -6513,30 +6612,33 @@ performance.
<para>The user specifies the desired chunking policy with the <samp>-P</samp> switch
(or its long option equivalents, <samp>--cnk_plc</samp> and
<samp>--chunk_policy</samp>) and its <var>cnk_plc</var> argument.
-Five chunking policies are currently implemented:&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="682"><samp>all</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="683"><samp>g2d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="684"><samp>g3d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="685"><samp>xpl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="686"><samp>xst</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="687"><samp>cnk_all</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="688"><samp>cnk_g2d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="689"><samp>cnk_g3d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="690"><samp>cnk_xpl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="691"><samp>cnk_xst</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="692"><samp>plc_all</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="693"><samp>plc_g2d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="694"><samp>plc_g3d</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="695"><samp>plc_xpl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="696"><samp>plc_xst</samp></indexterm></cindex>
+As of August, 2014, six chunking policies are currently implemented:&linebreak;
+<cindex index="cp" spaces=" "><indexterm index="cp" number="684"><samp>all</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="685"><samp>g2d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="686"><samp>g3d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="687"><samp>r1d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="688"><samp>xpl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="689"><samp>xst</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="690"><samp>cnk_all</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="691"><samp>cnk_g2d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="692"><samp>cnk_g3d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="693"><samp>cnk_r1d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="694"><samp>cnk_xpl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="695"><samp>cnk_xst</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="696"><samp>plc_all</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="697"><samp>plc_g2d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="698"><samp>plc_g3d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="699"><samp>plc_r1d</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="700"><samp>plc_xpl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="701"><samp>plc_xst</samp></indexterm></cindex>
</para><table commandarg="dfn" spaces=" " endspaces=" ">
-<tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk All Variables [<emph>default</emph>]</itemformat></item>
+<tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk All Variables</itemformat></item>
</tableterm><tableitem><para>Definition: Chunk all variables possible.
For obvious reasons, scalar variables cannot be chunked.&linebreak;
Alternate invocation: <code>ncchunk</code>&linebreak;
<var>cnk_plc</var> key values: <samp>all</samp>, <samp>cnk_all</samp>, <samp>plc_all</samp>&linebreak;
Mnemonic: All&linebreak;
-</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk Variables with at least Two Dimensions</itemformat></item>
+</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk Variables with at least Two Dimensions [<emph>default</emph>]</itemformat></item>
</tableterm><tableitem><para>Definition: Chunk all variables possible with at least two dimensions&linebreak;
Alternate invocation: none&linebreak;
<var>cnk_plc</var> key values: <samp>g2d</samp>, <samp>cnk_g2d</samp>, <samp>plc_g2d</samp>&linebreak;
@@ -6546,6 +6648,15 @@ Mnemonic: <emph>G</emph>reater than or equal to <emph>2</emph> <emph>D</emph>ime
Alternate invocation: none&linebreak;
<var>cnk_plc</var> key values: <samp>g3d</samp>, <samp>cnk_g3d</samp>, <samp>plc_g3d</samp>&linebreak;
Mnemonic: <emph>G</emph>reater than or equal to <emph>3</emph> <emph>D</emph>imensions&linebreak;
+</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk One-Dimensional Record Variables</itemformat></item>
+</tableterm><tableitem><para>Definition: Chunk all 1-D record variables&linebreak;
+Alternate invocation: none&linebreak;
+Any specified (with <samp>--cnk_dmn</samp>) record dimension chunksizes will
+be applied to 1-D record variables (and to no other variables).
+Other dimensions may be chunked with their own <samp>--cnk_dmn</samp> options
+that will apply to all variables.
+<var>cnk_plc</var> key values: <samp>r1d</samp>, <samp>cnk_r1d</samp>, <samp>plc_r1d</samp>&linebreak;
+Mnemonic: <emph>R</emph>ecord <emph>1</emph>-<emph>D</emph> variables&linebreak;
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunk Variables Containing Explicitly Chunked Dimensions</itemformat></item>
</tableterm><tableitem><para>Definition: Chunk all variables possible that contain at least one
dimension whose chunksize was explicitly set with the <samp>--cnk_dmn</samp> option.
@@ -6576,12 +6687,12 @@ Multiple equivalent options are provided to satisfy disparate needs
and tastes of <acronym><acronymword>NCO</acronymword></acronym> users working with scripts and from the
command line.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="697">chunking map</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="698">degenerate dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="699"><var>cnk_map</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="700"><code>-M <var>cnk_map</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="701"><code>--cnk_map <var>cnk_map</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="702"><code>--map <var>cnk_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="702">chunking map</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="703">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="704"><var>cnk_map</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="705"><code>-M <var>cnk_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="706"><code>--cnk_map <var>cnk_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="707"><code>--map <var>cnk_map</var></code></indexterm></cindex>
<para>The chunking algorithms must know the chunksizes of each dimension of
each variable to be chunked.
The correspondence between the input variable shape and the chunksizes
@@ -6590,26 +6701,26 @@ The user specifies the desired chunking map with the <samp>-M</samp> switch
(or its long option equivalents, <samp>--cnk_map</samp> and
<samp>--chunk_map</samp>) and its <var>cnk_map</var> argument.
Four chunking maps are currently implemented:&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="703"><samp>dmn</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="704"><samp>scl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="705"><samp>prd</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="706"><samp>lfp</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="707"><samp>rd1</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="708"><samp>xst</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="709"><samp>rew</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="710"><samp>cnk_dmn</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="711"><samp>cnk_scl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="712"><samp>cnk_prd</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="713"><samp>cnk_lfp</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="714"><samp>cnk_rd1</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="715"><samp>cnk_xst</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="716"><samp>map_dmn</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="717"><samp>map_scl</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="718"><samp>map_prd</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="719"><samp>map_lfp</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="720"><samp>map_rd1</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="721"><samp>map_xst</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="722">Chris Barker</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="708"><samp>dmn</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="709"><samp>scl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="710"><samp>prd</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="711"><samp>lfp</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="712"><samp>rd1</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="713"><samp>xst</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="714"><samp>rew</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="715"><samp>cnk_dmn</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="716"><samp>cnk_scl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="717"><samp>cnk_prd</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="718"><samp>cnk_lfp</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="719"><samp>cnk_rd1</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="720"><samp>cnk_xst</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="721"><samp>map_dmn</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="722"><samp>map_scl</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="723"><samp>map_prd</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="724"><samp>map_lfp</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="725"><samp>map_rd1</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="726"><samp>map_xst</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="727">Chris Barker</indexterm></cindex>
</para><table commandarg="dfn" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="dfn">Chunksize Equals Dimension Size [<emph>default</emph>]</itemformat></item>
</tableterm><tableitem><para>Definition: Chunksize defaults to dimension size.
@@ -6719,7 +6830,25 @@ ncwa -O -4 -D 4 -a time --cnk_plc=g2d --cnk_map=rd1 --cnk_dmn lat,32 \
--cnk_dmn lon,128 dstmch90_clm_0112.nc ~/foo.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="723">record dimension</indexterm></cindex>
+<html endspaces=" ">
+<a name="r1d"></a> <!&textndash; http://nco.sf.net/nco.html#r1d &textndash;>
+</html>
+<para>Chunking policy <samp>r1d</samp> changes the chunksize of 1-D record variables
+(and no other variables) to the specified (with <samp>--cnk_dmn</samp>)
+chunksize.
+Any specified record dimension chunksizes will be applied to 1-D
+record variables only.
+Other dimensions may be chunked with their own <samp>--cnk_dmn</samp> options
+that will apply to all variables.
+For example,
+</para><example endspaces=" ">
+<pre xml:space="preserve">ncks --cnk_plc=r1d --cnk_dmn=time,1000. in.nc out.nc
+</pre></example>
+<para>This sets <code>time</code> chunks to 1000 only in 1-D record variables.
+Without the <samp>r1d</samp> policy, <code>time</code> chunks would change in all
+variables.
+</para>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="728">record dimension</indexterm></cindex>
<para>It is appropriate to conclude by informing users about an aspect of
chunking that may not be expected.
Three types of variables are <emph>always</emph> chunked: Record variables,
@@ -6745,12 +6874,12 @@ variables.
</section>
<node name="Deflation" spaces=" "><nodename>Deflation</nodename><nodenext spaces=" ">MD5 digests</nodenext><nodeprev spaces=" ">Chunking</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Deflation</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="724"><code>-L</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="725"><code>--deflate</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="726"><code>--dfl_lvl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="727">Lempel-Ziv deflation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="728">compression</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="729">deflation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="729"><code>-L</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="730"><code>--deflate</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="731"><code>--dfl_lvl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="732">Lempel-Ziv deflation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="733">compression</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="734">deflation</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncecat</command>, <command>ncflint</command>, <command>ncks</command>, <command>ncpdq</command>,
@@ -6808,15 +6937,15 @@ ncpdq -4 -L 9 in.nc out.nc # Deflated packing (~80% compression)
</section>
<node name="MD5-digests" spaces=" "><nodename>MD5 digests</nodename><nodenext spaces=" ">Buffer sizes</nodenext><nodeprev spaces=" ">Deflation</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>MD5 digests</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="730"><code>--md5_digest</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="731"><code>--md5_dgs</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="732"><code>--md5_wrt_att</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="733"><code>--md5_write_attribute</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="734">integrity</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="735">security</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="736">digest</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="737">hash</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="738">MD5 digest</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="735"><code>--md5_digest</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="736"><code>--md5_dgs</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="737"><code>--md5_wrt_att</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="738"><code>--md5_write_attribute</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="739">integrity</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="740">security</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="741">digest</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="742">hash</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="743">MD5 digest</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability:
<command>ncecat</command>, <command>ncks</command>, <command>ncrcat</command>&linebreak;
@@ -6911,12 +7040,12 @@ We welcome feedback and suggestions from users.
</section>
<node name="Buffer-sizes" spaces=" "><nodename>Buffer sizes</nodename><nodenext spaces=" ">RAM disks</nodenext><nodeprev spaces=" ">MD5 digests</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Buffer sizes</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="739"><code>--bfr_sz_hnt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="740">Buffer sizes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="741">File buffers</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="742"><command>stat() system call</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="743">I/O block size</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="744">System calls</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="744"><code>--bfr_sz_hnt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="745">Buffer sizes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="746">File buffers</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="747"><command>stat() system call</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="748">I/O block size</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="749">System calls</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: All operators&linebreak;
Short options: &linebreak;
@@ -6956,19 +7085,19 @@ ncks: INFO nc__open() opened file with buffer size = 2097152 bytes
</section>
<node name="RAM-disks" spaces=" "><nodename>RAM disks</nodename><nodenext spaces=" ">Packed data</nodenext><nodeprev spaces=" ">Buffer sizes</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>RAM disks</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="745"><code>--ram_all</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="746"><code>--create_ram</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="747"><code>--open_ram</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="748"><code>--diskless_all</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="749"><acronym><acronymword>RAM</acronymword></acronym> disks</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="750"><acronym><acronymword>RAM</acronymword></acronym> files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="751"><code>NC_DISKLESS</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="752">diskless files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="753">memory requirements</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="754">memory available</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="755"><acronym><acronymword>RAM</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="756">swap space</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="757">peak memory usage</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="750"><code>--ram_all</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="751"><code>--create_ram</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="752"><code>--open_ram</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="753"><code>--diskless_all</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="754"><acronym><acronymword>RAM</acronymword></acronym> disks</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="755"><acronym><acronymword>RAM</acronymword></acronym> files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="756"><code>NC_DISKLESS</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="757">diskless files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="758">memory requirements</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="759">memory available</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="760"><acronym><acronymword>RAM</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="761">swap space</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="762">peak memory usage</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: All operators&linebreak;
Short options: &linebreak;
@@ -7017,7 +7146,7 @@ To be safe, use <samp>--open_ram</samp>, <samp>--ram_all</samp>, or
of four) smaller than your available system <acronym><acronymword>RAM</acronymword></acronym>.
See <ref label="Memory-Requirements"><xrefnodename>Memory Requirements</xrefnodename></ref> for further details.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="758"><acronym><acronymword>RAM</acronymword></acronym> variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="763"><acronym><acronymword>RAM</acronymword></acronym> variables</indexterm></cindex>
<para>The <samp>--create_ram</samp> switch causes output files to be created in RAM,
rather than on disk.
These files are copied to disk only when closed, i.e., when the
@@ -7048,17 +7177,19 @@ an arbitrary number (set to one hundred thousand) of files are all
symbolically linked to the same file.
Everything is on the local filesystem (not <acronym><acronymword>DAP</acronymword></acronym>).
</para><example endspaces=" ">
-<pre xml:space="preserve"># Create symbolic links for benchmark
-cd ${DATA}/nco # Do all work here
-for idx in {1..99999}; do
- idx_fmt=`printf "%05d" ${idx}`
- /bin/ln -s ${DATA}/nco/LPRM-AMSR_E_L3_D_SOILM3_V002-20120512T111931Z_20020619.nc \
- ${DATA}/nco/${idx_fmt}.nc
+<verbatim xml:space="preserve">
+# Create symbolic links for benchmark
+cd ${DATA}/nco # Do all work here
+for idx in {1..99999}; do
+ idx_fmt=`printf "%05d" ${idx}`
+ /bin/ln -s ${DATA}/nco/LPRM-AMSR_E_L3_D_SOILM3_V002-20120512T111931Z_20020619.nc \
+ ${DATA}/nco/${idx_fmt}.nc
done
# Benchmark time to ncecat one hundred thousand files
time ncecat --create_ram -O -u time -v ts -d Latitude,40.0 \
- -d Longitude,-105.0 -p ${DATA}/nco -n 99999,5,1 00001.nc ~/foo.nc
-</pre></example>
+ -d Longitude,-105.0 -p ${DATA}/nco -n 99999,5,1 00001.nc ~/foo.nc
+</verbatim>
+</example>
<para>Run normally on a laptop in 201303, this completes in <w>21 seconds</w>.
The <samp>--create_ram</samp> reduces the elapsed time to <w>9 seconds</w>.
Some of this speed may be due to using symlinks and caching.
@@ -7068,9 +7199,9 @@ It is not unreasonable to for <acronym><acronymword>NCO</acronymword></acronym>
like this in a few minutes.
However, there is no substitute for benchmarking with real files.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="759">temporary output files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="760">temporary files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="761"><code>--no_tmp_fl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="764">temporary output files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="765">temporary files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="766"><code>--no_tmp_fl</code></indexterm></cindex>
<para>A completely independent way to reduce time spent writing files is
to refrain from writing temporary output files.
This is accomplished with the <samp>--no_tmp_fl</samp> switch
@@ -7083,16 +7214,16 @@ This is accomplished with the <samp>--no_tmp_fl</samp> switch
</section>
<node name="Packed-data" spaces=" "><nodename>Packed data</nodename><nodenext spaces=" ">Operation Types</nodenext><nodeprev spaces=" ">RAM disks</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Packed data</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="762">packing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="763">unpacking</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="764"><code>add_offset</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="765"><code>scale_factor</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="766"><code>missing_value</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="767"><code>_FillValue</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="768"><command>pack(x)</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="769"><command>unpack(x)</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="770"><code>--hdf_upk</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="771"><code>--hdf_unpack</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="767">packing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="768">unpacking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="769"><code>add_offset</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="770"><code>scale_factor</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="771"><code>missing_value</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="772"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="773"><command>pack(x)</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="774"><command>unpack(x)</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="775"><code>--hdf_upk</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="776"><code>--hdf_unpack</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncflint</command>, <command>ncpdq</command>, <command>ncra</command>, <command>ncwa</command>&linebreak;
@@ -7195,8 +7326,8 @@ unpacked data, i.e., <code>int</code>, <code>float</code> or <code>double</code>
<a name="hdf_upk"></a> <!&textndash; http://nco.sf.net/nco.html#hdf_upk &textndash;>
<a name="hdf_unpack"></a> <!&textndash; http://nco.sf.net/nco.html#hdf_unpack &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="772">interoperability</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="773"><acronym><acronymword>HDF</acronymword></acronym> unpacking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="777">interoperability</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="778"><acronym><acronymword>HDF</acronymword></acronym> unpacking</indexterm></cindex>
<para>Most files originally written in <acronym><acronymword>HDF</acronymword></acronym> format use the
<acronym><acronymword>HDF</acronymword></acronym> packing/unpacking algorithm.
This algorithm is incompatible with the netCDF packing algorithm
@@ -7300,27 +7431,27 @@ Pack and unpack individual variables with <command>ncpdq</command> and the
</section>
<node name="Operation-Types" spaces=" "><nodename>Operation Types</nodename><nodenext spaces=" ">Type Conversion</nodenext><nodeprev spaces=" ">Packed data</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Operation Types</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="774">operation types</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="775"><code>avg</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="776"><code>sqravg</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="777"><code>avgsqr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="778"><code>min</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="779"><code>max</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="780"><code>rmssdn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="781"><code>rms</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="782"><code>ttl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="783"><code>sqrt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="784">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="785">mean</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="786">total</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="787">minimum</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="788">maximum</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="789">root-mean-square</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="790">standard deviation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="791">variance</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="792"><code>-y <var>op_typ</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="793"><code>--operation <var>op_typ</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="794"><code>--op_typ <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="779">operation types</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="780"><code>avg</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="781"><code>sqravg</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="782"><code>avgsqr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="783"><code>min</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="784"><code>max</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="785"><code>rmssdn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="786"><code>rms</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="787"><code>ttl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="788"><code>sqrt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="789">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="790">mean</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="791">total</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="792">minimum</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="793">maximum</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="794">root-mean-square</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="795">standard deviation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="796">variance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="797"><code>-y <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="798"><code>--operation <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="799"><code>--op_typ <var>op_typ</var></code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncap2</command>, <command>ncra</command>, <command>nces</command>, <command>ncwa</command>&linebreak;
Short options: <samp>-y</samp>&linebreak;
@@ -7351,7 +7482,7 @@ Set <var>op_typ</var> to the abbreviated key for the corresponding operation:
</tableterm><tableitem><para>Sum of values
</para></tableitem></tableentry></table>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="795">coordinate variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="800">coordinate variable</indexterm></cindex>
<para><acronym><acronymword>NCO</acronymword></acronym> assumes coordinate variables represent grid axes, e.g.,
longitude.
The only rank-reduction which makes sense for coordinate variables
@@ -7585,7 +7716,7 @@ ncwa -y rms -v prs_sfc -a time in.nc foo.nc
<noindent></noindent>
<para>The previous two commands give the same answer but <command>ncra</command> is
preferred because it has a smaller memory footprint.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="796">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="801">degenerate dimension</indexterm></cindex>
A dimension of size one is said to be <dfn>degenerate</dfn>.
By default, <command>ncra</command> leaves the (degenerate) <code>time</code>
dimension in the output file (which is usually useful) whereas
@@ -7610,7 +7741,7 @@ We can now find the three month maximium surface pressure at every point.
<a name="xmp_sdn"></a> <!&textndash; http://nco.sf.net/nco.html#xmp_sdn &textndash;>
</html>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="797">standard deviation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="802">standard deviation</indexterm></cindex>
<para>It is possible to use a combination of these operations to compute
the variance and standard deviation of a field stored in a single file
or across multiple files.
@@ -7701,7 +7832,7 @@ less required by the <command>ncbo</command> operation in the third step.
</section>
<node name="Type-Conversion" spaces=" "><nodename>Type Conversion</nodename><nodenext spaces=" ">Batch Mode</nodenext><nodeprev spaces=" ">Operation Types</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Type Conversion</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="798">type conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="803">type conversion</indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability (automatic type conversion): <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
<command>ncflint</command>, <command>ncra</command>, <command>ncwa</command>&linebreak;
@@ -7710,10 +7841,10 @@ Availability (manual type conversion): <command>nces</command>, <command>ncra</c
Short options: None&linebreak;
Long options: <samp>--dbl</samp>, <samp>--flt</samp>, <samp>--rth_dbl</samp>, <samp>--rth_flt</samp>&linebreak;
</para></cartouche>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="799">promotion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="800">demotion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="801">automatic type conversion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="802">manual type conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="804">promotion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="805">demotion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="806">automatic type conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="807">manual type conversion</indexterm></cindex>
<para>Type conversion refers to the casting or coercion of one fundamental or
atomic data type to another, e.g., converting <code>NC_SHORT</code> (two
bytes) to <code>NC_DOUBLE</code> (eight bytes).
@@ -7793,7 +7924,7 @@ This is why type conversion is limited to the operators <command>ncap2</command>
<command>ncwa</command>.
</para></listitem><listitem spaces=" "><para>The arithmetic operation could benefit from type conversion.
Operations that could benefit include averaging, summation, or any
-"hard" arithmetic that could overflow or underflow.
+&textldquo;hard&textrdquo; arithmetic that could overflow or underflow.
Larger representable sums help avoid overflow, and more precision
helps to avoid underflow.
Type conversion does not benefit searching for minima and maxima
@@ -7827,7 +7958,7 @@ Similarly, the total (e.g., <samp>-y ttl</samp>) of <code>17000s</code> and
the final result (the true total) of <math>34000</math> is outside the range
of type <code>NC_SHORT</code>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="803"><code>trunc()</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="808"><code>trunc()</code></indexterm></cindex>
<para>After arithmetic is computed in double-precision for promoted variables,
the intermediate double-precision values must be demoted to the
variables&textrsquo; original storage type (e.g., from <code>NC_DOUBLE</code> to
@@ -7835,7 +7966,7 @@ variables&textrsquo; original storage type (e.g., from <code>NC_DOUBLE</code> to
<acronym><acronymword>NCO</acronymword></acronym> has handled this demotion in three ways in its history.
Prior to October, 2011 (version 4.0.8), <acronym><acronymword>NCO</acronymword></acronym> employed the
<w>C library</w> truncate function, <code>trunc()</code>
-<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="804">C language</indexterm></cindex>
+<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="809">C language</indexterm></cindex>
<para>The actual type conversions with trunction were handled by intrinsic
type conversion, so the <code>trunc()</code> function was never explicitly
called, although the results would be the same if it were.</para></footnote>.
@@ -7848,7 +7979,7 @@ integer!
Yet truncation is how the <w>C language</w> performs implicit conversion of
real numbers to integers.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="805">Neil Davis</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="810">Neil Davis</indexterm></cindex>
<para><acronym><acronymword>NCO</acronymword></acronym> stopped using truncation for demotion when an alert user
(Neil Davis) informed us that this caused a small bias in the packing
algorithm employed by <command>ncpdq</command>.
@@ -7863,11 +7994,11 @@ These functions round <var>x</var> to the nearest integer, halfway cases away
from zero.
The problem with <code>lround()</code> is that it always rounds real values
ending in <code>.5</code> away from zero.
-This rounds, for example, <code>1.5d</code> and <code>2.5d</code> to <code>1s</code>
-and <code>2s</code>, respectively.
+This rounds, for example, <code>1.5d</code> and <code>2.5d</code> to <code>2s</code>
+and <code>3s</code>, respectively.
</para>
<findex index="fn" spaces=" "><indexterm index="fn" number="13" mergedindex="cp"><code>lrint()</code>.</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="806"><acronym><acronymword>IEEE</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="811"><acronym><acronymword>IEEE</acronymword></acronym></indexterm></cindex>
<para>Since April, 2013 (version 4.3.0), <acronym><acronymword>NCO</acronymword></acronym> has employed the
other <w>C library</w> family of rounding functions, <code>lrint()</code>.
This algorithm rounds <var>x</var> to the nearest integer, using the current
@@ -7895,12 +8026,12 @@ stores it on disk as
</subsection>
<node name="Promoting-Single_002dprecision-to-Double" spaces=" "><nodename>Promoting Single-precision to Double</nodename><nodenext spaces=" ">Manual type conversion</nodenext><nodeprev spaces=" ">Automatic type conversion</nodeprev><nodeup spaces=" ">Type Conversion</nodeup></node>
<subsection spaces=" "><sectiontitle>Promoting Single-precision to Double</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="807">promotion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="808">implicit conversion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="809"><code>--dbl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="810"><code>--rth_dbl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="811"><code>--flt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="812"><code>--rth_flt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="812">promotion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="813">implicit conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="814"><code>--dbl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="815"><code>--rth_dbl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="816"><code>--flt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="817"><code>--rth_flt</code></indexterm></cindex>
<para>Promotion of real numbers from single- to double-precision is
fundamental to scientific computing.
When it should occur depends on the precision of the inputs and the
@@ -7911,18 +8042,18 @@ More, err, precisely, the <acronym><acronymword>IEEE</acronymword></acronym> sin
gives from <w>6 to 9</w> significant decimal digits precision
<footnote><para>According to Wikipedia&textrsquo;s summary of <acronym><acronymword>IEEE</acronymword></acronym> standard
754, &textldquo;If a decimal string with at most 6 significant digits is
-converted to IEEE 754 single-precision and then converted back to the
+converted to <acronym><acronymword>IEEE</acronymword></acronym> 754 single-precision and then converted back to the
same number of significant decimal, then the final string should match
-the original; and if an IEEE 754 single-precision is converted to a
+the original; and if an <acronym><acronymword>IEEE</acronymword></acronym> 754 single-precision is converted to a
decimal string with at least 9 significant decimal and then converted
back to single, then the final number must match the original&textrdquo;.</para></footnote>.
And the <acronym><acronymword>IEEE</acronymword></acronym> double-precision representation
gives from <w>15 to 17</w> significant decimal digits precision
<footnote><para>According to Wikipedia&textrsquo;s summary of <acronym><acronymword>IEEE</acronymword></acronym> standard
754, &textldquo;If a decimal string with at most 15 significant digits is
-converted to IEEE 754 double-precision representation and then converted
+converted to <acronym><acronymword>IEEE</acronymword></acronym> 754 double-precision representation and then converted
back to a string with the same number of significant digits, then the
-final string should match the original; and if an IEEE 754 double
+final string should match the original; and if an <acronym><acronymword>IEEE</acronymword></acronym> 754 double
precision is converted to a decimal string with at least 17 significant
digits and then converted back to double, then the final number must
match the original&textrdquo;.</para></footnote>.
@@ -7931,8 +8062,8 @@ precision than single-precision numbers.
</para>
<para>Given these properties, there are at least two possible arithmetic
conventions for the treatment of real numbers:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="813">C language</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="814">Fortran</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="818">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="819">Fortran</indexterm></cindex>
</para><enumerate first="1" endspaces=" ">
<listitem spaces=" "><para>Conservative, aka Fortran Convention
Automatic type conversion during arithmetic in the Fortran language is,
@@ -8038,9 +8169,9 @@ seven significant figures for single precision floats (<code>tpt_flt</code>),
and sixteen significant figures for double precision (<code>tpt_dbl</code>).
The input precision determines the answer precision.
</para>
-<para>IEEE arithmetic guarantees that two methods will produce bit-for-bit
-identical answers only if they compute the same operations in the same
-order.
+<para><acronym><acronymword>IEEE</acronymword></acronym> arithmetic guarantees that two methods will produce
+bit-for-bit identical answers only if they compute the same operations
+in the same order.
Bit-for-bit identical answers may also occur by happenstance when
rounding errors exactly compensate one another.
This is demonstrated by repeating the example above with the
@@ -8103,9 +8234,9 @@ degrade the precision in such situtations.
Double-precision arithmetic mititgates this problem, so <samp>--dbl</samp>
would be warranted.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="815"><acronym><acronymword>TREFHT</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="816"><acronym><acronymword>CAM3</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="817"><acronym><acronymword>GCM</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="820"><acronym><acronymword>TREFHT</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="821"><acronym><acronymword>CAM3</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="822"><acronym><acronymword>GCM</acronymword></acronym></indexterm></cindex>
<para>This can be seen with another example, averaging a global surface
temperature field with <command>ncwa</command>.
The input contains a single-precision global temperature field
@@ -8184,8 +8315,8 @@ It means that the global mean temperature changes scientists are looking
for are comparable in size to the numerical artifacts produced by the
averaging procedure.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="818">rounding</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="819">random walk</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="823">rounding</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="824">random walk</indexterm></cindex>
<para>Why are the single-precision numerical artifacts so large?
Each global average is the result of multiplying almost 15,000 elements
each by its weight, summing those, and then dividing by the summed
@@ -8194,7 +8325,7 @@ Thus about 50,000 single-precision floating point operations caused
the loss of two to three significant digits of precision.
The net error of a series of independent rounding errors is a random
walk phenomena
-<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="820">Michael Prather</indexterm></cindex>
+<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="825">Michael Prather</indexterm></cindex>
<para>Thanks to <w>Michael J.</w> Prather for explaining this to me.</para></footnote>.
Successive rounding errors displace the answer further from the truth.
An ensemble of such averages will, on average, have no net bias.
@@ -8203,8 +8334,8 @@ rounding errors is zero.
And the error of any given sequence of rounding errors obeys, for large
series, a Gaussian distribution centered on zero.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="821">mantissa</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="822">exponent</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="826">mantissa</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="827">exponent</indexterm></cindex>
<para>Single-precision numbers use three of their four eight-bit bytes to
represent the mantissa so the smallest representable single-precision
mantissa is <math>\epsilon \equiv 2^{-23} = 1.19209 \times 10^{-7}</math>.
@@ -8237,7 +8368,7 @@ agreement.
<!-- c P(>=25500,50000)= ? -->
<!-- c fxm: Use Gaussian distribution/Random Walk -->
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="823">beer</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="828">beer</indexterm></cindex>
<para>The <acronym><acronymword>NCO</acronymword></acronym> results have been independently validated to the
extent possible in three other languages:
<w>C</w>, Matlab, and <acronym><acronymword>NCL</acronymword></acronym>.
@@ -8310,7 +8441,7 @@ Please let us know what you think of the selected defaults and options.
</subsection>
<node name="Manual-type-conversion" spaces=" "><nodename>Manual type conversion</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Promoting Single-precision to Double</nodeprev><nodeup spaces=" ">Type Conversion</nodeup></node>
<subsection spaces=" "><sectiontitle>Manual type conversion</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="824"><command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="829"><command>ncap2</command></indexterm></cindex>
<para><command>ncap2</command> provides intrinsic functions for performing manual type
conversions.
This, for example, converts variable <code>tpt</code> to external type
@@ -8329,17 +8460,17 @@ external type <code>NC_DOUBLE</code> (a C-type <code>double</code>).
</section>
<node name="Batch-Mode" spaces=" "><nodename>Batch Mode</nodename><nodenext spaces=" ">History Attribute</nodenext><nodeprev spaces=" ">Type Conversion</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Batch Mode</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="825">batch mode</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="826">overwriting files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="827">appending to files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="828">force overwrite</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="829">force append</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="830"><code>-O</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="831"><code>-A</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="832"><code>--overwrite</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="833"><code>--ovr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="834"><code>--apn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="835"><code>--append</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="830">batch mode</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="831">overwriting files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="832">appending to files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="833">force overwrite</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="834">force append</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="835"><code>-O</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="836"><code>-A</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="837"><code>--overwrite</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="838"><code>--ovr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="839"><code>--apn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="840"><code>--append</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: All operators&linebreak;
Short options: <samp>-O</samp>, <samp>-A</samp>&linebreak;
@@ -8370,13 +8501,13 @@ already contain the appended dimensions.
</section>
<node name="History-Attribute" spaces=" "><nodename>History Attribute</nodename><nodenext spaces=" ">File List Attributes</nodenext><nodeprev spaces=" ">Batch Mode</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>History Attribute</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="836"><code>history</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="837">timestamp</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="838">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="839">attributes, global</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="840"><code>-h</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="841"><code>--hst</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="842"><code>--history</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="841"><code>history</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="842">timestamp</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="843">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="844">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="845"><code>-h</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="846"><code>--hst</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="847"><code>--history</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: All operators&linebreak;
Short options: <samp>-h</samp>&linebreak;
@@ -8403,7 +8534,7 @@ attributes.
When more than one global attribute fits the case-insensitive search
for "history", the first one found will be used.
<code>history</code> attribute
-<cindex index="cp" spaces=" "><indexterm index="cp" number="843"><command>ncatted</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="848"><command>ncatted</command></indexterm></cindex>
To avoid information overkill, all operators have an optional switch
(<samp>-h</samp>, <samp>--hst</samp>, or <samp>--history</samp>) to override
automatically appending the <code>history</code> attribute
@@ -8418,14 +8549,14 @@ Note that the <samp>-h</samp> switch also turns off writing the
</section>
<node name="File-List-Attributes" spaces=" "><nodename>File List Attributes</nodename><nodenext spaces=" ">CF Conventions</nodenext><nodeprev spaces=" ">History Attribute</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>File List Attributes</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="844"><code>nco_input_file_list</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="845"><code>nco_input_file_number</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="846"><code>stdin</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="847">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="848">attributes, global</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="849"><code>-H</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="850"><code>--fl_lst_in</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="851"><code>--file_list</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="849"><code>nco_input_file_list</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="850"><code>nco_input_file_number</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="851"><code>stdin</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="852">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="853">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="854"><code>-H</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="855"><code>--fl_lst_in</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="856"><code>--file_list</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>nces</command>, <command>ncecat</command>, <command>ncra</command>, <command>ncrcat</command>&linebreak;
Short options: <samp>-H</samp>&linebreak;
@@ -8470,21 +8601,21 @@ may amount to many thousands of filenames in a metadata attribute.
</section>
<node name="CF-Conventions" spaces=" "><nodename>CF Conventions</nodename><nodenext spaces=" ">ARM Conventions</nodenext><nodeprev spaces=" ">File List Attributes</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle><acronym><acronymword>CF</acronymword></acronym> Conventions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="852"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="853"><acronym><acronymword>CCSM</acronymword></acronym> conventions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="854">UDUnits</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="855"><code>ORO</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="856"><code>area</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="857"><code>datesec</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="858"><code>date</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="859"><code>gw</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="860"><code>hyai</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="861"><code>hyam</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="862"><code>hybi</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="863"><code>hybm</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="864"><code>lat_bnds</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="865"><code>lon_bnds</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="866"><code>msk_*</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="857"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="858"><acronym><acronymword>CCSM</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="859">UDUnits</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="860"><code>ORO</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="861"><code>area</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="862"><code>datesec</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="863"><code>date</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="864"><code>gw</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="865"><code>hyai</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="866"><code>hyam</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="867"><code>hybi</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="868"><code>hybm</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="869"><code>lat_bnds</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="870"><code>lon_bnds</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="871"><code>msk_*</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncbo</command>, <command>nces</command>, <command>ncecat</command>,
<command>ncflint</command>, <command>ncpdq</command>, <command>ncra</command>, <command>ncwa</command>&linebreak;
@@ -8502,8 +8633,8 @@ Nevertheless, we refer to all such metadata collectively as <acronym><acronymwor
metadata.
Skip this section if you never work with <acronym><acronymword>CF</acronymword></acronym> metadata.
</para>
-<para>The <acronym><acronymword>CF</acronymword></acronym> netCDF conventions are described
-<uref><urefurl>http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
+<para>The latest <acronym><acronymword>CF</acronymword></acronym> netCDF conventions are described
+<uref><urefurl>http://cfconventions.org/1.6.html</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
Most <acronym><acronymword>CF</acronymword></acronym> netCDF conventions are transparent to <acronym><acronymword>NCO</acronymword></acronym>
<footnote spaces="\n"><para>The exception is appending/altering the attributes <code>x_op</code>,
<code>y_op</code>, <code>z_op</code>, and <code>t_op</code> for variables which have been
@@ -8548,7 +8679,7 @@ variables because of their usual meaning in <acronym><acronymword>CF</acronymwor
These variables contain scalar metadata such as the resolution of the
host geophysical model and it makes no sense to change their values.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="867">non-coordinate grid properties</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="872">non-coordinate grid properties</indexterm></cindex>
<para>Furthermore, the <dfn>size and rank-preserving arithmetic operators</dfn> try
not to operate on certain grid properties.
These operators are <command>ncap2</command>, <command>ncbo</command>, <command>nces</command>,
@@ -8592,12 +8723,12 @@ or alter the <code>Conventions</code> attribute.
<a name="cnv_CF_bnd"></a> <!&textndash; http://nco.sf.net/nco.html#cnv_CF_bnd &textndash;>
<a name="bnd"></a> <!&textndash; http://nco.sf.net/nco.html#bnd &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="868"><code>bounds</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="869">bounds convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="873"><code>bounds</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="874">bounds convention</indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.0.8 (April, 2011), <acronym><acronymword>NCO</acronymword></acronym>
supports the <acronym><acronymword>CF</acronymword></acronym> <code>bounds</code> convention for cell boundaries
described
-<uref><urefurl>http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#cell-boundaries</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
+<uref><urefurl>http://cfconventions.org/1.6.html#cell-boundaries</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
This convention allows coordinate variables (including multidimensional
coordinates) to describe the boundaries of their cells.
This is done by naming the variable which contains the bounds in
@@ -8607,31 +8738,54 @@ NCO-generated subsets of <acronym><acronymword>CF</acronymword></acronym>-compli
attributes will include the coordinates specified by the <code>bounds</code>
attribute, if any.
Hence the subsets will themselves be <acronym><acronymword>CF</acronymword></acronym>-compliant.
+Bounds are subject to the user-specified override switches
+(including <samp>-c</samp> and <samp>-C</samp>) described in
+<ref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></ref>.
+</para>
+<html endspaces=" ">
+<a name="cnv_CF_ncl"></a> <!&textndash; http://nco.sf.net/nco.html#cnv_CF_ncl &textndash;>
+<a name="ncl"></a> <!&textndash; http://nco.sf.net/nco.html#ncl &textndash;>
+</html>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="875"><code>ancillary_variables</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="876">ancillary variables convention</indexterm></cindex>
+<para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.4.5 (July, 2014), <acronym><acronymword>NCO</acronymword></acronym>
+supports the <acronym><acronymword>CF</acronymword></acronym> <code>ancillary_variables</code> convention for
+described
+<uref><urefurl>http://cfconventions.org/1.6.html#ancillary-data</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
+This convention allows ancillary variables to be associated with one or
+more primary variables.
+<acronym><acronymword>NCO</acronymword></acronym> attaches any such variables to the extraction list along
+with the primary variable and its usual (one-dimensional) coordinates,
+if any.
+Ancillary variables are subject to the user-specified override switches
+(including <samp>-c</samp> and <samp>-C</samp>) described in
+<ref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></ref>.
</para>
<html endspaces=" ">
<a name="cnv_CF_crd"></a> <!&textndash; http://nco.sf.net/nco.html#cnv_CF_crd &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="870"><code>coordinates</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="871">coordinates convention</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="872">coordinate variable</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="873">auxiliary coordinates</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="874">subsetting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="875"><code>-C</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="876"><code>-c</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="877"><code>--no-coords</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="878"><code>--no-crd</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="879"><code>--coords</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="880"><code>--crd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="877"><code>coordinates</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="878">coordinates convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="879">coordinate variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="880">auxiliary coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="881">subsetting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="882"><code>-C</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="883"><code>-c</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="884"><code>--no-coords</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="885"><code>--no-crd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="886"><code>--coords</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="887"><code>--crd</code></indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> version 3.9.6 (January, 2009), <acronym><acronymword>NCO</acronymword></acronym>
supports the <acronym><acronymword>CF</acronymword></acronym> <code>coordinates</code> convention described
-<uref><urefurl>http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.6/cf-conventions.html#coordinate-system</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
+<uref><urefurl>http://cfconventions.org/1.6.html#coordinate-system</urefurl><urefdesc spaces=" ">here</urefdesc></uref>.
This convention allows variables to specify additional coordinates
(including multidimensional coordinates) in a space-separated string
attribute named <code>coordinates</code>.
-NCO attaches any such coordinates to the extraction list along with
-variable and its usual (one-dimensional) coordinates, if any.
-These auxiliary coordinates are subject to the user-specified overrides
-described in <ref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></ref>.
+<acronym><acronymword>NCO</acronymword></acronym> attaches any such coordinates to the extraction list along
+with variable and its usual (one-dimensional) coordinates, if any.
+These auxiliary coordinates are subject to the user-specified override
+switches (including <samp>-c</samp> and <samp>-C</samp>) described in
+<ref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></ref>.
</para>
<html endspaces=" ">
<a name="cnv_CF_cll_mth"></a> <!&textndash; http://nco.sf.net/nco.html#cnv_CF_cll_mth &textndash;>
@@ -8639,15 +8793,15 @@ described in <ref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetti
<a name="no_cll_mth"></a> <!&textndash; http://nco.sf.net/nco.html#no_cll_mth &textndash;>
<a name="cell_methods"></a> <!&textndash; http://nco.sf.net/nco.html#cell_methods &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="881"><code>cell_methods</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="882"><code>--cll_mth</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="883"><code>--no_cll_mth</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="884"><code>--cell_methods</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="885"><code>--no_cell_methods</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="886">cell methods convention</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="888"><code>cell_methods</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="889"><code>--cll_mth</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="890"><code>--no_cll_mth</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="891"><code>--cell_methods</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="892"><code>--no_cell_methods</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="893">cell methods convention</indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.4.2 (February, 2014), <acronym><acronymword>NCO</acronymword></acronym>
supports some of the <acronym><acronymword>CF</acronymword></acronym> <code>cell_methods</code>
-<uref><urefurl>http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.7-draft1/cf-conventions.html#cell-methods</urefurl><urefdesc spaces=" ">convention</urefdesc></uref>
+<uref><urefurl>http://cfconventions.org/1.6.html#cell-methods</urefurl><urefdesc spaces=" ">convention</urefdesc></uref>
to describe the analysis procedures that have been applied to data.
The convention creates (or appends to an existing) <code>cell_methods</code>
attribute a space-separated list of couplets of the form <var>dmn: op</var>
@@ -8680,10 +8834,10 @@ These options are only available in the operators <command>ncwa</command> and
</section>
<node name="ARM-Conventions" spaces=" "><nodename>ARM Conventions</nodename><nodenext spaces=" ">Operator Version</nodenext><nodeprev spaces=" ">CF Conventions</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle><acronym><acronymword>ARM</acronymword></acronym> Conventions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="887"><acronym><acronymword>ARM</acronymword></acronym> conventions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="888"><code>time_offset</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="889"><code>base_time</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="890"><code>time</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="894"><acronym><acronymword>ARM</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="895"><code>time_offset</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="896"><code>base_time</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="897"><code>time</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: <command>ncrcat</command>&linebreak;
Short options: None&linebreak;
@@ -8719,9 +8873,9 @@ The values of <code>time</code> are defined by the <acronym><acronymword>ARM</ac
<math><var>time</var> = <var>base_time</var> + <var>time_offset</var></math>.
Thus, if <var>output-file</var> contains the <code>time_offset</code>
variable, it will also contain the <code>time</code> coordinate.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="891"><code>history</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="892">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="893">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="898"><code>history</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="899">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="900">attributes, global</indexterm></cindex>
<w>A short</w> message is added to the <code>history</code> global attribute
whenever these <acronym><acronymword>ARM</acronymword></acronym>-specific procedures are executed.
</para>
@@ -8732,12 +8886,12 @@ whenever these <acronym><acronymword>ARM</acronymword></acronym>-specific proced
</section>
<node name="Operator-Version" spaces=" "><nodename>Operator Version</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">ARM Conventions</nodeprev><nodeup spaces=" ">Common features</nodeup></node>
<section spaces=" "><sectiontitle>Operator Version</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="894">version</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="895"><acronym><acronymword>RCS</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="896"><code>-r</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="897"><code>--revision</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="898"><code>--version</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="899"><code>--vrs</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="901">version</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="902"><acronym><acronymword>RCS</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="903"><code>-r</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="904"><code>--revision</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="905"><code>--version</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="906"><code>--vrs</code></indexterm></cindex>
<cartouche endspaces=" ">
<para>Availability: All operators&linebreak;
Short options: <samp>-r</samp>&linebreak;
@@ -8771,7 +8925,7 @@ This tells you that <command>ncks</command> contains all patches up to version
<para>This chapter presents reference pages for each of the operators
individually.
The operators are presented in alphabetical order.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="900">command line switches</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="907">command line switches</indexterm></cindex>
All valid command line switches are included in the syntax statement.
Recall that descriptions of many of these command line switches are
provided only in <ref label="Common-features"><xrefnodename>Common features</xrefnodename></ref>, to avoid redundancy.
@@ -8800,12 +8954,11 @@ described in any detail in the sections below.
</html>
<node name="ncap2-netCDF-Arithmetic-Processor" spaces=" "><nodename>ncap2 netCDF Arithmetic Processor</nodename><nodenext spaces=" ">ncatted netCDF Attribute Editor</nodenext><nodeprev spaces=" ">Operator Reference Manual</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncap2</command> netCDF Arithmetic Processor</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="901">parser</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="902">lexer</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="903">arithmetic processor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="908">parser</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="909">lexer</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="910">arithmetic processor</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="14" mergedindex="cp">ncap</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="15" mergedindex="cp">ncap2</indexterm></findex>
-
<cartouche endspaces=" ">
<para><command>ncap2</command> understands a relatively full-featured
language of operations, including loops, conditionals, arrays,
@@ -8844,11 +8997,11 @@ This documentation refers to <command>ncap2</command>, which has a superset of
the <command>ncap</command> functionality.
Eventually <command>ncap</command> will be deprecated in favor <command>ncap2</command>.
<command>ncap2</command> may be renamed <command>ncap</command> in 2013.</para></footnote>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="904">script file</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="905"><code>--script-file</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="906"><code>--fl_spt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="907"><code>--script</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="908"><code>--spt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="911">script file</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="912"><code>--script-file</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="913"><code>--fl_spt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="914"><code>--script</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="915"><code>--spt</code></indexterm></cindex>
The processing instructions are contained either in the <acronym><acronymword>NCO</acronymword></acronym>
script file <file>fl.nco</file> or in a sequence of command line arguments.
The options <samp>-s</samp> (or long options <samp>--spt</samp> or <samp>--script</samp>)
@@ -8857,7 +9010,7 @@ are used for in-line scripts and <samp>-S</samp> (or long options
filename where (usually multiple) scripting commands are pre-stored.
<command>ncap2</command> was written to perform arbitrary algebraic
transformations of data and archive the results as easily as possible.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="909">derived fields</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="916">derived fields</indexterm></cindex>
<xref label="Missing-Values"><xrefnodename>Missing Values</xrefnodename></xref>, for treatment of missing values.
The results of the algebraic manipulations are called
<dfn>derived fields</dfn>.
@@ -8868,7 +9021,7 @@ variables to be operated on as an argument to <samp>-v</samp>
Rather, the <samp>-v</samp> switch takes no arguments and indicates
that <command>ncap2</command> should output <emph>only</emph> user-defined variables.
<command>ncap2</command> neither accepts nor understands the <var>-x</var> switch.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="910">appending variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="917">appending variables</indexterm></cindex>
NB: As of 20120515, <command>ncap2</command> is unable to append to files that
already contain the appended dimensions.
</para>
@@ -8909,7 +9062,7 @@ already contain the appended dimensions.
</html>
<para>Defining new variables in terms of existing variables is a powerful
feature of <command>ncap2</command>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="911">derived fields</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="918">derived fields</indexterm></cindex>
Derived fields inherit the metadata (i.e., attributes) of their
ancestors, if any, in the script or input file.
When the derived field is completely new (no identically-named ancestors
@@ -8929,49 +9082,49 @@ using left hand casting.
</html>
<node name="Syntax-of-ncap2-statements" spaces=" "><nodename>Syntax of ncap2 statements</nodename><nodenext spaces=" ">Expressions</nodenext><nodeprev spaces=" ">ncap2 netCDF Arithmetic Processor</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Syntax of <command>ncap2</command> statements</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="912">statement</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="913">syntax</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="919">statement</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="920">syntax</indexterm></cindex>
<para>Mastering <command>ncap2</command> is relatively simple.
Each valid statement <var>statement</var> consists of standard forward
algebraic expression.
The <file>fl.nco</file>, if present, is simply a list of such statements,
whitespace, and comments.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="914">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="921">C language</indexterm></cindex>
The syntax of statements is most like the computer <w>language C</w>.
The following characteristics <w>of C</w> are preserved:
</para><table commandarg="asis" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="asis">Array syntax</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="915">array syntax</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="916"><code>[]</code> (array delimiters)</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="922">array syntax</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="923"><code>[]</code> (array delimiters)</indexterm></cindex>
<para>Arrays elements are placed within <code>[]</code> characters;
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Array indexing</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="917">array indexing</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="924">array indexing</indexterm></cindex>
<para>Arrays are 0-based;
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Array storage</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="918">array storage</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="925">array storage</indexterm></cindex>
<para>Last dimension is most rapidly varying;
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Assignment statements</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="919">assignment statement</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="920">semi-colon</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="921"><code>;</code> (end of statement)</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="926">assignment statement</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="927">semi-colon</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="928"><code>;</code> (end of statement)</indexterm></cindex>
<para><w>A semi</w>-colon <samp>;</samp> indicates the end of an assignment statement.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Comments</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="922">comments</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="923"><code>/*...*/</code> (comment)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="924"><code>//</code> (comment)</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="929">comments</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="930"><code>/*...*/</code> (comment)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="931"><code>//</code> (comment)</indexterm></cindex>
<para>Multi-line comments are enclosed within <code>/* */</code> characters.
Single line comments are preceded by <code>//</code> characters.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Nesting</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="925">including files</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="926">nesting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="927"><code>#include</code></indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="932">including files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="933">nesting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="934"><code>#include</code></indexterm></cindex>
<para>Files may be nested in scripts using <code>#include <var>script</var></code>.
Note that the <code>#include</code> command is not followed by a semi-colon
because it is a pre-processor directive, not an assignment statement.
The filename <file>script</file> is interpreted relative to the run directory.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Attribute syntax</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="928">attribute syntax</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="929"><code>&arobase;</code> (attribute)</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="935">attribute syntax</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="936"><code>&arobase;</code> (attribute)</indexterm></cindex>
<para>The at-sign <code>&arobase;</code> is used to delineate an attribute name from a
variable name.
</para></tableitem></tableentry></table>
@@ -8981,12 +9134,12 @@ variable name.
</html>
</subsection>
<node name="Expressions" spaces=" "><nodename>Expressions</nodename><nodenext spaces=" ">Dimensions</nodenext><nodeprev spaces=" ">Syntax of ncap2 statements</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="930">expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="937">expressions</indexterm></cindex>
<subsection spaces=" "><sectiontitle>Expressions</sectiontitle>
<para>Expressions are the fundamental building block of <command>ncap2</command>.
Expressions are composed of variables, numbers, literals, and
attributes.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="931">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="938">C language</indexterm></cindex>
The following <w>C operators</w> are &textldquo;overloaded&textrdquo; and work with scalars
and multi-dimensional arrays:
</para><example endspaces=" ">
@@ -9015,8 +9168,8 @@ When either type is <code>NC_DOUBLE</code>, the result is also <code>NC_DOUBLE</
</para></listitem></itemize>
<!-- c csz got to here editing -->
-<cindex index="cp" spaces=" "><indexterm index="cp" number="932">broadcasting variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="933">rank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="939">broadcasting variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="940">rank</indexterm></cindex>
<para><strong>Rank</strong>
</para><itemize commandarg="bullet" spaces=" " endspaces=" "><itemprepend><formattingcommand command="bullet"/> </itemprepend>
<listitem spaces=" "><prepend>•</prepend><para>The Rank of the result is generally equal to Rank of the operand
@@ -9039,7 +9192,8 @@ to precision and rank.&linebreak;
Examples:
</para>
<example endspaces=" ">
-<pre xml:space="preserve">dimensions: time=10, lat=2, lon=4
+<verbatim xml:space="preserve">
+dimensions: time=10, lat=2, lon=4
Suppose we have the two variables:
double P(time,lat,lon);
@@ -9064,15 +9218,16 @@ PZ0 =
Once the expression is evaluated then PZ will be of type double;
Consider now
- start=four-att_var&arobase;double_att; // start =-69 and is of type intger;
+ start=four-att_var at double_att; // start =-69 and is of type intger;
four_pow=four^3.0f // four_pow=64 and is of type float
three_nw=three_dmn_var_sht*1.0f; // type is now float
- start&arobase;n1=att_var&arobase;short_att*att_var&arobase;int_att;
- // start&arobase;n1=5329 and is type int
-</pre></example>
+ start at n1=att_var at short_att*att_var at int_att;
+ // start at n1=5329 and is type int
+</verbatim>
+</example>
<noindent></noindent> <para><strong>Binary Operators</strong> &linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="934">binary Operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="941">binary Operators</indexterm></cindex>
Unlike C the binary operators return an array of values.
There is no such thing as short circuiting with the AND/OR operators.
Missing values are carried into the result in the same way they are with
@@ -9134,7 +9289,7 @@ n4=--time; n4=time=0.,1.,2.,3.,4.,5.,6.,7.,8.,9.;
</pre></example>
<noindent></noindent> <para><strong>Conditional Operator ?: </strong> &linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="935">conditional Operator</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="942">conditional Operator</indexterm></cindex>
<noindent></noindent> <emph>exp1 ? exp2 : exp3 </emph> &linebreak;
The conditional operator (or ternary Operator) is a succinct way
of writing an if/then/else. If exp1 evaluates to true then exp2 is
@@ -9142,17 +9297,19 @@ returned else exp3 is returned.
</para>
<para>Example:
</para><example endspaces=" ">
-<pre xml:space="preserve">weight_avg=weight.avg();
-weight_avg&arobase;units= (weight_avg == 1 ? "kilo" : "kilos");
+<verbatim xml:space="preserve">
+weight_avg=weight.avg();
+weight_avg at units= (weight_avg == 1 ? "kilo" : "kilos");
PS_nw=PS-(PS.min() > 100000 ? 100000 : 0);
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="clp"></a> <!&textndash; http://nco.sf.net/nco.html#clp &textndash;>
<a name="clipping"></a> <!&textndash; http://nco.sf.net/nco.html#clipping &textndash;>
</html>
<noindent></noindent> <para><strong>Clipping Operators</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="936">clipping operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="943">clipping operators</indexterm></cindex>
</para><table commandarg="asis" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="asis"><< Less-than Clipping&linebreak;</itemformat></item>
</tableterm><tableitem><para>For arrays, the less-than selection operator selects all values in the
@@ -9183,8 +9340,8 @@ RDM2=RDM << 90s // 1, 9, 36, 84, 90, 90, 84, 36, 9, 1 int
</subsection>
<node name="Dimensions" spaces=" "><nodename>Dimensions</nodename><nodenext spaces=" ">Left hand casting</nodenext><nodeprev spaces=" ">Expressions</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Dimensions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="937">defining dimensions in <command>ncap2</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="938"><code>defdim()</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="944">defining dimensions in <command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="945"><code>defdim()</code></indexterm></cindex>
<para>Dimensions are defined in Output using the <code>defdim()</code> function.
</para><example endspaces=" ">
<pre xml:space="preserve">defdim("cnt",10);
@@ -9249,9 +9406,9 @@ A1['$a--list.A']=30.0;
</subsection>
<node name="Left-hand-casting" spaces=" "><nodename>Left hand casting</nodename><nodenext spaces=" ">Arrays and hyperslabs</nodenext><nodeprev spaces=" ">Dimensions</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Left hand casting</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="939">hybrid coordinate system</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="940">left hand casting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="941"><acronym><acronymword>LHS</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="946">hybrid coordinate system</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="947">left hand casting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="948"><acronym><acronymword>LHS</acronymword></acronym></indexterm></cindex>
<para>The following examples demonstrate the utility of the
<dfn>left hand casting</dfn> ability of <command>ncap2</command>.
Consider first this simple, artificial, example.
@@ -9315,10 +9472,10 @@ coordinate system is easy with left hand casting.
<subsection spaces=" "><sectiontitle>Arrays and hyperslabs</sectiontitle>
<findex index="fn" spaces=" "><indexterm index="fn" number="16" mergedindex="cp">array</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="942"><code>array</code> function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="943">arrays</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="944">findgen-equivalent</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="945">indgen-equivalent</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="949"><code>array</code> function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="950">arrays</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="951">findgen-equivalent</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="952">indgen-equivalent</indexterm></cindex>
<para>Generating a regularly spaced one-dimensional array with <command>ncap2</command>
is simple with the <code>array()</code> function.
The syntax is
@@ -9356,7 +9513,7 @@ var_out=array(1+2-2,one,$time); // 1,2,3,4,5,6,7,8,9,10
var_out=array(1,2,three_dmn_rec_var); // 1,3,5,...155,157,159
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="946">hyperslabs</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="953">hyperslabs</indexterm></cindex>
<para>Hyperslabs in <command>ncap2</command> are more limited than hyperslabs with the
other <acronym><acronymword>NCO</acronymword></acronym> operators.
<command>ncap2</command> does not understand the shell command-line syntax
@@ -9387,8 +9544,9 @@ The number of hyperslab arguments MUST equal the variable&textrsquo;s rank.
</para>
<para>A simple 1D example:
</para><example endspaces=" ">
-<pre xml:space="preserve">($time.size=10)
-od[$time]={20,22,24,26,28,30,32,34,36,38};
+<verbatim xml:space="preserve">
+($time.size=10)
+od[$time]={20,22,24,26,28,30,32,34,36,38};
od(7); // 34
od(7:); // 34,36,38
@@ -9396,13 +9554,15 @@ od(:7); // 20,22,24,26,28,30,32,34
od(::4); // 20,28,36
od(1:6:2) // 22,26,30
od(:) // 20,22,24,26,28,30,32,34,36,38
-</pre></example>
+</verbatim>
+</example>
<para>A more complex three dimensional example:
</para><example endspaces=" ">
-<pre xml:space="preserve">($lat.size=2,$lon.size=4)
+<verbatim xml:space="preserve">
+($lat.size=2,$lon.size=4)
th[$time,$lat,$lon]=
- {1, 2, 3, 4, 5, 6, 7, 8,
+ {1, 2, 3, 4, 5, 6, 7, 8,
9,10,11,12,13,14,15,16,
17,18,19,20,21,22,23,24,
-99,-99,-99,-99,-99,-99,-99,-99,
@@ -9411,13 +9571,14 @@ th[$time,$lat,$lon]=
49,50,51,52,53,54,55,56,
-99,58,59,60,61,62,63,64,
65,66,67,68,69,70,71,72,
- -99,74,75,76,77,78,79,-99 };
+ -99,74,75,76,77,78,79,-99 };
th(1,1,3); // 16
th(2,0,:); // 17, 18, 19, 20
th(:,1,3); // 8, 16, 24, -99, 40, 48, 56, 64, 72, -99
th(::5,:,0:3:2); // 1, 3, 5, 7, 41, 43, 45, 47
-</pre></example>
+</verbatim>
+</example>
<para>If hyperslab arguments collapse to a single value (a cross-section has
been specified), then that dimension is removed from the returned
@@ -9469,17 +9630,19 @@ prs(:,1,:,:)=th1
</pre></example>
<noindent></noindent> <para><strong>Reverse method</strong>&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="947">reverse()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="954">reverse()</indexterm></cindex>
Use the <code>reverse()</code> method to reverse a dimension&textrsquo;s elements in a
variable with at least one dimension.
This is equivalent to a negative stride, e.g.,
</para><example endspaces=" ">
-<pre xml:space="preserve">th_rv=th(1 ,:,:).reverse($lon); // {12,11,10,9 }, {16,15,14,13}
-od_rv=od.reverse($time); // {38,36,34,32,30,28,26,24,22,20}
-</pre></example>
+<verbatim xml:space="preserve">
+th_rv=th(1 ,:,:).reverse($lon); // {12,11,10,9 }, {16,15,14,13}
+od_rv=od.reverse($time); // {38,36,34,32,30,28,26,24,22,20}
+</verbatim>
+</example>
<noindent></noindent> <para><strong>Permute method</strong>p&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="948">permute()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="955">permute()</indexterm></cindex>
Use the <code>permute()</code> method to swap the dimensions of a variable.
The number and names of dimension arguments must match the dimensions in
the variable.
@@ -9510,27 +9673,31 @@ three_dmn_var_prm=
</subsection>
<node name="Attributes" spaces=" "><nodename>Attributes</nodename><nodenext spaces=" ">Number literals</nodenext><nodeprev spaces=" ">Arrays and hyperslabs</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Attributes</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="949">attributes<command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="956">attributes<command>ncap2</command></indexterm></cindex>
<noindent></noindent> <para>Attributes are referred to by <emph>var_nm&arobase;att_nm</emph> &linebreak;
All the following are valid statements:
</para><example endspaces=" ">
-<pre xml:space="preserve">global&arobase;text="Test Attributes"; /* Assign a global variable attribute */
+<verbatim xml:space="preserve">
+global at text="Test Attributes"; /* Assign a global variable attribute */
a1[$time]=time*20;
-a1&arobase;long_name="Kelvin";
-a1&arobase;min=a1.min();
-a1&arobase;max=a1.max();
-a1&arobase;min++;
---a1&arobase;max; q
-a1(0)=a1&arobase;min;
-a1($time.size-1)=a1&arobase;max;
-</pre></example>
+a1 at long_name="Kelvin";
+a1 at min=a1.min();
+a1 at max=a1.max();
+a1 at min++;
+--a1 at max; q
+a1(0)=a1 at min;
+a1($time.size-1)=a1 at max;
+</verbatim>
+</example>
<para>A <emph>value list</emph> can be used on the RHS of an assign...
-<cindex index="cp" spaces=" "><indexterm index="cp" number="950">value list</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="957">value list</indexterm></cindex>
</para><example endspaces=" ">
-<pre xml:space="preserve">a1&arobase;trip1={1,2,3} ;
-a1&arobase;triplet={a1&arobase;min,(a1&arobase;min+a1&arobase;max)/2,a1&arobase;max};
-</pre></example>
+<verbatim xml:space="preserve">
+a1 at trip1={1,2,3} ;
+a1 at triplet={a1 at min,(a1 at min+a1@max)/2,a1 at max};
+</verbatim>
+</example>
<para>The netCDF specification allows all attribute types to have a size
greater than one.
The maximum is defined by <code>NC_MAX_ATTRS</code>.
@@ -9547,15 +9714,17 @@ The following is an <command>ncdump</command> of the metadata for variable <var>
<para>The <code>size()</code> method can be used with attributes.
For example, to save an attribute text string in a variable,
</para><example endspaces=" ">
-<pre xml:space="preserve">defdim("sng_len", a1&arobase;long_name.size());
-sng_arr[$sng_len]=a1&arobase;long_name; // sng_arr now contains "Kelvin"
-</pre></example>
+<verbatim xml:space="preserve">
+defdim("sng_len", a1 at long_name.size());
+sng_arr[$sng_len]=a1 at long_name; // sng_arr now contains "Kelvin"
+</verbatim>
+</example>
<para>Attributes defined in a script are stored in memory and are written to Output after script completion.
To stop the attribute being written use the ram_delete() method or use a bogus variable name.
</para>
<noindent></noindent> <para><strong>Attribute Propagation and Inheritance</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="951">attribute propagation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="952">attribute inheritance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="958">attribute propagation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="959">attribute inheritance</indexterm></cindex>
</para><itemize commandarg="bullet" spaces=" " endspaces=" "><itemprepend><formattingcommand command="bullet"/></itemprepend>
<beforefirstitem> </beforefirstitem><listitem spaces=" "><prepend>•</prepend><para>Attribute propagation occurs in a regular assign statement. The variable being defined on the LHS gets copies of the attributes from the leftermost variable on the RHS.
</para></listitem><listitem spaces=" "><prepend>•</prepend><para>Attribute Inheritance: The LHS variable "inherits" attributes from an Input variable with the same name
@@ -9571,8 +9740,10 @@ th_min=1.0 + 2*three_dmn_var_dbl.min($time);
<para>If the attribute name contains non-regular characters use ID quoting. See <pxref label="ID-Quoting"><xrefnodename>ID Quoting</xrefnodename></pxref>
</para><example endspaces=" ">
-<pre xml:space="preserve">'b..m1&arobase;c--lost'=23;
-</pre></example>
+<verbatim xml:space="preserve">
+'b..m1 at c--lost'=23;
+</verbatim>
+</example>
<html endspaces=" ">
<a name="ncap_num"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_num &textndash;>
@@ -9580,33 +9751,37 @@ th_min=1.0 + 2*three_dmn_var_dbl.min($time);
</subsection>
<node name="Number-literals" spaces=" "><nodename>Number literals</nodename><nodenext spaces=" ">if statement</nodenext><nodeprev spaces=" ">Attributes</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Number literals</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="953">number literals <command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="960">number literals <command>ncap2</command></indexterm></cindex>
<para>The table below lists the postfix character(s) to add to a number
literal for type cohesion.
To use the new netCDF4 types <acronym><acronymword>NCO</acronymword></acronym> must be compiled/linked to
the netCDF4 library and the output file must be <acronym><acronymword>HDF5</acronymword></acronym>.
</para>
<example endspaces=" ">
-<pre xml:space="preserve">n1[$time]=1UL; // n1 will now by type <code>NC_UINT</code>
-n2[$lon]=4b; // n2 will be of type <code>NC_BYTE</code>
-n3[$lat]=5ull; // n3 will be of type <code>NC_UINT64</code>
-n3&arobase;a1=6.0d; // attribute will be type <code>NC_DOUBLE</code>
-n3&arobase;a2=-666L; // attribute will be type <code>NC_INT</code>
-</pre></example>
+<verbatim xml:space="preserve">
+n1[$time]=1UL; // n1 will now by type @code{NC_UINT}
+n2[$lon]=4b; // n2 will be of type @code{NC_BYTE}
+n3[$lat]=5ull; // n3 will be of type @code{NC_UINT64}
+n3 at a1=6.0d; // attribute will be type @code{NC_DOUBLE}
+n3 at a2=-666L; // attribute will be type @code{NC_INT}
+</verbatim>
+</example>
<para>A floating point number without a postfix will default to
<code>NC_DOUBLE</code>.
An integer without a postfix will default to type <code>NC_INT</code>.
There is no postfix for characters, use a quoted string instead.
</para><example endspaces=" ">
-<pre xml:space="preserve">n4[$rlev]=0.1 // n4 will be of type <code>NC_DOUBLE</code>
-n5[$lon_grd]=2.0 // n5 will be of type <code>NC_DOUBLE</code>
-n6[$gds_crd]=2e3; // n6 will be of type <code>NC_DOUBLE</code>
-n7[$gds_crd]=2e3f; // n7 will be of type <code>NC_FLOAT</code>
-n6&arobase;a1=41; // attribute will be type <code>NC_INT</code>
-n6&arobase;a2=-21; // attribute will be type <code>NC_INT</code>
-n6&arobase;units="kelvin" // attribute will be type <code>NC_CHAR</code>
-</pre></example>
+<verbatim xml:space="preserve">
+n4[$rlev]=0.1 // n4 will be of type @code{NC_DOUBLE}
+n5[$lon_grd]=2.0 // n5 will be of type @code{NC_DOUBLE}
+n6[$gds_crd]=2e3; // n6 will be of type @code{NC_DOUBLE}
+n7[$gds_crd]=2e3f; // n7 will be of type @code{NC_FLOAT}
+n6 at a1=41; // attribute will be type @code{NC_INT}
+n6 at a2=-21; // attribute will be type @code{NC_INT}
+n6 at units="kelvin" // attribute will be type @code{NC_CHAR}
+</verbatim>
+</example>
<table commandarg="asis" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="asis"><strong>netCDF3/4 Types</strong></itemformat></item>
@@ -9641,12 +9816,13 @@ n6&arobase;units="kelvin" // attribute will be type <code>NC_CHAR</cod
</subsection>
<node name="if-statement" spaces=" "><nodename>if statement</nodename><nodenext spaces=" ">print statement</nodenext><nodeprev spaces=" ">Number literals</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>if statement</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="954">if()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="961">if()</indexterm></cindex>
<para>The syntax of the if statement is similar to its C counterpart.
The <emph>Conditional Operator (ternary operator)</emph> has also been
implemented.
</para><example endspaces=" ">
-<pre xml:space="preserve">if(exp1)
+<verbatim xml:space="preserve">
+if(exp1)
stmt1;
else if(exp2)
stmt2;
@@ -9654,18 +9830,19 @@ else
stmt3;
# Can use code blocks as well:
-if(exp1){
+if(exp1){
stmt1;
stmt1a;
stmt1b;
-} else if(exp2)
+}else if(exp2)
stmt2;
-else {
+else{
stmt3;
stmt3a;
stmt3b;
-}
-</pre></example>
+}
+</verbatim>
+</example>
<!-- comment Truth -->
<noindent></noindent> <para>For a variable or attribute expression to be logically true
@@ -9677,35 +9854,37 @@ OR (<code>||</code>) and AND (<code>&&</code>) operators.
The whole expression is evaluated regardless if one of the AND/OR
operands are True/False.
</para><example endspaces=" ">
-<pre xml:space="preserve"># Simple example
+<verbatim xml:space="preserve">
+# Simple example
if(time>0)
print("All values of time are greater than zero\n");
else if( time<0)
print("All values of time are less than zero\n");
-else {
+else {
time_max=time.max();
time_min=time.min();
print("min value of time=");print(time_min,"%f");
print("max value of time=");print(time_max,"%f");
-}
+}
# Example from ddra.nco
-if(fl_typ==fl_typ_gcm){
+if(fl_typ==fl_typ_gcm){
var_nbr_apx=32;
lmn_nbr=1.0*var_nbr_apx*varsz_gcm_4D; /* [nbr] Variable size */
- if(nco_op_typ==nco_op_typ_avg){
+ if(nco_op_typ==nco_op_typ_avg){
lmn_nbr_avg=1.0*var_nbr_apx*varsz_gcm_4D; // Block size
lmn_nbr_wgt=dmnsz_gcm_lat; /* [nbr] Weight size */
- } // !nco_op_typ_avg
-}else if(fl_typ==fl_typ_stl){
+ } // !nco_op_typ_avg
+}else if(fl_typ==fl_typ_stl){
var_nbr_apx=8;
lmn_nbr=1.0*var_nbr_apx*varsz_stl_2D; /* [nbr] Variable size */
- if(nco_op_typ==nco_op_typ_avg){
+ if(nco_op_typ==nco_op_typ_avg){
lmn_nbr_avg=1.0*var_nbr_apx*varsz_stl_2D; // Block size
lmn_nbr_wgt=dmnsz_stl_lat; /* [nbr] Weight size */
- } // !nco_op_typ_avg
-} // !fl_typ
-</pre></example>
+ } // !nco_op_typ_avg
+} // !fl_typ
+</verbatim>
+</example>
<noindent></noindent> <para><strong>Conditional Operator &linebreak;</strong>
</para><example endspaces=" ">
@@ -9720,7 +9899,7 @@ th_nw=(three_dmn_var_sht >= 0 ? three_dmn_var_sht.uint() : \
</subsection>
<node name="print-statement" spaces=" "><nodename>print statement</nodename><nodenext spaces=" ">Missing values ncap2</nodenext><nodeprev spaces=" ">if statement</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>print statement</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="955">print() <command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="962">print() <command>ncap2</command></indexterm></cindex>
<example endspaces=" ">
<pre xml:space="preserve">print(variable_name/attribute name/string, format string);
</pre></example>
@@ -9736,7 +9915,8 @@ will be saved and can be printed), and then print the variable.
</para>
<noindent></noindent> <para>examples
</para><example endspaces=" ">
-<pre xml:space="preserve">print(lon);
+<verbatim xml:space="preserve">
+print(lon);
lon[0]=0
lon[1]=90
lon[2]=180
@@ -9745,12 +9925,13 @@ lon[3]=270
print(lon_2D_rrg,"%3.2f,");
0.00,0.00,180.00,0.00,180.00,0.00,180.00,0.00,
-print(mss_val_fst&arobase;_FillValue);
-mss_val_fst&arobase;_FillValue, size = 1 NC_FLOAT, value = -999
+print(mss_val_fst at _FillValue);
+mss_val_fst at _FillValue, size = 1 NC_FLOAT, value = -999
print("This function \t is monotonic\n");
This function is monotonic
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="ncap_miss"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_miss &textndash;>
@@ -9758,7 +9939,7 @@ This function is monotonic
</subsection>
<node name="Missing-values-ncap2" spaces=" "><nodename>Missing values ncap2</nodename><nodenext spaces=" ">Methods and functions</nodenext><nodeprev spaces=" ">print statement</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Missing values ncap2</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="956">missing values ncap2</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="963">missing values ncap2</indexterm></cindex>
<para>Missing values operate slightly differently in <command>ncap2</command>
Consider the expression where op is any of the following operators (excluding &textrsquo;=&textrsquo;)
</para><example endspaces=" ">
@@ -9801,7 +9982,7 @@ with a variable.
They only work on variables in Output.
</para><table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">set_miss(expr)</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="957"><code>set_miss()</code></indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="964"><code>set_miss()</code></indexterm></cindex>
<para>The numeric argument <var>expr</var> becomes the new missing value,
overwriting the old missing value, if any.
The argument given is converted if necessary to the variable type.
@@ -9814,28 +9995,29 @@ They only work on variables in Output.
The intrinsic function <code>change_miss()</code> (see below) is typically
used to edit values of existing variables.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">change_miss(expr)</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="958"><code>change_miss()</code></indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="965"><code>change_miss()</code></indexterm></cindex>
<para>Sets or changes (any pre-existing) missing value attribute and missing
data values to <var>expr</var>.
NB: This is an expensive function since all values must be examined.
Use this function when changing missing values for pre-existing
variables.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">get_miss() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="959"><code>get_miss()</code></indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="966"><code>get_miss()</code></indexterm></cindex>
<para>Returns the missing value of a variable.
If the variable exists in Input and Output then the missing value of
the variable in Output is returned.
If the variable has no missing value then an error is returned.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">delete_miss()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="960"><code>delete_miss()</code></indexterm></cindex>
- <para>Deletes the missing value associated with a variable.
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="967"><code>delete_miss()</code></indexterm></cindex>
+ <para>Delete the missing value associated with a variable.
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">number_miss()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="961"><code>number_miss()</code></indexterm></cindex>
- <para>Counts the number of missing values a variable contains.
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="968"><code>number_miss()</code></indexterm></cindex>
+ <para>Count the number of missing values a variable contains.
</para></tableitem></tableentry></table>
<example endspaces=" ">
-<pre xml:space="preserve">th=three_dmn_var_dbl;
+<verbatim xml:space="preserve">
+th=three_dmn_var_dbl;
th.change_miss(-1e10d);
/* Set values less than 0 or greater than 50 to missing value */
where(th < 0.0 || th > 50.0) th=th.get_miss();
@@ -9852,11 +10034,12 @@ elsewhere
// Print missing value and variable summary
mss_val_nbr=three_dmn_var_dbl.number_miss();
-print(three_dmn_var_dbl&arobase;_FillValue);
+print(three_dmn_var_dbl at _FillValue);
print("Number of missing values in three_dmn_var_dbl: ");
print(mss_val_nbr,"%d");
print(three_dmn_var_dbl);
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="ncap_mtd"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_mtd &textndash;>
@@ -9891,26 +10074,26 @@ type double, average it, then convert this back to type short:
</para>
<table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">avg()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="962">avg()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="969">avg()</indexterm></cindex>
<para>Mean value
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">sqravg()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="963">sqravg()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="970">sqravg()</indexterm></cindex>
<para>Square of the mean
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">avgsqr()</itemformat></item>
</tableterm><tableitem><para>Mean of sum of squares
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">max()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="964">max()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="971">max()</indexterm></cindex>
<para>Maximum value
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">min()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="965">min()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="972">min()</indexterm></cindex>
<para>Minimum value
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">rms()</itemformat></item>
</tableterm><tableitem><para>Root-mean-square (normalize by <var>N</var>)
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">rmssdn()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="966">rmssdn()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="973">rmssdn()</indexterm></cindex>
<para>Root-mean square (normalize by <var>N-1</var>)
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">ttl() or total()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="967">ttl()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="974">ttl()</indexterm></cindex>
<para>Sum of values
</para></tableitem></tableentry></table>
@@ -9924,19 +10107,19 @@ four_time_avg=four_dmn_rec_var($time);
For more information see <pxref label="Packed-data"><xrefnodename>Packed data</xrefnodename></pxref> and <pxref label="ncpdq-netCDF-Permute-Dimensions-Quickly"><xrefnodename>ncpdq netCDF Permute Dimensions Quickly</xrefnodename></pxref>&linebreak;
</para><table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">pack() & pack_short()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="968">pack()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="975">pack()</indexterm></cindex>
<para>The default packing algorithm is applied and variable is packed to <code>NC_SHORT</code>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">pack_byte()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="969">pack_byte()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="976">pack_byte()</indexterm></cindex>
<para>Variable is packed to <code>NC_BYTE</code>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">pack_short()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="970">pack_short()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="977">pack_short()</indexterm></cindex>
<para>Variable is packed to <code>NC_SHORT</code>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">pack_int()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="971">pack_int()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="978">pack_int()</indexterm></cindex>
<para>Variable is packed to <code>NC_INT</code>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">unpack()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="972">unpack()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="979">unpack()</indexterm></cindex>
<para>The standard unpacking algorithm is applied.
</para></tableitem></tableentry></table>
@@ -9945,13 +10128,13 @@ These methods work with variables and attributes. They have no arguments
</para>
<table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">size() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="973">size()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="980">size()</indexterm></cindex>
<para>Total number of elements
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">ndims()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="974">ndims()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="981">ndims()</indexterm></cindex>
<para>Number of dimensions in variable
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">type() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="975">type()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="982">type()</indexterm></cindex>
<para>Returns the netcdf type (see previous section)
</para></tableitem></tableentry></table>
@@ -9997,38 +10180,38 @@ lat_2D_rrg_new=0,90,-30,30,-30,30,-90,0
<table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code"><strong>netCDF3/4 Types</strong></itemformat></item>
</tableterm></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">byte() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="976">byte()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="983">byte()</indexterm></cindex>
<para>convert to <code>NC_BYTE</code>, a signed 1-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">char()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="977">char()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="984">char()</indexterm></cindex>
<para>convert to <code>NC_CHAR</code>, an ISO/ASCII character
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">short() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="978">sshort()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="985">sshort()</indexterm></cindex>
<para>convert to <code>NC_SHORT</code>, a signed 2-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">int() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="979">int()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="986">int()</indexterm></cindex>
<para>convert to <code>NC_INT</code>, a signed 4-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">float()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="980">float()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="987">float()</indexterm></cindex>
<para>convert to <code>NC_FLOAT</code>, a single-precision (4-byte) floating point number
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">double() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="981">double()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="988">double()</indexterm></cindex>
<para>convert to <code>NC_DOUBLE</code>, a double-precision (8-byte) floating point number
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code"><strong>netCDF4 Types</strong></itemformat></item>
</tableterm></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">ubyte() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="982">ubyte()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="989">ubyte()</indexterm></cindex>
<para>convert to <code>NC_UBYTE</code>, an unsigned 1-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">ushort() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="983">ushort()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="990">ushort()</indexterm></cindex>
<para>convert to <code>NC_USHORT</code>, an unsigned 2-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">uint()</itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="984">uint()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="991">uint()</indexterm></cindex>
<para>convert to <code>NC_UINT</code>, an unsigned 4-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">int64() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="985">int64()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="992">int64()</indexterm></cindex>
<para>convert to <code>NC_INT64</code>, a signed 8-byte integer
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">uint64() </itemformat></item>
-</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="986">unit64()</indexterm></cindex>
+</tableterm><tableitem><cindex index="cp" spaces=" "><indexterm index="cp" number="993">unit64()</indexterm></cindex>
<para>convert to <code>NC_UINT64</code>, an unsigned 8-byte integer
</para></tableitem></tableentry></table>
@@ -10052,7 +10235,7 @@ n3=1/(three_dmn_var_dbl.cos().pow(2))-tan(three_dmn_var_dbl)^2; // n3 type doubl
<html endspaces=" ">
<a name="ncap_ram"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_ram &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="987"><acronym><acronymword>RAM</acronymword></acronym> variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="994"><acronym><acronymword>RAM</acronymword></acronym> variables</indexterm></cindex>
</subsection>
<node name="RAM-variables" spaces=" "><nodename>RAM variables</nodename><nodenext spaces=" ">Where statement</nodenext><nodeprev spaces=" ">Methods and functions</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle><acronym><acronymword>RAM</acronymword></acronym> variables</sectiontitle>
@@ -10067,8 +10250,8 @@ To delete a <acronym><acronymword>RAM</acronymword></acronym> variables (and rec
<code>ram_delete()</code> method.
To write a <acronym><acronymword>RAM</acronymword></acronym> variable to disk (like a regular variable) use
<code>ram_write()</code>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="988">ram_write()</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="989">ram_delete()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="995">ram_write()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="996">ram_delete()</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">*temp[$time,$lat,$lon]=10.0; // Cast
*temp_avg=temp.avg($time); // Regular assign
@@ -10090,29 +10273,31 @@ temp_avg.ram_write(); // Write Variable to output
</subsection>
<node name="Where-statement" spaces=" "><nodename>Where statement</nodename><nodenext spaces=" ">Loops</nodenext><nodeprev spaces=" ">RAM variables</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Where statement</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="990">where()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="997">where()</indexterm></cindex>
<para>A <code>where()</code> combines the definition and application of a mask all in one go and can lead to succinct code.
The full syntax of a <code>where()</code> statement is as follows:
</para>
<example endspaces=" ">
-<pre xml:space="preserve">// Single assign (the 'elsewhere' block is optional)
+<verbatim xml:space="preserve">
+// Single assign (the 'elsewhere' block is optional)
where(mask)
var1=expr1;
elsewhere
var1=expr2;
// Multiple assigns
-where(mask){
+where(mask){
var1=expr1;
var2=expr2;
...
-}elsewhere{
+}elsewhere{
var1=expr3
var2=expr4
var3=expr5;
...
-}
-</pre></example>
+}
+</verbatim>
+</example>
<itemize commandarg="bullet" spaces=" " endspaces=" "><itemprepend><formattingcommand command="bullet"/></itemprepend>
<listitem spaces=" "><prepend>•</prepend><para>The only expression allowed in the predicate of a where is assign,
@@ -10151,31 +10336,99 @@ to set its values less than 8 or greater than 80 <w>to 0</w>:
<pre xml:space="preserve">where(RDM < 8 || RDM > 80) RDM=0;
</pre></example>
+<html endspaces=" ">
+<a name="WRF"></a> <!&textndash; http://nco.sf.net/nco.html#WRF &textndash;>
+<a name="SLD"></a> <!&textndash; http://nco.sf.net/nco.html#SLD &textndash;>
+<a name="wrf"></a> <!&textndash; http://nco.sf.net/nco.html#wrf &textndash;>
+<a name="sld"></a> <!&textndash; http://nco.sf.net/nco.html#sld &textndash;>
+</html>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="998">Weather and Research Forecast (<acronym><acronymword>WRF</acronymword></acronym>) Model</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="999">Swath-like Data (<acronym><acronymword>SLD</acronymword></acronym>)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1000"><acronym><acronymword>WRF</acronymword></acronym> (Weather and Research Forecast Model)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1001"><acronym><acronymword>SLD</acronymword></acronym> (Swath-like Data)</indexterm></cindex>
<para>Consider irregularly gridded data, described using <w>rank 2</w> coordinates:
<code>double lat(south_north,east_west)</code>,
<code>double lon(south_north,east_west)</code>,
<code>double temperature(south_north,east_west)</code>.
+This type of structure is often found in regional weather/climate model
+(such as <acronym><acronymword>WRF</acronymword></acronym>) output, and in satellite swath data.
+For this reason we call it &textldquo;Swath-like Data&textrdquo;, or <acronym><acronymword>SLD</acronymword></acronym>.
To find the average temperature in a region bounded by
[<var>lat_min</var>,<var>lat_max</var>] and [<var>lon_min</var>,<var>lon_max</var>]:
</para><example endspaces=" ">
-<pre xml:space="preserve">temperature_msk[$south_north,$east_west]=0.0;
-where(lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max)
+<verbatim xml:space="preserve">
+temperature_msk[$south_north,$east_west]=0.0;
+where((lat >= lat_min && lat <= lat_max) && (lon >= lon_min && lon <= lon_max))
temperature_msk=temperature;
elsewhere
- temperature_msk=temperature&arobase;_FillValue;
+ temperature_msk=temperature at _FillValue;
temp_avg=temperature_msk.avg();
temp_max=temperature.max();
-</pre></example>
+</verbatim>
+</example>
+
+<html endspaces=" ">
+<a name="NARR"></a> <!&textndash; http://nco.sf.net/nco.html#NARR &textndash;>
+<a name="narr"></a> <!&textndash; http://nco.sf.net/nco.html#narr &textndash;>
+</html>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1002"><acronym><acronymword>NARR</acronymword></acronym> (North American Regional Reanalysis)a</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1003">North American Regional Reanalysis (<acronym><acronymword>NARR</acronymword></acronym>)</indexterm></cindex>
+<para>For North American Regional Reanalysis (<acronym><acronymword>NARR</acronymword></acronym>) data
+(example
+<uref><urefurl>http://dust.ess.uci.edu/diwg/narr_uwnd.199605.nc</urefurl><urefdesc spaces=" ">dataset</urefdesc></uref>)
+the procedure looks like this
+</para><example endspaces=" ">
+<verbatim xml:space="preserve">
+ncap2 -O -v -S ~/narr.nco ${DATA}/hdf/narr_uwnd.199605.nc ~/foo.nc
+</verbatim>
+</example>
+<para>where <file>narr.nco</file> is an <command>ncap2</command> script like this:
+</para><example endspaces=" ">
+<verbatim xml:space="preserve">
+/* North American Regional Reanalysis (NARR) Statistics
+ NARR stores grids with 2-D latitude and longitude, aka Swath-like Data (SLD)
+ Here we work with three variables:
+ lat(y,x), lon(y,x), and uwnd(time,level,y,x);
+ To study sub-regions of SLD, we use masking techniques:
+ 1. Define mask as zero times variable to be masked
+ Then mask automatically inherits variable attributes
+ And average below will inherit mask attributes
+ 2. Optionally, create mask as RAM variable (as below with asterisk *)
+ NCO does not write RAM variable to output
+ Masks are often unwanted, and can be big, so this speeds execution
+ 3. Example could be extended to preserve mean lat and lon of sub-region
+ Follow uwnd example to do this: lat_msk=0.0*lat ... lat_avg=lat.avg($y,$x) */
+*uwnd_msk=0.0*uwnd;
+where((lat >= 35.6 && lat <= 37.0) && (lon >= -100.5 && lon <= -99.0))
+ uwnd_msk=uwnd;
+elsewhere
+ uwnd_msk=uwnd at _FillValue;
+// Average only over horizontal dimensions x and y (preserve level and time)
+uwnd_avg=uwnd_msk.avg($y,$x);
+</verbatim>
+</example>
+<para>Stripped of comments and formatting, this example is a three-statement
+script executed by a one-line command.
+<acronym><acronymword>NCO</acronymword></acronym> needs only this meagre input to unpack and copy the input
+data and attributes, compute the statistics, and then define and write
+the output file.
+Unless the comments pointed out that wind variable (<code>uwnd</code>) was
+four-dimensional and the latitude/longitude grid variables were both
+two-dimensional, there would be no way to tell.
+This shows how <acronym><acronymword>NCO</acronymword></acronym> hides from the user the complexity of
+analyzing multi-dimensional <acronym><acronymword>SLD</acronymword></acronym>.
+We plan to extend such <acronym><acronymword>SLD</acronymword></acronym> features to more operators soon.
+</para>
<html endspaces=" ">
<a name="ncap_lop"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_lop &textndash;>
</html>
</subsection>
<node name="Loops" spaces=" "><nodename>Loops</nodename><nodenext spaces=" ">Include files</nodenext><nodeprev spaces=" ">Where statement</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Loops</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="991">while()</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="992">for()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1004">while()</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1005">for()</indexterm></cindex>
<para><command>ncap2</command> supplies <command>for()</command> loops and <command>while()</command> loops.
They are completely unoptimized so use them only with <acronym><acronymword>RAM</acronymword></acronym>
variables unless you want thrash your disk to death.
@@ -10183,7 +10436,8 @@ To break out of a loop use the <command>break</command> command.
To iterate to the next cycle use the <command>continue</command> command.
</para>
<example endspaces=" ">
-<pre xml:space="preserve">// Set elements in variable double temp(time,lat)
+<verbatim xml:space="preserve">
+// Set elements in variable double temp(time,lat)
// If element < 0 set to 0, if element > 100 set to 100
*sz_idx=$time.size;
*sz_jdx=$lat.size;
@@ -10207,14 +10461,15 @@ if(idx == sz) print("lat co-ordinate is monotonic\n");
*sz=$lat_nw.size;
*sum=0.0;
-while(idx<sz){
+while(idx<sz){
if(lat(idx)%2) sum+=lat(idx);
idx++;
-}
+}
ram_write(sum);
print("Total of odd elements ");print(sum);print("\n");
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="ncap_inc"></a> <!&textndash; http://nco.sf.net/nco.html#ncap_inc &textndash;>
@@ -10222,7 +10477,7 @@ print("Total of odd elements ");print(sum);print("\n");
</subsection>
<node name="Include-files" spaces=" "><nodename>Include files</nodename><nodenext spaces=" ">Sort methods</nodenext><nodeprev spaces=" ">Loops</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Include files</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="993"><command>include</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1006"><command>include</command></indexterm></cindex>
<para>The syntax of an <var>include-file</var> is:
</para><example endspaces=" ">
<pre xml:space="preserve">#include "script.nco"
@@ -10248,12 +10503,12 @@ e=2.71828; // Regular (disk) variable, written to output
</subsection>
<node name="Sort-methods" spaces=" "><nodename>Sort methods</nodename><nodenext spaces=" ">Irregular grids</nodenext><nodeprev spaces=" ">Include files</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle><command>sort</command> methods</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="994"><command>sort</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="995"><command>asort</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="996"><command>dsort</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="997"><command>remap</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="998"><command>unmap</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="999"><command>invert_map</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1007"><command>sort</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1008"><command>asort</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1009"><command>dsort</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1010"><command>remap</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1011"><command>unmap</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1012"><command>invert_map</command></indexterm></cindex>
<para>In <acronym><acronymword>ncap2</acronymword></acronym> there are multiple ways to sort data.
Beginning with <acronym><acronymword>NCO</acronymword></acronym> 4.1.0 (March, 2012), <acronym><acronymword>ncap2</acronymword></acronym>
support six sorting functions:
@@ -10293,18 +10548,20 @@ de-sorting map <var>dsr_map</var> which is inverse map of the input map
This gives the user access to both the forward and inverse sorting maps
which can be useful in special situations.
</para><example endspaces=" ">
-<pre xml:space="preserve">a1[$time]={10,2,3,4,6,5,7,3,4,1};
+<verbatim xml:space="preserve">
+a1[$time]={10,2,3,4,6,5,7,3,4,1};
a1_sort=sort(a1);
print(a1_sort);
// 1, 2, 3, 3, 4, 4, 5, 6, 7, 10;
-a2[$lon]={2,1,4,3};
+a2[$lon]={2,1,4,3};
a2_sort=sort(a2,&a2_map);
print(a2);
// 1, 2, 3, 4
print(a2_map);
// 1, 0, 3, 2;
-</pre></example>
+</verbatim>
+</example>
<para>If the map variable does not exist prior to the <command>sort()</command> call,
then it will be created with the same shape as the input variable and be
@@ -10313,15 +10570,16 @@ If the map variable already exists, then the only restriction is that it
be of at least the same size as the input variable.
To apply a map use <code>remap(var_in,srt_map)</code>.
</para><example endspaces=" ">
-<pre xml:space="preserve">defdim("nlat",5);
+<verbatim xml:space="preserve">
+defdim("nlat",5);
-a3[$lon]={2,5,3,7};
-a4[$nlat,$lon]={
+a3[$lon]={2,5,3,7};
+a4[$nlat,$lon]={
1, 2, 3, 4,
5, 6, 7, 8,
9,10,11,12,
13,14,15,16,
- 17,18,19,20};
+ 17,18,19,20};
a3_sort=sort(a3,&a3_map);
print(a3_map);
@@ -10335,7 +10593,7 @@ print(a4_sort);
// 13,15,14,16,
// 17,19,18,20;
-a3_map2[$nlat]={4,3,0,2,1};
+a3_map2[$nlat]={4,3,0,2,1};
a4_sort2=remap(a4,a3_map2);
print(a4_sort2);
@@ -10343,7 +10601,8 @@ print(a4_sort2);
// 8, 10, 9,7, 6,
// 13,15,14,12,11,
// 18,20,19,17,16
-</pre></example>
+</verbatim>
+</example>
<para>As in the above example you may create your own sort map.
To sort in descending order, apply the <code>reverse()</code> method after the
<command>sort()</command>.
@@ -10523,11 +10782,11 @@ ncap2 -O -v -S ~/ncap2_foo.nco ~/nco/data/in.nc ~/foo.nc
</subsection>
<node name="Irregular-grids" spaces=" "><nodename>Irregular grids</nodename><nodenext spaces=" ">Bilinear interpolation</nodenext><nodeprev spaces=" ">Sort methods</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>Irregular Grids</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1000">irregular grids</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1001">rectangular grids</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1002">non-rectangular grids</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1003">non-standard grids</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1004">mask</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1013">irregular grids</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1014">rectangular grids</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1015">non-rectangular grids</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1016">non-standard grids</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1017">mask</indexterm></cindex>
<!-- c fxm need to edit rrg sxn beginning here -->
<para><acronym><acronymword>NCO</acronymword></acronym> is capable of analyzing datasets for many different
underlying coordinate grid types.
@@ -10563,7 +10822,7 @@ analysis software like <acronym><acronymword>NCO</acronymword></acronym>.
are independent of these grid properties (regularity,
rectangularity).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1005">wrapped coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1018">wrapped coordinates</indexterm></cindex>
<para>The preferred <acronym><acronymword>NCO</acronymword></acronym> technique to analyze data on non-standard
coordinate grids is to create a region mask with <command>ncap2</command>, and
then to use the mask within <command>ncap2</command> for variable-specific
@@ -10635,23 +10894,19 @@ ncap2 -S ncap2.in in.nc out.nc
</verbatim>
</example>
-<html endspaces=" ">
-<a name="wrf"></a> <!&textndash; http://nco.sf.net/nco.html#wrf &textndash;>
-<a name="WRF"></a> <!&textndash; http://nco.sf.net/nco.html#WRF &textndash;>
-</html>
<ignore>
http://foehn.colorado.edu/wrfout_to_cf/wrfout_to_cf.ncl
ncl 'file_in="wrfout.nc"' 'file_out="wrfpost.nc"' wrfout_to_cf.ncl
ncl 'file_in="wrfout_d02_2013-10-04_20:00:00"' 'file_out="wrfout_d02_2013-10-04_20:00:00_cf.nc"' wrfout_to_cf.ncl
ncl 'file_in="wrfout_v2_Lambert"' 'file_out="wrfout_v2_Lambert.nc"' wrfout_to_cf.ncl
</ignore>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1006"><acronym><acronymword>WRF</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1019"><acronym><acronymword>WRF</acronymword></acronym></indexterm></cindex>
<para>Grids like those produced by the <acronym><acronymword>WRF</acronymword></acronym> model are complex because
one must use global metadata to determine the grid staggering and
offsets to translate <code>XLAT</code> and <code>XLONG</code> into real latitudes,
longitudes, and missing points.
The <acronym><acronymword>WRF</acronymword></acronym> grid documentation should describe this.
-For <acronym><acronymword>WRF</acronymword></acronym> files creating regional masks looks like
+For <acronym><acronymword>WRF</acronymword></acronym> files creating regional masks looks, in general, like
</para><example endspaces=" ">
<pre xml:space="preserve">mask_var = (XLAT >= lat_min && XLAT <= lat_max) && (XLONG >= lon_min && XLONG <= lon_max);
</pre></example>
@@ -10716,34 +10971,38 @@ After calculations <code>var_out</code> is converted to the input type of
</para>
<para>Suppose the first part of an <command>ncap2</command> script is
</para><example endspaces=" ">
-<pre xml:space="preserve">defdim("X",4);
+<verbatim xml:space="preserve">
+defdim("X",4);
defdim("Y",5);
// Temperature
T_in[$X,$Y]=
- {100, 200, 300, 400, 500,
+ {100, 200, 300, 400, 500,
101, 202, 303, 404, 505,
102, 204, 306, 408, 510,
- 103, 206, 309, 412, 515.0 };
+ 103, 206, 309, 412, 515.0 };
// Coordinate variables
-x_in[$X]={0.0,1.0,2.0,3.01};
-y_in[$Y]={1.0,2.0,3.0,4.0,5};
-</pre></example>
+x_in[$X]={0.0,1.0,2.0,3.01};
+y_in[$Y]={1.0,2.0,3.0,4.0,5};
+</verbatim>
+</example>
<para>Now we interpolate with the following variables:
</para><example endspaces=" ">
-<pre xml:space="preserve">defdim("Xn",3);
+<verbatim xml:space="preserve">
+defdim("Xn",3);
defdim("Yn",4);
T_out[$Xn,$Yn]=0.0;
-x_out[$Xn]={0.0,0.02,3.01};
-y_out[$Yn]={1.1,2.0,3,4};
+x_out[$Xn]={0.0,0.02,3.01};
+y_out[$Yn]={1.1,2.0,3,4};
var_out=bilinear_interp(T_in,T_out,x_out,y_out,x_in,y_in);
print(var_out);
// 110, 200, 300, 400,
// 110.022, 200.04, 300.06, 400.08,
// 113.3, 206, 309, 412 ;
-</pre></example>
+</verbatim>
+</example>
<para>It is possible to interpolate a single point:
</para><example endspaces=" ">
@@ -10767,27 +11026,28 @@ typically these are in the range (-90,90).
This <command>ncap2</command> script illustrates both wrapping and extrapolation
of end points:
</para><example endspaces=" ">
-<pre xml:space="preserve">defdim("lat_in",6);
+<verbatim xml:space="preserve">
+defdim("lat_in",6);
defdim("lon_in",5);
// Coordinate input vars
-lat_in[$lat_in]={-80,-40,0,30,60.0,85.0};
-lon_in[$lon_in]={30, 110, 190, 270, 350.0};
+lat_in[$lat_in]={-80,-40,0,30,60.0,85.0};
+lon_in[$lon_in]={30, 110, 190, 270, 350.0};
T_in[$lat_in,$lon_in]=
- {10,40,50,30,15,
+ {10,40,50,30,15,
12,43,52,31,16,
14,46,54,32,17,
16,49,56,33,18,
18,52,58,34,19,
- 20,55,60,35,20.0 };
+ 20,55,60,35,20.0 };
defdim("lat_out",4);
defdim("lon_out",3);
// Coordinate variables
-lat_out[$lat_out]={-90,0,70,88.0};
-lon_out[$lon_out]={0,190,355.0};
+lat_out[$lat_out]={-90,0,70,88.0};
+lon_out[$lon_out]={0,190,355.0};
T_out[$lat_out,$lon_out]=0.0;
@@ -10797,7 +11057,8 @@ print(T_out);
// 16.25, 54, 16.625,
// 19.25, 58.8, 19.325,
// 20.15, 60.24, 20.135 ;
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="gsl"></a> <!&textndash; http://nco.sf.net/nco.html#gsl &textndash;>
@@ -10805,7 +11066,7 @@ print(T_out);
</subsection>
<node name="GSL-special-functions" spaces=" "><nodename>GSL special functions</nodename><nodenext spaces=" ">GSL interpolation</nodenext><nodeprev spaces=" ">Bilinear interpolation</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>GSL special functions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1007"><acronym><acronymword>GSL</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1020"><acronym><acronymword>GSL</acronymword></acronym></indexterm></cindex>
<noindent></noindent> <para>As of version 3.9.6 (released January, 2009), <acronym><acronymword>NCO</acronymword></acronym>
can link to the GNU Scientific Library (<acronym><acronymword>GSL</acronymword></acronym>).
<command>ncap2</command> can access most <acronym><acronymword>GSL</acronymword></acronym> special functions including
@@ -10833,17 +11094,19 @@ The slow-down due to calling the error-handling version of the
<acronym><acronymword>GSL</acronymword></acronym> numerical functions was found to be negligible (please let
us know if you find otherwise).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1008">gamma function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1009"><var>gsl_sf_gamma</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1021">gamma function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1022"><var>gsl_sf_gamma</var></indexterm></cindex>
<noindent></noindent> <para>Consider the gamma function.&linebreak;
<noindent></noindent> The <acronym><acronymword>GSL</acronymword></acronym> function prototype is &linebreak;
<code>int gsl_sf_gamma_e(const double x, gsl_sf_result * result)</code>
The <command>ncap2</command> script would be:
</para><example endspaces=" ">
-<pre xml:space="preserve">lon_in[lon]={-1,0.1,0,2,0.3};
+<verbatim xml:space="preserve">
+lon_in[lon]={-1,0.1,0,2,0.3};
lon_out=gsl_sf_gamma(lon_in);
lon_out= _, 9.5135, 4.5908, 2.9915
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent> <para>The first value is set to <code>_FillValue</code> since the gamma
function is undefined for negative integers.
@@ -10852,8 +11115,8 @@ Otherwise, the default double fill value is used
(defined in the netCDF header <file>netcdf.h</file> as
<code>NC_FILL_DOUBLE = 9.969e+36</code>).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1010">Bessel function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1011"><var>gsl_sf_bessel_Jn</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1023">Bessel function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1024"><var>gsl_sf_bessel_Jn</var></indexterm></cindex>
<noindent></noindent> <para>Consider a call to a Bessel function with <acronym><acronymword>GSL</acronymword></acronym>
prototype&linebreak;
<code>int gsl_sf_bessel_Jn_e(int n, double x, gsl_sf_result * result)</code>
@@ -10868,10 +11131,12 @@ lon_out=0.11490, 0.0012, 0.00498, 0.011165
The Bessel order argument, an integer, can also be a non-scalar
variable, i.e., an array.
</para><example endspaces=" ">
-<pre xml:space="preserve">n_in[lon]={0,1,2,3};
+<verbatim xml:space="preserve">
+n_in[lon]={0,1,2,3};
lon_out=gsl_sf_bessel_Jn(n_in,0.5);
lon_out= 0.93846, 0.24226, 0.03060, 0.00256
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent> <para>Arguments to <acronym><acronymword>GSL</acronymword></acronym> wrapper functions in <command>ncap2</command>
must conform to one another, i.e., they must share the same sub-set of
@@ -10882,7 +11147,7 @@ dimension, so <code>n_in</code> in can be broadcast to conform to
<code>three_dmn_var_dbl</code>.
However <code>time_out=gsl_sf_bessel_Jn(n_in,time)</code> is invalid.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1012">Elliptic integrals</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1025">Elliptic integrals</indexterm></cindex>
<para>Consider the elliptical integral with prototype
<code>int gsl_sf_ellint_RD_e(double x, double y, double z, gsl_mode_t mode, gsl_sf_result * result)</code>
</para><example endspaces=" ">
@@ -10923,7 +11188,7 @@ Zero indicates success.
</para>
<noindent></noindent> <para>Consider another array function &linebreak;
<code>int gsl_sf_legendre_Pl_array( int lmax, double x, double *result_array);</code>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1013">Legendre polynomial</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1026">Legendre polynomial</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="17" mergedindex="cp">gsl_sf_legendre_Pl</indexterm></findex>
</para><example endspaces=" ">
<pre xml:space="preserve">a1=time.double();
@@ -11235,7 +11500,7 @@ prototypes look at the spreadsheet <strong>doc/nco_gsl.ods</strong>. &linebreak;
</subsection>
<node name="GSL-interpolation" spaces=" "><nodename>GSL interpolation</nodename><nodenext spaces=" ">GSL least-squares fitting</nodenext><nodeprev spaces=" ">GSL special functions</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>GSL interpolation</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1014"><acronym><acronymword>GSL</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1027"><acronym><acronymword>GSL</acronymword></acronym></indexterm></cindex>
<noindent></noindent> <para>As of version 3.9.9 (released July, 2009), <acronym><acronymword>NCO</acronymword></acronym> has wrappers to the <acronym><acronymword>GSL</acronymword></acronym> interpolation functions.
</para>
<noindent></noindent> <para>Given a set of data points (x1,y1)...(xn, yn) the <acronym><acronymword>GSL</acronymword></acronym> functions computes a continuous interpolating function <acronym><acronymword>Y(x)</acronymword></acronym> such that <acronym><acronymword>Y(xi) = yi</acronymword></acronym>. The interpolation is piecewise smooth, and its behavior at the end-points is determined by the type of interpolation used. For more information consult the <acronym><acronymword>GSL</acrony [...]
@@ -11245,13 +11510,14 @@ prototypes look at the spreadsheet <strong>doc/nco_gsl.ods</strong>. &linebreak;
<noindent></noindent> <para>A simple example
</para>
<example endspaces=" ">
-<pre xml:space="preserve">x_in[$lon]={1.0,2.0,3.0,4.0};
-y_in[$lon]={1.1,1.2,1.5,1.8};
+<verbatim xml:space="preserve">
+x_in[$lon]={1.0,2.0,3.0,4.0};
+y_in[$lon]={1.1,1.2,1.5,1.8};
// Ram variable is declared and defined here
gsl_interp_cspline(&ram_sp,x_in,y_in);
-x_out[$lon_grd]={1.1,2.0,3.0,3.1,3.99};
+x_out[$lon_grd]={1.1,2.0,3.0,3.1,3.99};
y_out=gsl_spline_eval(ram_sp,x_out);
y2=gsl_spline_eval(ram_sp,1.3);
@@ -11261,7 +11527,8 @@ ram_delete(ram_sp);
print(y_out); // 1.10472, 1.2, 1.4, 1.42658, 1.69680002
print(y2); // 1.12454
print(y3); // '_'
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent> <para>Note in the above example y3 is set to &textrsquo;missing value&textrsquo; because 0.0 isn&textrsquo;t within the input X range.
</para>
@@ -11338,22 +11605,24 @@ If data_x or data_y is less than type <code>double</code> then it is converted t
<noindent></noindent> <para>The below example shows <strong>gsl_fit_linear()</strong> in action
</para>
<example endspaces=" ">
-<pre xml:space="preserve">defdim("d1",10);
-xin[d1]={1,2,3,4,5,6,7,8,9,10.0};
-yin[d1]={3.1,6.2,9.1,12.2,15.1,18.2,21.3,24.0,27.0,30.0};
+<verbatim xml:space="preserve">
+defdim("d1",10);
+xin[d1]={1,2,3,4,5,6,7,8,9,10.0};
+yin[d1]={3.1,6.2,9.1,12.2,15.1,18.2,21.3,24.0,27.0,30.0};
gsl_fit_linear(xin,1,yin,1,$d1.size,&c0,&c1,&cov00,&cov01,&cov11,&sumsq);
print(c0); // 0.2
print(c1); // 2.98545454545
defdim("e1",4);
-xout[e1]={1.0,3.0,4.0,11};
+xout[e1]={1.0,3.0,4.0,11};
yout[e1]=0.0;
yout=gsl_fit_linear_est(xout, c0,c1, cov00,cov01, cov11, sumsq);
print(yout); // 3.18545454545 ,9.15636363636, ,12.1418181818 ,33.04
-</pre></example>
+</verbatim>
+</example>
&linebreak; &linebreak;
@@ -11392,7 +11661,8 @@ double gsl_stats_quantile_from_sorted_data (var_sorted_data, data_stride, n, var
<para>Some examples
</para>
<example endspaces=" ">
-<pre xml:space="preserve">a1[time]={1,2,3,4,5,6,7,8,9,10 };
+<verbatim xml:space="preserve">
+a1[time]={1,2,3,4,5,6,7,8,9,10};
a1_avg=gsl_stats_mean(a1,1,10);
print(a1_avg); // 5.5
@@ -11402,8 +11672,8 @@ print(a1_var); // 16.0
// bounding error, vector attempts to access element a1(10)
a1_sd=gsl_stats_sd(a1,5,3);
-
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent> <para>For functions with the signature
<strong>func_nm(var_data,data_stride,n)</strong>,
@@ -11568,8 +11838,10 @@ for more complete demonstrations of <command>ncap2</command> functionality
as twice the existing attribute <var>double_att</var> of variable
<var>att_var</var>:
</para><example endspaces=" ">
-<pre xml:space="preserve">ncap2 -s 'one&arobase;new=2*att_var&arobase;double_att' in.nc out.nc
-</pre></example>
+<verbatim xml:space="preserve">
+ncap2 -s 'one at new=2*att_var at double_att' in.nc out.nc
+</verbatim>
+</example>
<para>Average variables of mixed types (result is of type <code>double</code>):
</para><example endspaces=" ">
@@ -11600,8 +11872,8 @@ statements chained together as a single <samp>-s</samp> argument.
<html endspaces=" ">
<a name="xmp_grw"></a> <!&textndash; http://nco.sf.net/nco.html#xmp_grw &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1015">growing dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1016">dimensions, growing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1028">growing dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1029">dimensions, growing</indexterm></cindex>
<para><command>ncap2</command> may be used to &textldquo;grow&textrdquo; dimensions, i.e., to increase
dimension sizes without altering existing data.
Say <file>in.nc</file> has <code>ORO(lat,lon)</code> and the user wishes a new
@@ -11624,7 +11896,7 @@ and then execute the script with
<html endspaces=" ">
<a name="flg"></a> <!&textndash; http://nco.sf.net/nco.html#flg &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1017">flags</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1030">flags</indexterm></cindex>
<para>Imagine you wish to create a binary flag based on the value of
an array.
The flag should have <w>value 1.0</w> where the array <w>exceeds 1.0</w>,
@@ -11639,7 +11911,7 @@ from the continuous array named <code>ORO</code> in <file>in.nc</file>.
</para><example endspaces=" ">
<pre xml:space="preserve">ncap2 -s 'ORO_msk=(ORO==2.0);ORO=ORO_msk*3.0+!ORO_msk*ORO' in.nc out.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1018">mask</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1031">mask</indexterm></cindex>
<para>This creates and uses <code>ORO_msk</code> to mask the subsequent arithmetic
operation.
Values of <code>ORO</code> are only changed where <code>ORO_msk</code> is true,
@@ -11656,7 +11928,7 @@ Using the <code>where</code> statement the above code simplifies to :
variables.
Let the variables <var>u</var> and <var>v</var> be the horizontal
wind components.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1019">covariance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1032">covariance</indexterm></cindex>
<!-- c fxm 20030423: texi2html 1.64 has problems with this legal syntax but makeinfo -html does not -->
The <dfn>covariance</dfn> of <var>u</var> and <var>v</var> is defined
as the time mean product of the deviations of <var>u</var> and
@@ -11679,7 +11951,7 @@ where <math>[<var>x</var>]</math> denotes the time-average of
denotes the deviation from the time-mean.
The covariance tells us how much of the correlation of two signals
arises from the signal fluctuations versus the mean signals.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1020">eddy covariance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1033">eddy covariance</indexterm></cindex>
Sometimes this is called the <dfn>eddy covariance</dfn>.
We will store the covariance in the variable <code>uprmvprm</code>.
</para><example endspaces=" ">
@@ -11704,11 +11976,11 @@ can compute averages, and thus covariances, by itself:
<para>We have not seen a simpler method to script and execute powerful
arithmetic than <command>ncap2</command>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1021">globbing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1022">shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1023">quotes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1024">extended regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1025">regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1034">globbing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1035">shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1036">quotes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1037">extended regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1038">regular expressions</indexterm></cindex>
<para><command>ncap2</command> utilizes many meta-characters
(e.g., <samp>$</samp>, <samp>?</samp>, <samp>;</samp>, <samp>()</samp>, <samp>[]</samp>)
that can confuse the command-line shell if not quoted properly.
@@ -11739,13 +12011,14 @@ variables in <command>ncap2</command> command-line scripts
In such cases it may be necessary to use the shell backslash character
<samp>\</samp> to protect the <command>ncap2</command> meta-character.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1026">appending data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1027">time-averaging</indexterm></cindex>
+
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1039">appending data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1040">time-averaging</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="18" mergedindex="cp">ncks</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="19" mergedindex="cp">ncwa</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="20" mergedindex="cp">ncra</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1028">degenerate dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1029"><samp>-b</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1041">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1042"><samp>-b</samp></indexterm></cindex>
<para>A dimension of size one is said to be <emph>degenerate</emph>.
Whether a degenerate record dimension is desirable or not
depends on the application.
@@ -11763,7 +12036,7 @@ and <code>vavg</code> to the size of the non-degenerate <var>time</var> dimensio
in the input file.
Thus the append (<command>ncks -A</command>) command would be undefined (and
should fail) in this case.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1030"><code>-C</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1043"><code>-C</code></indexterm></cindex>
Equally important is the <samp>-C</samp> argument
(<pxref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></pxref>) to <command>ncwa</command> to prevent
any scalar <var>time</var> variable from being written to the output file.
@@ -11778,78 +12051,78 @@ Knowing when to use <command>ncwa -a time</command> rather than the default
<subsection spaces=" "><sectiontitle>Intrinsic mathematical methods</sectiontitle>
<para><command>ncap2</command> supports the standard mathematical functions supplied with
most operating systems.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1031">addition</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1032">subtraction</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1033">multiplication</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1034">division</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1035">exponentiation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1036">power</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1037">modulus</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1038"><code>+</code> (addition)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1039"><code>-</code> (subtraction)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1040"><code>*</code> (multiplication)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1041"><code>/</code> (division)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1042"><code>^</code> (power)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1043"><code>%</code> (modulus)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1044">addition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1045">subtraction</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1046">multiplication</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1047">division</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1048">exponentiation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1049">power</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1050">modulus</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1051"><code>+</code> (addition)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1052"><code>-</code> (subtraction)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1053"><code>*</code> (multiplication)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1054"><code>/</code> (division)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1055"><code>^</code> (power)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1056"><code>%</code> (modulus)</indexterm></cindex>
Standard calculator notation is used for addition <kbd>+</kbd>, subtraction
<kbd>-</kbd>, multiplication <kbd>*</kbd>, division <kbd>/</kbd>, exponentiation
<kbd>^</kbd>, and modulus <kbd>%</kbd>.
The available elementary mathematical functions are:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1044"><var>abs</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1045"><var>acosh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1046"><var>acos</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1047"><var>asinh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1048"><var>asin</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1049"><var>atanh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1050"><var>atan</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1051"><var>ceil</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1052"><var>cosh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1053"><var>cos</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1054"><var>erfc</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1055"><var>erf</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1056"><var>exp</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1057"><var>floor</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1058"><var>gamma</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1059"><var>ln</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1060"><var>log10</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1061"><var>log</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1062"><var>nearbyint</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1063"><var>pow</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1064"><var>rint</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1065"><var>round</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1066"><var>sinh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1067"><var>sin</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1068"><var>sqrt</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1069"><var>tanh</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1070"><var>tan</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1071"><var>trunc</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1072">mathematical functions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1073">nearest integer function (inexact)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1074">nearest integer function (exact)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1075">rounding functions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1076">truncation function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1077">absolute value</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1078">arccosine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1079">arcsine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1080">arctangent function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1081">ceiling function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1082">complementary error function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1083">cosine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1084">error function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1085">exponentiation function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1086">floor function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1087">gamma function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1088">hyperbolic arccosine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1089">hyperbolic arcsine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1090">hyperbolic arctangent function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1091">hyperbolic cosine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1092">hyperbolic sine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1093">hyperbolic tangent</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1094">logarithm, base 10</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1095">logarithm, natural</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1096">power function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1097">sine function</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1098">square root function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1057"><var>abs</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1058"><var>acosh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1059"><var>acos</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1060"><var>asinh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1061"><var>asin</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1062"><var>atanh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1063"><var>atan</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1064"><var>ceil</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1065"><var>cosh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1066"><var>cos</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1067"><var>erfc</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1068"><var>erf</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1069"><var>exp</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1070"><var>floor</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1071"><var>gamma</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1072"><var>ln</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1073"><var>log10</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1074"><var>log</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1075"><var>nearbyint</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1076"><var>pow</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1077"><var>rint</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1078"><var>round</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1079"><var>sinh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1080"><var>sin</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1081"><var>sqrt</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1082"><var>tanh</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1083"><var>tan</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1084"><var>trunc</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1085">mathematical functions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1086">nearest integer function (inexact)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1087">nearest integer function (exact)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1088">rounding functions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1089">truncation function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1090">absolute value</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1091">arccosine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1092">arcsine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1093">arctangent function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1094">ceiling function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1095">complementary error function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1096">cosine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1097">error function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1098">exponentiation function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1099">floor function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1100">gamma function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1101">hyperbolic arccosine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1102">hyperbolic arcsine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1103">hyperbolic arctangent function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1104">hyperbolic cosine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1105">hyperbolic sine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1106">hyperbolic tangent</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1107">logarithm, base 10</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1108">logarithm, natural</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1109">power function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1110">sine function</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1111">square root function</indexterm></cindex>
</para><table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">abs(x)</itemformat></item>
</tableterm><tableitem><para><dfn>Absolute value</dfn>
@@ -12048,7 +12321,7 @@ log$(10.0) = 1.0$
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">nearbyint(x)</itemformat></item>
</tableterm><tableitem><para><dfn>Round inexactly</dfn>
Nearest integer to <var>x</var> is returned in floating point format.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1099">inexact conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1112">inexact conversion</indexterm></cindex>
No exceptions are raised for <dfn>inexact conversions</dfn>.
Example:
<tex endspaces=" ">
@@ -12057,8 +12330,8 @@ nearbyint$(0.1) = 0.0$
<math>nearbyint(0.1) = 0.0</math>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">pow(x,y)</itemformat></item>
</tableterm><tableitem><para><dfn>Power</dfn>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1100">promotion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1101">automatic type conversion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1113">promotion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1114">automatic type conversion</indexterm></cindex>
Value of <var>x</var> is raised to the power of <var>y</var>.
Exceptions are raised for <dfn>domain errors</dfn>.
Due to type-limitations in the <w>C language</w> <code>pow</code> function,
@@ -12081,7 +12354,8 @@ rint$(0.1) = 0$
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">round(x)</itemformat></item>
</tableterm><tableitem><para><dfn>Round</dfn>
Nearest integer to <var>x</var> is returned in floating point format.
-Round halfway cases away from zero, regardless of current IEEE rounding direction.
+Round halfway cases away from zero, regardless of current <acronym><acronymword>IEEE</acronymword></acronym>
+rounding direction.
Example:
<tex endspaces=" ">
round$(0.5) = 1.0$
@@ -12134,7 +12408,8 @@ tanh$(1.0) = 0.761594155956$
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="code">trunc(x)</itemformat></item>
</tableterm><tableitem><para><dfn>Truncate</dfn>
Nearest integer to <var>x</var> is returned in floating point format.
-Round halfway cases toward zero, regardless of current IEEE rounding direction.
+Round halfway cases toward zero, regardless of current <acronym><acronymword>IEEE</acronymword></acronym>
+rounding direction.
Example:
<tex endspaces=" ">
trunc$(0.5) = 0.0$
@@ -12147,14 +12422,14 @@ platform-specific.
Functions mandated by <w>ANSI C</w> are <emph>guaranteed</emph> to be present
and are indicated with an asterisk
<!-- c fxm No they're not, not yet -->
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1102"><code>ANSI C</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1103"><code>float</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1104">precision</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1105">quadruple-precision</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1106">single-precision</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1107">double-precision</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1108"><code>long double</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1109"><code>NC_DOUBLE</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1115"><code>ANSI C</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1116"><code>float</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1117">precision</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1118">quadruple-precision</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1119">single-precision</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1120">double-precision</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1121"><code>long double</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1122"><code>NC_DOUBLE</code></indexterm></cindex>
<footnote spaces="\n"><para><w>ANSI C</w> compilers are guaranteed to support double-precision versions
of these functions.
These functions normally operate on netCDF variables of type <code>NC_DOUBLE</code>
@@ -12172,12 +12447,12 @@ performing the operation, and then re-casting.
available, and uses the casting method when they are not.
</para></footnote>.
and are indicated with an asterisk.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1110"><code>-f</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1111"><code>--prn_fnc_tbl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1112"><code>--fnc_tbl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1123"><code>-f</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1124"><code>--prn_fnc_tbl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1125"><code>--fnc_tbl</code></indexterm></cindex>
Use the <samp>-f</samp> (or <samp>fnc_tbl</samp> or <samp>prn_fnc_tbl</samp>) switch
to print a complete list of functions supported on your platform.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1113">Linux</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1126">Linux</indexterm></cindex>
<footnote><para>Linux supports more of these intrinsic functions than
other OSs.</para></footnote>
</para>
@@ -12238,7 +12513,7 @@ other OSs.</para></footnote>
</subsection>
<node name="ID-Quoting" spaces=" "><nodename>ID Quoting</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" " trailingspaces=" ">Operator precedence and associativity</nodeprev><nodeup spaces=" ">ncap2 netCDF Arithmetic Processor</nodeup></node>
<subsection spaces=" "><sectiontitle>ID Quoting</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1114">ID Quoting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1127">ID Quoting</indexterm></cindex>
<para>In this section when I refer to a name I mean a variable name, attribute name or a dimension name
The allowed characters in a valid netCDF name vary from release to release. (See end section). If you want to use metacharacters in a name or use a method name as a variable name then the name has to be quoted wherever it occurs.
</para>
@@ -12273,24 +12548,27 @@ netcdf-3.6.0-p1 &linebreak;
netcdf-3.6.1 &linebreak;
netcdf-3.6.2 &linebreak;
</para><example endspaces=" ">
-<pre xml:space="preserve">/*
- * ( [a-zA-Z]|[0-9]|'_'|'-'|'+'|'.'|'|':'|'&arobase;'|'('|')' )+
+<verbatim xml:space="preserve">
+/*
+ * ( [a-zA-Z]|[0-9]|'_'|'-'|'+'|'.'|'|':'|'@'|'('|')' )+
* Verify that name string is valid CDL syntax, i.e., all characters are
* alphanumeric, '-', '_', '+', or '.'.
- * Also permit ':', '&arobase;', '(', or ')' in names for chemists currently making
+ * Also permit ':', '@', '(', or ')' in names for chemists currently making
* use of these characters, but don't document until ncgen and ncdump can
* also handle these characters in names.
*/
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent> <para>netcdf-3.6.3&linebreak;
netcdf-4.0 Final 2008/08/28&linebreak;
</para><example endspaces=" ">
-<pre xml:space="preserve">/*
+<verbatim xml:space="preserve">
+/*
* Verify that a name string is valid syntax. The allowed name
* syntax (in RE form) is:
*
- * ([a-zA-Z_]|{UTF8})([^\x00-\x1F\x7F/]|{UTF8})*
+ * ([a-zA-Z_]|{UTF8})([^\x00-\x1F\x7F/]|{UTF8})*
*
* where UTF8 represents a multibyte UTF-8 encoding. Also, no
* trailing spaces are permitted in names. This definition
@@ -12300,7 +12578,8 @@ netcdf-4.0 Final 2008/08/28&linebreak;
* character can occur anywhere within an identifier. We later
* normalize UTF-8 strings to NFC to facilitate matching and queries.
*/
-</pre></example>
+</verbatim>
+</example>
<!-- c End HMB documentation -->
<page></page>
@@ -12311,9 +12590,9 @@ netcdf-4.0 Final 2008/08/28&linebreak;
</section>
<node name="ncatted-netCDF-Attribute-Editor" spaces=" "><nodename>ncatted netCDF Attribute Editor</nodename><nodenext spaces=" ">ncbo netCDF Binary Operator</nodenext><nodeprev spaces=" ">ncap2 netCDF Arithmetic Processor</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncatted</command> netCDF Attribute Editor</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1115">attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1116">attribute names</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1117">editing attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1128">attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1129">attribute names</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1130">editing attributes</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="21" mergedindex="cp">ncatted</indexterm></findex>
<noindent></noindent>
@@ -12327,7 +12606,7 @@ netcdf-4.0 Final 2008/08/28&linebreak;
<noindent></noindent>
<para>DESCRIPTION
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1118"><command>ncattget</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1131"><command>ncattget</command></indexterm></cindex>
<para><command>ncatted</command> edits attributes in a netCDF file.
If you are editing attributes then you are spending too much time in the
world of metadata, and <command>ncatted</command> was written to get you back out as
@@ -12342,16 +12621,16 @@ To <emph>read</emph> attribute values in plain text, use <command>ncks -m -M</co
or define something like <command>ncattget</command> as a shell command
(<pxref label="Filters-for-ncks"><xrefnodename>Filters for <command>ncks</command></xrefnodename></pxref>).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1119"><code>history</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1120"><code>-h</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1132"><code>history</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1133"><code>-h</code></indexterm></cindex>
<para>Because repeated use of <command>ncatted</command> can considerably increase the size
of the <code>history</code> global attribute (<pxref label="History-Attribute"><xrefnodename>History Attribute</xrefnodename></pxref>), the
<samp>-h</samp> switch is provided to override automatically appending the
command to the <code>history</code> global attribute in the <var>output-file</var>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1121">missing values</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1122">data, missing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1123"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1134">missing values</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1135">data, missing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1136"><code>_FillValue</code></indexterm></cindex>
<para>When <command>ncatted</command> is used to change the <code>_FillValue</code> attribute,
it changes the associated missing data self-consistently.
If the internal floating point representation of a missing value,
@@ -12379,10 +12658,10 @@ Example: <code>units</code>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="var">var_nm</itemformat></item>
</tableterm><tableitem><para>Variable name.
Example: <code>pressure</code>, <code>'^H2O'</code>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1124">extended regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1125">regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1126">pattern matching</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1127">wildcards</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1137">extended regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1138">regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1139">pattern matching</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1140">wildcards</indexterm></cindex>
Regular expressions (<pxref label="Subsetting-Files"><xrefnodename>Subsetting Files</xrefnodename></pxref>) are accepted and will
select any matching variable names.
The names <code>global</code> and <code>group</code> have special meaning.
@@ -12413,8 +12692,8 @@ If <var>att_nm</var> is omitted (i.e., left blank) and <dfn>Delete</dfn> mode is
selected, then all attributes associated with the specified variable
will be deleted.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1128">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1129">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1141">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1142">attributes, global</indexterm></cindex>
<para>The value of <var>var_nm</var> is the name of the variable containing the
attribute (named <var>att_nm</var>) that you want to edit.
There are three very important and useful exceptions to this rule.
@@ -12442,12 +12721,12 @@ conventions you use for describing the data.
<para>The value of <var>mode</var> is a single character abbreviation (<code>a</code>,
<code>c</code>, <code>d</code>, <code>m</code>, or <code>o</code>) standing for one of
five editing modes:&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1130">attributes, appending</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1131">attributes, creating</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1132">attributes, deleting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1133">attributes, modifying</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1134">attributes, editing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1135">attributes, overwriting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1143">attributes, appending</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1144">attributes, creating</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1145">attributes, deleting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1146">attributes, modifying</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1147">attributes, editing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1148">attributes, overwriting</indexterm></cindex>
</para><table commandarg="code" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="code">a </itemformat></item>
</tableterm><tableitem><para><dfn>Append</dfn>.
@@ -12567,15 +12846,15 @@ The quotes are strictly unnecessary around <var>att_val</var> except
when <var>att_val</var> contains characters which would confuse the calling
shell, such as spaces, commas, and wildcard characters.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1136">Perl</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1137"><acronym><acronymword>ASCII</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1149">Perl</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1150"><acronym><acronymword>ASCII</acronymword></acronym></indexterm></cindex>
<para><acronym><acronymword>NCO</acronymword></acronym> processing of <code>NC_CHAR</code> attributes is a bit like Perl in
that it attempts to do what you want by default (but this sometimes
causes unexpected results if you want unusual data storage).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1138"><code>printf()</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1139"><code>\n</code> (<acronym><acronymword>ASCII</acronymword></acronym> LF, linefeed)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1140">characters, special</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1141"><code>\t</code> (<acronym><acronymword>ASCII</acronymword></acronym> HT, horizontal tab)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1151"><code>printf()</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1152"><code>\n</code> (<acronym><acronymword>ASCII</acronymword></acronym> LF, linefeed)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1153">characters, special</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1154"><code>\t</code> (<acronym><acronymword>ASCII</acronymword></acronym> HT, horizontal tab)</indexterm></cindex>
If the <var>att_type</var> is <code>NC_CHAR</code> then the argument is interpreted as a
string and it may contain C-language escape sequences, e.g., <code>\n</code>,
which <acronym><acronymword>NCO</acronymword></acronym> will interpret before writing anything to disk.
@@ -12589,27 +12868,27 @@ The most frequently used C-language escape sequences are <code>\n</code> (for
linefeed) and <code>\t</code> (for horizontal tab).
These sequences in particular allow convenient editing of formatted text
attributes.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1142"><code>\a</code> (<acronym><acronymword>ASCII</acronymword></acronym> BEL, bell)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1143"><code>\b</code> (<acronym><acronymword>ASCII</acronymword></acronym> BS, backspace)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1144"><code>\f</code> (<acronym><acronymword>ASCII</acronymword></acronym> FF, formfeed)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1145"><code>\r</code> (<acronym><acronymword>ASCII</acronymword></acronym> CR, carriage return)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1146"><code>\v</code> (<acronym><acronymword>ASCII</acronymword></acronym> VT, vertical tab)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1147"><code>\\</code> (<acronym><acronymword>ASCII</acronymword></acronym> \, backslash)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1155"><code>\a</code> (<acronym><acronymword>ASCII</acronymword></acronym> BEL, bell)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1156"><code>\b</code> (<acronym><acronymword>ASCII</acronymword></acronym> BS, backspace)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1157"><code>\f</code> (<acronym><acronymword>ASCII</acronymword></acronym> FF, formfeed)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1158"><code>\r</code> (<acronym><acronymword>ASCII</acronymword></acronym> CR, carriage return)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1159"><code>\v</code> (<acronym><acronymword>ASCII</acronymword></acronym> VT, vertical tab)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1160"><code>\\</code> (<acronym><acronymword>ASCII</acronymword></acronym> \, backslash)</indexterm></cindex>
The other valid <acronym><acronymword>ASCII</acronymword></acronym> codes are <code>\a</code>, <code>\b</code>, <code>\f</code>,
<code>\r</code>, <code>\v</code>, and <code>\\</code>.
<xref label="ncks-netCDF-Kitchen-Sink"><xrefnodename>ncks netCDF Kitchen Sink</xrefnodename></xref>, for more examples of string formatting
(with the <command>ncks</command> <samp>-s</samp> option) with special characters.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1148"><code>\'</code> (protected end quote)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1149"><code>\"</code> (protected double quote)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1150"><code>\?</code> (protected question mark)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1151"><code>\\</code> (protected backslash)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1152"><code>'</code> (end quote)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1153"><code>"</code> (double quote)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1154"><code>?</code> (question mark)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1155"><code>\</code> (backslash)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1156">special characters</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1157"><acronym><acronymword>ASCII</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1161"><code>\'</code> (protected end quote)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1162"><code>\"</code> (protected double quote)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1163"><code>\?</code> (protected question mark)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1164"><code>\\</code> (protected backslash)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1165"><code>'</code> (end quote)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1166"><code>"</code> (double quote)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1167"><code>?</code> (question mark)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1168"><code>\</code> (backslash)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1169">special characters</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1170"><acronym><acronymword>ASCII</acronymword></acronym></indexterm></cindex>
<para>Analogous to <code>printf</code>, other special characters are also allowed by
<command>ncatted</command> if they are "protected" by a backslash.
The characters <code>"</code>, <code>'</code>, <code>?</code>, and <code>\</code> may be
@@ -12621,11 +12900,11 @@ Backslashes which precede any other character (e.g., <code>3</code>, <code>m</co
<code>$</code>, <code>|</code>, <code>&</code>, <code>&arobase;</code>, <code>%</code>, <code>{</code>, and
<code>}</code>) will not be filtered and will be included in the attribute.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1158">strings</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1159">NUL-termination</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1160">NUL</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1161">C language</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1162"><code>0</code> (NUL)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1171">strings</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1172">NUL-termination</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1173">NUL</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1174">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1175"><code>0</code> (NUL)</indexterm></cindex>
<para>Note that the NUL character <code>\0</code> which terminates <w>C language</w>
strings is assumed and need not be explicitly specified.
<!-- comment If @code{\0} is input, it will not be translated (because it would -->
@@ -12665,23 +12944,30 @@ from whatever it currently is to "temperature":
<html endspaces=" ">
<a name="NaN"></a> <!&textndash; http://nco.sf.net/nco.html#NaN &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1163">NaN</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1164">IEEE NaN</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1165">Not-a-Number</indexterm></cindex>
-<para><acronym><acronymword>NCO</acronymword></acronym> arithmetic operators will not work as expected on IEEE
-NaN (short for Not-a-Number) and NaN-like numbers such as positive
-infinity and negative infinity.
-One way to work-around this problem is to change IEEE NaNs to normal
-missing values.
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1176">NaN</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1177"><acronym><acronymword>IEEE</acronymword></acronym> NaN</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1178">Not-a-Number</indexterm></cindex>
+<para><acronym><acronymword>NCO</acronymword></acronym> arithmetic operators may not work as expected on
+<acronym><acronymword>IEEE</acronymword></acronym> NaN (short for Not-a-Number) and NaN-like numbers such as
+positive infinity and negative infinity
+<footnote><para>Arithmetic comparisons to NaN and NaN-like numbers always
+return False, contrary to the behavior of all other numbers.
+This is difficult to inuit, yet is the behavior defined for NaN by
+<acronym><acronymword>IEEE</acronymword></acronym> 754.
+Using NaN for the missing value in datasets is legal.
+We strongly discourage it.</para></footnote>.
+One way to work-around this problem is to change <acronym><acronymword>IEEE</acronymword></acronym> NaNs to
+normal missing values.
As of <acronym><acronymword>NCO</acronymword></acronym> 4.1.0 (March, 2012), <command>ncatted</command> works with
NaNs.
First set the missing value (i.e., the value of the <code>_FillValue</code>
-attribute) for the variable(s) in question to the IEEE NaN value.
+attribute) for the variable(s) in question to the <acronym><acronymword>IEEE</acronymword></acronym> NaN value.
</para><example endspaces=" ">
<pre xml:space="preserve">ncatted -a _FillValue,,o,f,NaN in.nc
</pre></example>
-<para>Then change the missing value from the IEEE NaN value to a normal IEEE
-number, like 1.0e36 (or to whatever the original missing value was).
+<para>Then change the missing value from the <acronym><acronymword>IEEE</acronymword></acronym> NaN value to a
+normal <acronym><acronymword>IEEE</acronymword></acronym> number, like 1.0e36 (or to whatever the original
+missing value was).
</para><example endspaces=" ">
<pre xml:space="preserve">ncatted -a _FillValue,,m,f,1.0e36 in.nc
</pre></example>
@@ -12696,9 +12982,9 @@ variables in the file.
The values of <var>att_type</var> and <var>att_val</var> were left blank because
they are superfluous in <dfn>Delete</dfn> mode.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1166"><code>global</code> attribute</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1167">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1168">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1179"><code>global</code> attribute</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1180">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1181">attributes, global</indexterm></cindex>
<para>Delete all attributes associated with the <code>tpt</code> variable, and
delete all global attributes
</para><example endspaces=" ">
@@ -12710,13 +12996,13 @@ attributes associated with the variable.
To delete all global attributes, simply replace <code>tpt</code> with
<code>global</code> in the above.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1169"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1182"><code>units</code></indexterm></cindex>
<para>Modify all existing <code>units</code> attributes to "meter second-1":
</para><example endspaces=" ">
<pre xml:space="preserve">ncatted -a units,,m,c,"meter second-1" in.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1170"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1183"><code>units</code></indexterm></cindex>
<para>Add a <code>units</code> attribute of "kilogram kilogram-1" to all variables
whose first three characters are <samp>H2O</samp>:
</para><example endspaces=" ">
@@ -12729,10 +13015,10 @@ whose first three characters are <samp>H2O</samp>:
<pre xml:space="preserve">ncatted -O -a quanta,energy,o,s,"010,101,111,121" in.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1171">extended regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1172">regular expressions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1173">pattern matching</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1174">wildcards</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1184">extended regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1185">regular expressions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1186">pattern matching</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1187">wildcards</indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> 3.9.6 (January, 2009), <command>ncatted</command> accepts
<dfn>extended regular expressions</dfn> as arguments for variable names.
Create <code>isotope</code> attributes for all variables containing <samp>H2O</samp>
@@ -12742,7 +13028,7 @@ in their names.
</pre></example>
<para>See <ref label="Subsetting-Files"><xrefnodename>Subsetting Files</xrefnodename></ref> for more details.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1175">groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1188">groups</indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> 4.3.8 (November, 2013), <command>ncatted</command>
accepts full and partial group paths in names of attributes,
variables, dimensions, and groups.
@@ -12801,14 +13087,14 @@ omitted in batch scripts.
<findex index="fn" spaces=" "><indexterm index="fn" number="27" mergedindex="cp">ncmult</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="28" mergedindex="cp">ncmultiply</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="29" mergedindex="cp">ncdivide</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1176">binary operations</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1177">addition</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1178">subtraction</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1179">multiplication</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1180">adding data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1181">subtracting data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1182">multiplying data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1183">dividing data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1189">binary operations</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1190">addition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1191">subtraction</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1192">multiplication</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1193">adding data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1194">subtracting data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1195">multiplying data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1196">dividing data</indexterm></cindex>
<noindent></noindent>
<para>SYNTAX
@@ -12835,18 +13121,18 @@ variables).
One of the four standard arithmetic binary operations currently
supported must be selected with the <samp>-y <var>op_typ</var></samp> switch (or
long options <samp>--op_typ</samp> or <samp>--operation</samp>).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1184"><code>add</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1185"><code>subtract</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1186"><code>multiply</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1187"><code>divide</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1188"><code>+</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1189"><code>-</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1190"><code>*</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1191"><code>/</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1192"><code>-y <var>op_typ</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1193"><code>--operation <var>op_typ</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1194"><code>--op_typ <var>op_typ</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1195">alternate invocations</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1197"><code>add</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1198"><code>subtract</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1199"><code>multiply</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1200"><code>divide</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1201"><code>+</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1202"><code>-</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1203"><code>*</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1204"><code>/</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1205"><code>-y <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1206"><code>--operation <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1207"><code>--op_typ <var>op_typ</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1208">alternate invocations</indexterm></cindex>
The valid binary operations for <command>ncbo</command>, their definitions,
corresponding values of the <var>op_typ</var> key, and alternate invocations
are:
@@ -12877,12 +13163,12 @@ Examples: <samp>ncbo --op_typ=/ 1.nc 2.nc 3.nc</samp>, <samp>ncdivide 1.nc 2.nc
<para>Care should be taken when using the shortest form of key values,
i.e., <samp>+</samp>, <samp>-</samp>, <samp>*</samp>, <w>and <samp>/</samp></w>.
Some of these single characters may have special meanings to the shell
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1196">naked characters</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1209">naked characters</indexterm></cindex>
<footnote><para><w>A naked</w> (i.e., unprotected or unquoted) <samp>*</samp> is a
wildcard character.
<w>A naked</w> <samp>-</samp> may confuse the command line parser.
<w>A naked</w> <samp>+</samp> and <samp>/</samp> are relatively harmless.</para></footnote>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1197">Bash shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1210">Bash shell</indexterm></cindex>
Place these characters inside quotes to keep them from being interpreted
(globbed) by the shell
<footnote><para>The widely used shell Bash correctly interprets all these
@@ -12892,9 +13178,9 @@ the intended arithmetic operation when the following arguments are given
(without quotes) to <command>ncbo</command>:
<samp>--op_typ=+</samp>, <samp>--op_typ=-</samp>, <samp>--op_typ=*</samp>,
and <samp>--op_typ=/</samp></para></footnote>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1198">globbing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1199">shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1200">quotes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1211">globbing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1212">shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1213">quotes</indexterm></cindex>
For example, the following commands are equivalent
</para><example endspaces=" ">
<pre xml:space="preserve">ncbo --op_typ=* 1.nc 2.nc 3.nc # Dangerous (shell may try to glob)
@@ -12910,9 +13196,9 @@ ncmultiply 1.nc 2.nc 3.nc # First do 'ln -s ncbo ncmultiply'
<para>No particular argument or invocation form is preferred.
Users are encouraged to use the forms which are most intuitive to them.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1201"><command>alias</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1202"><command>ln -s</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1203">symbolic links</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1214"><command>alias</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1215"><command>ln -s</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1216">symbolic links</indexterm></cindex>
<para>Normally, <command>ncbo</command> will fail unless an operation type is specified
with <samp>-y</samp> (equivalent to <samp>--op_typ</samp>).
You may create exceptions to this rule to suit your particular tastes,
@@ -12954,12 +13240,12 @@ This ensures portability of scripts between users and sites.
<html endspaces=" ">
<a name="brd_var"></a> <!&textndash; http://nco.sf.net/nco.html#brd_var &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1204">broadcasting variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1205">rank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1217">broadcasting variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1218">rank</indexterm></cindex>
<para><command>ncbo</command> operates (e.g., adds) variables in <var>file_2</var> with the
corresponding variables (those with the same name) in <var>file_1</var> and
stores the results in <var>file_3</var>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1206">broadcasting variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1219">broadcasting variables</indexterm></cindex>
Variables in <var>file_1</var> or <var>file_2</var> are <dfn>broadcast</dfn> to conform
to the corresponding variable in the other input file if
necessary<footnote spaces="\n"><para>Prior to <acronym><acronymword>NCO</acronymword></acronym> version 4.3.1 (May, 2013), <command>ncbo</command>
@@ -12982,12 +13268,12 @@ by copying data in existing dimensions.
For example, a two dimensional variable in <var>file_2</var> can be
subtracted from a four, three, or two (not one or zero)
dimensional variable (of the same name) in <code>file_1</code>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1207">anomalies</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1220">anomalies</indexterm></cindex>
This functionality allows the user to compute anomalies from the mean.
In the future, we will broadcast variables in <var>file_1</var>, if necessary
to conform to their counterparts in <var>file_2</var>.
<!-- c TODO #268 -->
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1208">rank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1221">rank</indexterm></cindex>
Thus, presently, the number of dimensions, or <dfn>rank</dfn>, of any
processed variable in <var>file_1</var> must be greater than or equal to the
rank of the same variable in <var>file_2</var>.
@@ -13002,13 +13288,13 @@ In these cases, creating <var>file_2</var> with <command>ncra</command> rather t
<command>ncwa</command> will cause the <command>ncbo</command> operation to fail.
For concreteness say the record dimension in <code>file_1</code> is
<code>time</code>.
-If <var>file_2</var> were created by averaging <var>file_1</var> over the
-<code>time</code> dimension with the <command>ncra</command> operator rather than with
-the <command>ncwa</command> operator, then <var>file_2</var> will have a <code>time</code>
+If <var>file_2</var> was created by averaging <var>file_1</var> over the
+<code>time</code> dimension with the <command>ncra</command> operator (rather than with
+the <command>ncwa</command> operator), then <var>file_2</var> will have a <code>time</code>
dimension of <w>size 1</w> rather than having no <code>time</code> dimension at
all
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1209">degenerate dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1210"><samp>-b</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1222">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1223"><samp>-b</samp></indexterm></cindex>
<footnote><para>This is because <command>ncra</command> collapses the record dimension
to a size <w>of 1</w> (making it a <dfn>degenerate</dfn> dimension), but does
not remove it, while, unless <samp>-b</samp> is given, <command>ncwa</command> removes
@@ -13022,14 +13308,14 @@ To prevent this from occuring, use <command>ncwa</command> to remove the
<code>time</code> dimension from <var>file_2</var>.
See the example below.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1211">coordinate variable</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1212"><code>NC_CHAR</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1224">coordinate variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1225"><code>NC_CHAR</code></indexterm></cindex>
<para><command>ncbo</command> never operates on coordinate variables or variables
of type <code>NC_CHAR</code> or <code>NC_STRING</code>.
This ensures that coordinates like (e.g., latitude and longitude) are
physically meaningful in the output file, <var>file_3</var>.
This behavior is hardcoded.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1213"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1226"><acronym><acronymword>CF</acronymword></acronym> conventions</indexterm></cindex>
<command>ncbo</command> applies special rules to some
<acronym><acronymword>CF</acronymword></acronym>-defined (and/or <acronym><acronymword>NCAR CCSM</acronymword></acronym> or <acronym><acronymword>NCAR CCM</acronymword></acronym>
fields) such as <code>ORO</code>.
@@ -13045,7 +13331,7 @@ albeit in a more convoluted way than <command>ncbo</command>.
<a name="gb"></a> <!&textndash; http://nco.sf.net/nco.html#gb &textndash;>
<a name="GB"></a> <!&textndash; http://nco.sf.net/nco.html#GB &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1214">broadcasting groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1227">broadcasting groups</indexterm></cindex>
<para>Beginning with <acronym><acronymword>NCO</acronymword></acronym> version 4.3.1 (May, 2013), <command>ncbo</command>
supports <dfn>group broadcasting</dfn>.
Group broadcasting means processing data based on group patterns in the
@@ -13080,8 +13366,8 @@ ncbo --op_typ='-' 86_0112.nc 85_0112.nc 86m85_0112.nc
<noindent></noindent>
<para>These commands are all different ways of expressing the same thing.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1215">broadcasting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1216">rank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1228">broadcasting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1229">rank</indexterm></cindex>
<para>The following examples demonstrate the broadcasting feature of
<command>ncbo</command>.
Say we wish to compute the monthly anomalies of <code>T</code> from the yearly
@@ -13128,7 +13414,7 @@ ncdiff 85_0112.nc 85_x.nc tx_anm_85_0112.nc
<code>time</code> and <code>lon</code>, and that <file>85_x.nc</file> has no <code>time</code>
or <code>lon</code> dimension.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1217">broadcasting groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1230">broadcasting groups</indexterm></cindex>
<para>Group broadcasting simplifies evaluation of multiple models against
observations.
Consider the input file <file>cmip5.nc</file> which contains multiple
@@ -13181,30 +13467,34 @@ one file, and use <command>ncra</command> to create the average anomaly for all
five Januarys.
These commands are embedded in a shell loop so they are repeated for all
twelve months:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1218">Bash Shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1219">Bourne Shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1220">C Shell</indexterm></cindex>
-</para><example endspaces=" ">
-<pre xml:space="preserve">for idx in {1..12}; do # Bash Shell (version 3.0+)
- idx=`printf "%02d" ${idx}` # Zero-pad to preserve order
- ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
- ncra foo.${idx} t_anm_8589_${idx}.nc
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1231">Bash Shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1232">Bourne Shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1233">C Shell</indexterm></cindex>
+</para><example endspaces=" ">
+<verbatim xml:space="preserve">
+for idx in {1..12}; do # Bash Shell (version 3.0+)
+ idx=`printf "%02d" ${idx}` # Zero-pad to preserve order
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
done
for idx in 01 02 03 04 05 06 07 08 09 10 11 12; do # Bourne Shell
- ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
- ncra foo.${idx} t_anm_8589_${idx}.nc
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
done
foreach idx (01 02 03 04 05 06 07 08 09 10 11 12) # C Shell
- ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
- ncra foo.${idx} t_anm_8589_${idx}.nc
+ ncks -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+ ncra foo.${idx} t_anm_8589_${idx}.nc
end
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent>
<para>Note that <command>ncra</command> understands the <code>stride</code> argument so the
two commands inside the loop may be combined into the single command
</para><example endspaces=" ">
-<pre xml:space="preserve">ncra -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
-</pre></example>
+<verbatim xml:space="preserve">
+ncra -F -d time,${idx},,12 t_anm_8501_8912.nc foo.${idx}
+</verbatim>
+</example>
<noindent></noindent>
<para>Finally, use <command>ncrcat</command> to concatenate the <w>12 average</w> monthly
anomaly files into one twelve-record file which contains the entire
@@ -13222,8 +13512,8 @@ seasonal cycle of the monthly anomalies:
</section>
<node name="nces-netCDF-Ensemble-Statistics" spaces=" "><nodename>nces netCDF Ensemble Statistics</nodename><nodenext spaces=" ">ncecat netCDF Ensemble Concatenator</nodenext><nodeprev spaces=" ">ncbo netCDF Binary Operator</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>nces</command> netCDF Ensemble Statistics</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1221">averaging data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1222">ensemble average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1234">averaging data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1235">ensemble average</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="30" mergedindex="cp">nces</indexterm></findex>
<noindent></noindent>
@@ -13253,7 +13543,7 @@ released December, 2013.
<acronym><acronymword>NCO</acronymword></acronym> will attempt to maintain back-compatibility and work
as expected with invocations of <command>ncea</command> for as long as possible.
Please replace <command>ncea</command> by <command>nces</command> in all future work.</para></footnote>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1223">ensemble</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1236">ensemble</indexterm></cindex>
For example, <command>nces</command> will average a set of files or groups,
weighting each file or group evenly.
This is distinct from <command>ncra</command>, which performs statistics only
@@ -13283,17 +13573,17 @@ the hypserslabs may (and usually do) change the size of the dimensions
from the input to the output files.
Prior to this, <command>nces</command> was only guaranteed to work on hyperslabs
in the record dimension that resolved to the same size.</para></footnote>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1224">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1225">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1237">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1238">hyperslab</indexterm></cindex>
<command>nces</command> does allow files to differ in the record dimension size
if the requested record hyperslab (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>) resolves to the
same size for all files.
<command>nces</command> recomputes the record dimension hyperslab limits for
each input file so that coordinate limits may be used to select equal
length timeseries from unequal length files.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1226"><acronym><acronymword>IPCC</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1227"><acronym><acronymword>AR4</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1228"><acronym><acronymword>CMIP</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1239"><acronym><acronymword>IPCC</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1240"><acronym><acronymword>AR4</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1241"><acronym><acronymword>CMIP</acronymword></acronym></indexterm></cindex>
This simplifies analysis of unequal length timeseries from simulation
ensembles (e.g., the <acronym><acronymword>CMIP3</acronymword></acronym> <acronym><acronymword>IPCC</acronymword></acronym> <acronym><acronymword>AR4</acronymword></acronym>
archive).
@@ -13303,12 +13593,12 @@ archive).
<a name="nsm_grp"></a> <!&textndash; http://nco.sf.net/nco.html#nsm_grp &textndash;>
<a name="nsm_sfx"></a> <!&textndash; http://nco.sf.net/nco.html#nsm_sfx &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1229"><code>--nsm_fl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1230"><code>--nsm_grp</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1231"><code>--ensemble_file</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1232"><code>--ensemble_group</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1233"><code>--nsm_sfx</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1234"><code>--ensemble_suffix</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1242"><code>--nsm_fl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1243"><code>--nsm_grp</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1244"><code>--ensemble_file</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1245"><code>--ensemble_group</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1246"><code>--nsm_sfx</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1247"><code>--ensemble_suffix</code></indexterm></cindex>
<para><command>nces</command> works in one of two modes, file ensembles
or group ensembles.
File ensembles are the default (equivalent to the old <command>ncea</command>)
@@ -13346,9 +13636,9 @@ nces --nsm_grp --nsm_sfx='_avg' mdl1.nc mdl2.nc mdl3.nc out.nc
<para><xref label="Statistics-vs_002e-Concatenation"><xrefnodename>Statistics vs. Concatenation</xrefnodename></xref>, for a description of the
distinctions between the statistics tools and concatenators.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1235">multi-file operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1236">standard input</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1237"><code>stdin</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1248">multi-file operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1249">standard input</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1250"><code>stdin</code></indexterm></cindex>
As a multi-file operator, <command>nces</command> will read the list of
<var>input-files</var> from <code>stdin</code> if they are not specified
as positional arguments on the command line
@@ -13446,8 +13736,8 @@ member in the first file.
</section>
<node name="ncecat-netCDF-Ensemble-Concatenator" spaces=" "><nodename>ncecat netCDF Ensemble Concatenator</nodename><nodenext spaces=" ">ncflint netCDF File Interpolator</nodenext><nodeprev spaces=" ">nces netCDF Ensemble Statistics</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncecat</command> netCDF Ensemble Concatenator</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1238">concatenation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1239">ensemble concatenation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1251">concatenation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1252">ensemble concatenation</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="31" mergedindex="cp">ncecat</indexterm></findex>
<noindent></noindent>
@@ -13484,8 +13774,8 @@ subsetting simultaneously (<pxref label="Subsetting-Files"><xrefnodename>Subsett
<html endspaces=" ">
<a name="rag"></a> <!&textndash; http://nco.sf.net/nco.html#rag &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1240">record aggregation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1241"><acronym><acronymword>RAG</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1253">record aggregation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1254"><acronym><acronymword>RAG</acronymword></acronym></indexterm></cindex>
<para><acronym><acronymword>RAG</acronymword></acronym> makes each variable (except coordinate variables) in each
input file into a single record of the same variable in the output file.
Coordinate variables are not concatenated, they are instead simply
@@ -13498,27 +13788,27 @@ data.
The new record dimension is defined in the root group of the output file
so it is visible to all sub-groups.
Its name is, by default, &textldquo;record&textrdquo;.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1242">unlimited dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1243">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1244"><samp>-u <var>ulm_nm</var></samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1245"><samp>--ulm_nm <var>ulm_nm</var></samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1246"><samp>--rcd_nm <var>ulm_nm</var></samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1255">unlimited dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1256">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1257"><samp>-u <var>ulm_nm</var></samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1258"><samp>--ulm_nm <var>ulm_nm</var></samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1259"><samp>--rcd_nm <var>ulm_nm</var></samp></indexterm></cindex>
This default name can be overridden with the <samp>-u <var>ulm_nm</var></samp>
short option (or the <samp>--ulm_nm</samp> or <samp>rcd_nm</samp> long options).
</para>
<para>Each extracted variable must be constant in size and rank across all
<var>input-files</var>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1247">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1248">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1260">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1261">hyperslab</indexterm></cindex>
The only exception is that <command>ncecat</command> allows files to differ in
the record dimension size if the requested record hyperslab
(<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>) resolves to the same size for all files.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1249"><acronym><acronymword>CMIP</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1262"><acronym><acronymword>CMIP</acronymword></acronym></indexterm></cindex>
This allows easier gluing/averaging of unequal length timeseries from
simulation ensembles (e.g., the <acronym><acronymword>CMIP</acronymword></acronym> rchive).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1250">fixed dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1251">fix record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1263">fixed dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1264">fix record dimension</indexterm></cindex>
<para>Classic (i.e., all netCDF3 and <code>NETCDF4_CLASSIC</code>) output files
can contain only one record dimension.
<command>ncecat</command> makes room for the new glue record dimension by
@@ -13531,8 +13821,8 @@ if any, of the input files as it copies them to the output file.
<html endspaces=" ">
<a name="gag"></a> <!&textndash; http://nco.sf.net/nco.html#gag &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1252">group aggregation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1253"><acronym><acronymword>GAG</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1265">group aggregation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1266"><acronym><acronymword>GAG</acronymword></acronym></indexterm></cindex>
<para><dfn>Group AGgregation</dfn> (<acronym><acronymword>GAG</acronymword></acronym>) stores <var>input-files</var> as
top-level groups in the <var>output-file</var>.
No assumption is made about the size or shape or type of a given
@@ -13541,7 +13831,7 @@ The entire contents of the extracted portion of each input file
is placed in its own top-level group in <var>output-file</var>, which
is automatically made as a netCDF4-format file.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1254"><option>--gag</option></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1267"><option>--gag</option></indexterm></cindex>
<para><acronym><acronymword>GAG</acronymword></acronym> has two methods to specify group names for the
<var>output-file</var>.
The <samp>-G</samp> option, or its long-option equivalent <samp>--gpe</samp>,
@@ -13570,17 +13860,17 @@ ncecat -G 85/ a.nc b.nc c.nc 8589.nc # Output groups 85/00, 85/01, 85/02
the sum of the sizes of the extracted variables in the input files.
<xref label="Statistics-vs_002e-Concatenation"><xrefnodename>Statistics vs. Concatenation</xrefnodename></xref>, for a description of the
distinctions between the various statistics tools and concatenators.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1255">multi-file operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1256">standard input</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1257"><code>stdin</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1268">multi-file operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1269">standard input</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1270"><code>stdin</code></indexterm></cindex>
As a multi-file operator, <command>ncecat</command> will read the list of
<var>input-files</var> from <code>stdin</code> if they are not specified
as positional arguments on the command line
(<pxref label="Large-Numbers-of-Files"><xrefnodename>Large Numbers of Files</xrefnodename></pxref>).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1258"><code>-M</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1259"><code>--glb_mtd_spp</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1260">metadata, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1271"><code>-M</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1272"><code>--glb_mtd_spp</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1273">metadata, global</indexterm></cindex>
<para>Suppress global metadata copying.
By default <acronym><acronymword>NCO</acronymword></acronym>&textrsquo;s multi-file operators copy the global metadata
from the first input file into <var>output-file</var>.
@@ -13594,7 +13884,7 @@ metadata.
metadata via the <samp>-M</samp> switch (or its long option equivalents,
<samp>--glb_mtd_spp</samp> and <samp>--global_metadata_suppress</samp>).
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1261">climate model</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1274">climate model</indexterm></cindex>
<para>Consider five realizations, <file>85a.nc</file>, <file>85b.nc</file>,
<w>&dots; <file>85e.nc</file></w> of 1985 predictions from the same climate
model.
@@ -13609,10 +13899,10 @@ Normally this means all the input files are the same size, and contain
data on different realizations of the same variables.
</para>
<findex index="fn" spaces=" "><indexterm index="fn" number="32" mergedindex="cp">ncpdq</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1262">packing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1263">unpacking</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1264"><code>add_offset</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1265"><code>scale_factor</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1275">packing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1276">unpacking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1277"><code>add_offset</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1278"><code>scale_factor</code></indexterm></cindex>
<para>Concatenating a variable packed with different scales across multiple
datasets is beyond the capabilities of <command>ncecat</command> (and
<command>ncrcat</command>, the other concatenator (<ref label="Concatenation"><xrefnodename>Concatenation</xrefnodename></ref>).
@@ -13673,10 +13963,10 @@ such descriptive coordinates are used.
<html endspaces=" ">
<a name="dmn_rcd_rm"></a> <!&textndash; http://nco.sf.net/nco.html#dmn_rcd_rm &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1266">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1267">fixed dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1268">fix record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1269"><code>--mk_rec_dmn <var>dim</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1279">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1280">fixed dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1281">fix record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1282"><code>--mk_rec_dmn <var>dim</var></code></indexterm></cindex>
<para>Consider a file with an existing record dimension named <code>time</code>.
and suppose the user wishes to convert <code>time</code> from a record
dimension to a non-record dimension.
@@ -13685,7 +13975,7 @@ record variable.
The simplest method is to use <samp>ncks --fix_rec_dmn</samp> but another
possibility is to use <command>ncecat</command> followed by
<command>ncwa</command>:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1270">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1283">degenerate dimension</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncecat in.nc out.nc # Convert time to non-record dimension
ncwa -a record in.nc out.nc # Remove new degenerate record dimension
@@ -13703,10 +13993,10 @@ of changing variable dimensionality, including the record dimension.
</section>
<node name="ncflint-netCDF-File-Interpolator" spaces=" "><nodename>ncflint netCDF File Interpolator</nodename><nodenext spaces=" ">ncks netCDF Kitchen Sink</nodenext><nodeprev spaces=" ">ncecat netCDF Ensemble Concatenator</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncflint</command> netCDF File Interpolator</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1271">interpolation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1272">adding data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1273">multiplying data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1274">addition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1284">interpolation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1285">adding data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1286">multiplying data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1287">addition</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="33" mergedindex="cp">ncflint</indexterm></findex>
<noindent></noindent>
@@ -13749,9 +14039,9 @@ $val3 = wgt1 \times val1 + wgt2 \times val2$
Here at least <var>wgt1</var>, and, optionally, <var>wgt2</var>, are specified on
the command line with the <samp>-w</samp> (or <samp>--weight</samp> or
<samp>--wgt_var</samp>) switch.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1275"><code>-w <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1276"><code>--weight <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1277"><code>--wgt_var <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1288"><code>-w <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1289"><code>--weight <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1290"><code>--wgt_var <var>wgt1</var>[,<var>wgt2</var>]</code></indexterm></cindex>
If only <var>wgt1</var> is specified then <var>wgt2</var> is automatically
computed as <math><var>wgt2</var> = 1 − <var>wgt1</var></math>.
Note that weights larger <w>than 1</w> are allowed.
@@ -13770,7 +14060,7 @@ weights and adding together the results to produce the output values.
It makes sense to use this when the weights are known
<emph><w>a priori</w></emph>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1278">arrival value</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1291">arrival value</indexterm></cindex>
<para>Another class of problems has the <dfn>arrival value</dfn> (i.e., <var>val3</var>)
of a particular variable <var>var</var> known <emph><w>a priori</w></emph>.
In this case, the implied weights can always be inferred by examining
@@ -13793,7 +14083,7 @@ and <var>val3</var> with the <samp>-i</samp> option.
weights on all variables to generate the output file.
Although <var>var</var> may have any number of dimensions in the input
files, it must represent a single, scalar value.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1279">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1292">degenerate dimension</indexterm></cindex>
Thus any dimensions associated with <var>var</var> must be <dfn>degenerate</dfn>,
i.e., of size one.
</para>
@@ -13820,8 +14110,8 @@ in <acronym><acronymword>NCO</acronymword></acronym> version 4.2.6 (March, 2013)
It prevents <command>ncflint</command> from multiplying or interpolating any
coordinate variables, including record coordinate variables.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1280">missing values</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1281"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1293">missing values</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1294"><code>_FillValue</code></indexterm></cindex>
<para>Depending on your intuition, <command>ncflint</command> may treat missing values
unexpectedly.
Consider a point where the value in one input file, say <var>val1</var>,
@@ -13897,13 +14187,13 @@ together to make <file>tst.nc</file>:
<pre xml:space="preserve">ncflint -w 3,-2 85.nc 85.nc tst.nc
</pre></example>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1282">null operation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1295">null operation</indexterm></cindex>
<para>This is an example of a null operation, so <file>tst.nc</file> should be
identical (within machine precision) to <file>85.nc</file>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1283">multiplication</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1284">file multiplication</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1285">scaling</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1296">multiplication</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1297">file multiplication</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1298">scaling</indexterm></cindex>
<para>Multiply all the variables except the coordinate variables in the file
<file>emissions.nc</file> by <w>by 0.8</w>:
</para><example endspaces=" ">
@@ -13923,14 +14213,14 @@ ncdiff 85.nc 86.nc 85m86.nc
<noindent></noindent>
<para>Thus <command>ncflint</command> can be used to mimic some <command>ncbo</command>
operations.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1286">broadcasting variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1299">broadcasting variables</indexterm></cindex>
However this is not a good idea in practice because <command>ncflint</command>
does not broadcast (<pxref label="ncbo-netCDF-Binary-Operator"><xrefnodename>ncbo netCDF Binary Operator</xrefnodename></pxref>) conforming
variables during arithmetic.
Thus the final two commands would produce identical results except that
<command>ncflint</command> would fail if any variables needed to be broadcast.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1287"><code>units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1300"><code>units</code></indexterm></cindex>
<para>Rescale the dimensional units of the surface pressure <code>prs_sfc</code>
from Pascals to hectopascals (millibars)
</para><example endspaces=" ">
@@ -13946,9 +14236,9 @@ ncatted -a units,prs_sfc,o,c,millibar out.nc
</section>
<node name="ncks-netCDF-Kitchen-Sink" spaces=" "><nodename>ncks netCDF Kitchen Sink</nodename><nodenext spaces=" ">ncpdq netCDF Permute Dimensions Quickly</nodenext><nodeprev spaces=" ">ncflint netCDF File Interpolator</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncks</command> netCDF Kitchen Sink</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1288">kitchen sink</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1289">printing files contents</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1290">printing variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1301">kitchen sink</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1302">printing files contents</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1303">printing variables</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="34" mergedindex="cp">ncks</indexterm></findex>
<noindent></noindent>
@@ -13957,7 +14247,7 @@ ncatted -a units,prs_sfc,o,c,millibar out.nc
<pre xml:space="preserve">ncks [-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b <var>binary-file</var>] [-C] [-c] [--cdl]
[--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz]
[-D <var>dbg</var>] [-d <var>dim</var>,[<var>min</var>][,[<var>max</var>][,[<var>stride</var>]]] [-F] [--fix_rec_dmn <var>dim</var>]
-[-G <var>gpe_dsc</var>] [-g <var>grp</var>[,&dots;]] [-H] [-h] [--hdn] [--hdr_pad <var>nbr</var>]
+[-G <var>gpe_dsc</var>] [-g <var>grp</var>[,&dots;]] [--grp_xtr_var_xcl] [-H] [-h] [--hdn] [--hdr_pad <var>nbr</var>]
[-L <var>dfl_lvl</var>] [-l <var>path</var>] [-M] [-m] [--mk_rec_dmn <var>dim</var>] [--md5_digest]
[--no_blank] [--no_tmp_fl] [-O] [-o <var>output-file</var>] [-P] [-p <var>path</var>]
[-Q] [-q] [-R] [-r] [--rad] [--ram_all] [-s <var>format</var>]
@@ -13968,7 +14258,7 @@ ncatted -a units,prs_sfc,o,c,millibar out.nc
<noindent></noindent>
<para>DESCRIPTION
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1291"><command>ncextr</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1304"><command>ncextr</command></indexterm></cindex>
<para>The nickname &textldquo;kitchen sink&textrdquo; is a catch-all because <command>ncks</command>
combines most features of <command>ncdump</command> and <command>nccopy</command> with
extra features to extract, hyperslab, multi-slab, sub-set, and translate
@@ -13997,8 +14287,8 @@ including <acronym><acronymword>CDL</acronymword></acronym> and <acronym><acrony
<samp>-s</samp>, <samp>-u</samp>, <samp>--xml</samp> (and their long option counterparts)
control the formatted appearance of the data.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1292">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1293">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1305">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1306">attributes, global</indexterm></cindex>
<para><command>ncks</command> extracts (and optionally creates a new netCDF file
comprised of) only selected variables from the input file
(similar to the old <command>ncextr</command> specification).
@@ -14015,8 +14305,8 @@ Input dimensions that are not associated with any output variable do
not appear in the output netCDF.
This feature removes superfluous dimensions from netCDF files.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1294">appending data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1295">merging files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1307">appending data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1308">merging files</indexterm></cindex>
<para><command>ncks</command> will append variables and attributes from the
<var>input-file</var> to <var>output-file</var> if <var>output-file</var> is a
pre-existing netCDF file whose relevant dimensions conform to dimension
@@ -14043,8 +14333,8 @@ with the members of <var>output-file</var> then it will be added to
<var>output-file</var>.
In this case the relevant dimensions must agree (conform) between the
two files; new dimensions are created in <var>output-file</var> as required.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1296">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1297">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1309">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1310">attributes, global</indexterm></cindex>
When a name conflict occurs, a global attribute from <var>input-file</var>
will overwrite the corresponding global attribute from
<var>output-file</var>.
@@ -14094,7 +14384,7 @@ Features common to many operators are described in
<a name="-5"></a> <!&textndash; http://nco.sf.net/nco.html#-5 &textndash;>
<a name="5"></a> <!&textndash; http://nco.sf.net/nco.html#5 &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1298"><code>-5</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1311"><code>-5</code></indexterm></cindex>
</beforefirstitem><tableentry><tableterm><item spaces=" "><itemformat command="samp">-5 </itemformat></item>
</tableterm><tableitem><para>Print data to screen alphabetically by group, and alphabetically by
variable within each group.
@@ -14107,11 +14397,11 @@ the future).
<a name="abc"></a> <!&textndash; http://nco.sf.net/nco.html#abc &textndash;>
<a name="alphabetize"></a> <!&textndash; http://nco.sf.net/nco.html#alphabetize &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1299">alphabetization</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1300">sort alphabetically</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1301"><code>-a</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1302"><code>--abc</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1303"><code>--alphabetize</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1312">alphabetization</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1313">sort alphabetically</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1314"><code>-a</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1315"><code>--abc</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1316"><code>--alphabetize</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-a</itemformat></item>
</tableterm><tableitem><para>Do not alphabetize extracted fields.
By default, the specified output variables are extracted, printed, and
@@ -14128,11 +14418,11 @@ Also <samp>--abc</samp> and <samp>--alphabetize</samp>.
<a name="bnr"></a> <!&textndash; http://nco.sf.net/nco.html#bnr &textndash;>
<a name="binary"></a> <!&textndash; http://nco.sf.net/nco.html#binary &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1304">binary format</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1305"><code>-b</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1306"><code>--fl_bnr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1307"><code>--bnr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1308"><code>--binary</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1317">binary format</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1318"><code>-b</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1319"><code>--fl_bnr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1320"><code>--bnr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1321"><code>--binary</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-b <file>file</file></itemformat></item>
</tableterm><tableitem><para>Activate native machine binary output writing to binary file
<file>file</file>.
@@ -14156,10 +14446,10 @@ coordinates to the binary file:
<a name="dmn_fix_mk"></a> <!&textndash; http://nco.sf.net/nco.html#dmn_fix_mk &textndash;>
<a name="fix_rec_dmn"></a> <!&textndash; http://nco.sf.net/nco.html#fix_rec_dmn &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1309">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1310">fixed dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1311"><code>--fix_rec_dmn <var>dim</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1312"><code>--no_rec_dmn <var>dim</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1322">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1323">fixed dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1324"><code>--fix_rec_dmn <var>dim</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1325"><code>--no_rec_dmn <var>dim</var></code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--fix_rec_dmn</itemformat></item>
</tableterm><tableitem><para>Change record dimension <var>dim</var> in the input file into a fixed
dimension in the output file.
@@ -14191,18 +14481,18 @@ limited to at most one record dimension) (<pxref label="Group-Path-Editing"><xre
<a name="hdn"></a> <!&textndash; http://nco.sf.net/nco.html#hdn &textndash;>
<a name="hidden"></a> <!&textndash; http://nco.sf.net/nco.html#hidden &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1313">hidden attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1314">special attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1315"><code>--hdn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1316"><code>--hidden</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1317"><code>_Format</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1318"><code>_DeflateLevel</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1319"><code>_Shuffle</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1320"><code>_Storage</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1321"><code>_ChunkSizes</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1322"><code>_Endianness</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1323"><code>_Fletcher32</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1324"><code>_NOFILL</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1326">hidden attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1327">special attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1328"><code>--hdn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1329"><code>--hidden</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1330"><code>_Format</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1331"><code>_DeflateLevel</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1332"><code>_Shuffle</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1333"><code>_Storage</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1334"><code>_ChunkSizes</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1335"><code>_Endianness</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1336"><code>_Fletcher32</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1337"><code>_NOFILL</code></indexterm></cindex>
<para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.4.0 (January, 2014), the <samp>--hdn</samp>
or <samp>--hidden</samp> options print hidden (aka special) attributes.
This is equivalent to <samp>ncdump -s</samp>.
@@ -14223,15 +14513,15 @@ detailed descriptions of the meanings of these attributes.
<a name="hncgen"></a> <!&textndash; http://nco.sf.net/nco.html#hncgen &textndash;>
<a name="ncgen-hdf"></a> <!&textndash; http://nco.sf.net/nco.html#ncgen-hdf &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1325"><command>hdp</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1326"><command>ncgen</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1327"><command>ncgen-hdf</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1328"><command>hncgen</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1329"><command>ncdump</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1330"><code>--cdl</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1331"><acronym><acronymword>CDL</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1332"><acronym><acronymword>HDF</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1333"><acronym><acronymword>HDF4</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1338"><command>hdp</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1339"><command>ncgen</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1340"><command>ncgen-hdf</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1341"><command>hncgen</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1342"><command>ncdump</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1343"><code>--cdl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1344"><acronym><acronymword>CDL</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1345"><acronym><acronymword>HDF</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1346"><acronym><acronymword>HDF4</acronymword></acronym></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--cdl </itemformat></item>
</tableterm><tableitem><para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.3.3 (July, 2013), <command>ncks</command> can
print extracted data and metadata to screen (i.e., <code>stdout</code>) as
@@ -14240,15 +14530,16 @@ valid <acronym><acronymword>CDL</acronymword></acronym> (network Common data for
<command>ncgen</command> and excreted by <command>ncdump</command>.
Compare <command>ncks</command> &textldquo;traditional&textrdquo; with <acronym><acronymword>CDL</acronymword></acronym> printing:
</para><example endspaces=" ">
-<pre xml:space="preserve">zender&arobase;roulee:~$ ncks -v one ~/nco/data/in.nc
+<verbatim xml:space="preserve">
+zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
one = 1
-zender&arobase;roulee:~$ ncks --cdl -v one ~/nco/data/in.nc
-netcdf in {
+zender at roulee:~$ ncks --cdl -v one ~/nco/data/in.nc
+netcdf in {
variables:
float one ;
@@ -14257,8 +14548,9 @@ netcdf in {
data:
one = 1 ;
-} // group /
-</pre></example>
+} // group /
+</verbatim>
+</example>
<para><command>ncgen</command> converts <acronym><acronymword>CDL</acronymword></acronym>-mode output into a netCDF file:
</para><example endspaces=" ">
<pre xml:space="preserve">ncks --cdl -v one ~/nco/data/in.nc > ~/in.cdl
@@ -14285,10 +14577,10 @@ name installed, is not robust and can fail on valid netCDF3
<a name="dmn_rec_mk"></a> <!&textndash; http://nco.sf.net/nco.html#dmn_rec_mk &textndash;>
<a name="mk_rec_dmn"></a> <!&textndash; http://nco.sf.net/nco.html#mk_rec_dmn &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1334">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1335">fixed dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1336">fix record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1337"><code>--mk_rec_dmn <var>dim</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1347">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1348">fixed dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1349">fix record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1350"><code>--mk_rec_dmn <var>dim</var></code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--mk_rec_dmn <var>dim</var></itemformat></item>
</tableterm><tableitem><para>Change existing dimension <var>dim</var> to a record dimension in the output file.
This is the most straightforward way of changing a dimension to a/the
@@ -14301,9 +14593,9 @@ changing variable dimensionality, including the record dimension.
<a name="H"></a> <!&textndash; http://nco.sf.net/nco.html#H &textndash;>
<a name="data"></a> <!&textndash; http://nco.sf.net/nco.html#data &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1338"><code>-H</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1339"><code>--data</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1340"><code>--hieronymus</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1351"><code>-H</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1352"><code>--data</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1353"><code>--hieronymus</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-H </itemformat></item>
</tableterm><tableitem><para>Turn-on printing to screen or turn-off copying data (not metadata).
Also activated using <samp>--print</samp> or <samp>--prn</samp>.
@@ -14363,10 +14655,10 @@ lat[0]=90 lev[0]=1000 lon[3]=270 three_dmn_var[3]=23
<a name="Metadata"></a> <!&textndash; http://nco.sf.net/nco.html#Metadata &textndash;>
<a name="M"></a> <!&textndash; http://nco.sf.net/nco.html#M &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1341"><code>-M</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1342"><code>--Mtd</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1343"><code>--Metadata</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1344">metadata, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1354"><code>-M</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1355"><code>--Mtd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1356"><code>--Metadata</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1357">metadata, global</indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-M</itemformat></item>
</tableterm><tableitem><para>Turn-on printing to screen or turn-off copying global and group metadata.
This includes file summary information and global and group attributes.
@@ -14422,20 +14714,20 @@ attributes, respectively.
<a name="mtd"></a> <!&textndash; http://nco.sf.net/nco.html#mtd &textndash;>
<a name="metadata"></a> <!&textndash; http://nco.sf.net/nco.html#metadata &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1345"><command>ncdump</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1346"><code>-m</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1347"><code>--mtd</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1348"><code>--metadata</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1349">metadata</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1358"><command>ncdump</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1359"><code>-m</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1360"><code>--mtd</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1361"><code>--metadata</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1362">metadata</indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-m</itemformat></item>
</tableterm><tableitem><para>Turn-on printing to screen or turn-off copying variable metadata.
Using <samp>-m</samp> will print variable metadata to screen (similar to
<kbd>ncdump -h</kbd>).
This displays all metadata pertaining to each variable, one variable
at a time.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1350">chunking</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1351">compression</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1352">deflation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1363">chunking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1364">compression</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1365">deflation</indexterm></cindex>
This includes information on the storage properties of the variable,
such as whether it employs chunking, compression, or packing.
Also activated using <samp>--mtd</samp> and <samp>--metadata</samp>.
@@ -14451,11 +14743,11 @@ file.
<a name="noblank"></a> <!&textndash; http://nco.sf.net/nco.html#noblank &textndash;>
<a name="no-blank"></a> <!&textndash; http://nco.sf.net/nco.html#no-blank &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1353"><code>--no_blank</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1354"><code>--noblank</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1355"><code>--no-blank</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1356">blank</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1357">missing values</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1366"><code>--no_blank</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1367"><code>--noblank</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1368"><code>--no-blank</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1369">blank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1370">missing values</indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--no_blank</itemformat></item>
</tableterm><tableitem><para>Print numeric representation of missing values.
As of <acronym><acronymword>NCO</acronymword></acronym>
@@ -14469,9 +14761,9 @@ Also activated using <samp>--noblank</samp> or <samp>--no-blank</samp>.
<a name="P"></a> <!&textndash; http://nco.sf.net/nco.html#P &textndash;>
<a name="prn"></a> <!&textndash; http://nco.sf.net/nco.html#prn &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1358"><code>-P</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1359"><code>--print</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1360"><code>--prn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1371"><code>-P</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1372"><code>--print</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1373"><code>--prn</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-P </itemformat></item>
</tableterm><tableitem><para>Print data, metadata, and units to screen.
The <samp>-P</samp> switch is a convenience abbreviation for
@@ -14482,7 +14774,7 @@ This set of switches is useful for exploring file contents.
<html endspaces=" ">
<a name="Q"></a> <!&textndash; http://nco.sf.net/nco.html#Q &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1361"><code>-Q</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1374"><code>-Q</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-Q </itemformat></item>
</tableterm><tableitem><para>Toggle printing of dimension indices and coordinate values when printing
arrays.
@@ -14494,9 +14786,9 @@ different dimensions.
<a name="q"></a> <!&textndash; http://nco.sf.net/nco.html#q &textndash;>
<a name="quiet"></a> <!&textndash; http://nco.sf.net/nco.html#quiet &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1362"><code>-q</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1363"><code>--quiet</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1364">quiet</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1375"><code>-q</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1376"><code>--quiet</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1377">quiet</indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-q </itemformat></item>
</tableterm><tableitem><para>Turn off all printing to screen.
This overrides the setting of all print-related switches, equivalent to
@@ -14512,11 +14804,11 @@ Also <samp>--quiet</samp>.
<a name="orphan"></a> <!&textndash; http://nco.sf.net/nco.html#orphan &textndash;>
<a name="rph_dmn"></a> <!&textndash; http://nco.sf.net/nco.html#rph_dmn &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1365"><code>--rad</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1366">orphan dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1367"><code>--retain_all_dimensions</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1368"><code>--orphan_dimensions</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1369"><code>--rph_dmn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1378"><code>--rad</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1379">orphan dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1380"><code>--retain_all_dimensions</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1381"><code>--orphan_dimensions</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1382"><code>--rph_dmn</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--rad</itemformat></item>
</tableterm><tableitem><para>Retain all dimensions.
When invoked with <code>--rad</code> (Retain All Dimensions),
@@ -14535,11 +14827,11 @@ Also <samp>--retain_all_dimensions</samp>, <samp>--orphan_dimensions</samp>, and
<a name="sng_fmt"></a> <!&textndash; http://nco.sf.net/nco.html#sng_fmt &textndash;>
<a name="string"></a> <!&textndash; http://nco.sf.net/nco.html#string &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1370"><code>-s</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1371"><code>--string</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1372"><code>--sng_fmt</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1373"><code>printf()</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1374">C language</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1383"><code>-s</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1384"><code>--string</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1385"><code>--sng_fmt</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1386"><code>printf()</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1387">C language</indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-s <var>format</var></itemformat></item>
</tableterm><tableitem><para>String format for text output.
Accepts <w>C language</w> escape sequences and <code>printf()</code> formats.
@@ -14549,8 +14841,8 @@ Also <samp>--string</samp> and <samp>--sng_fmt</samp>.
<a name="units"></a> <!&textndash; http://nco.sf.net/nco.html#units &textndash;>
<a name="u"></a> <!&textndash; http://nco.sf.net/nco.html#u &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1375"><code>-u</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1376"><code>--units</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1388"><code>-u</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1389"><code>--units</code></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">-u </itemformat></item>
</tableterm><tableitem><para>Toggle the printing of a variable&textrsquo;s <code>units</code> attribute, if any,
with its values.
@@ -14560,11 +14852,11 @@ Also <samp>--units</samp>.
<a name="xml"></a> <!&textndash; http://nco.sf.net/nco.html#xml &textndash;>
<a name="ncmnl"></a> <!&textndash; http://nco.sf.net/nco.html#ncml &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1377"><code>--xml</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1378"><code>--ncml</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1379"><command>ncdump</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1380"><acronym><acronymword>XML</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1381"><acronym><acronymword>NcML</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1390"><code>--xml</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1391"><code>--ncml</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1392"><command>ncdump</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1393"><acronym><acronymword>XML</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1394"><acronym><acronymword>NcML</acronymword></acronym></indexterm></cindex>
</tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="samp">--xml, --ncml</itemformat></item>
</tableterm><tableitem><para>As of <acronym><acronymword>NCO</acronymword></acronym> version 4.3.3 (July, 2013), <command>ncks</command> can
print extracted metadata to screen (i.e., <code>stdout</code>) as
@@ -14577,7 +14869,7 @@ into <acronym><acronymword>NcML</acronymword></acronym>, including metadata and
Compare <command>ncks</command> &textldquo;traditional&textrdquo; with <acronym><acronymword>XML</acronymword></acronym> printing:
</para><example endspaces=" ">
<verbatim xml:space="preserve">
-zender@@roulee:~$ ncks -v one ~/nco/data/in.nc
+zender at roulee:~$ ncks -v one ~/nco/data/in.nc
one: type NC_FLOAT, 0 dimensions, 1 attribute, chunked? no, compressed? no, packed? no
one size (RAM) = 1*sizeof(NC_FLOAT) = 1*4 = 4 bytes
one attribute 0: long_name, size = 3 NC_CHAR, value = one
@@ -14603,10 +14895,10 @@ comparison to output from Unidata&textrsquo;s <command>toolsUI</command> Java pr
Please let us know how to improve <acronym><acronymword>XML</acronymword></acronym>/<acronym><acronymword>NcML</acronymword></acronym>
features.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1382"><code>--xml_no_location</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1383"><code>--xml_spr_chr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1384"><code>--xml_spr_nmr</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1385">separator</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1395"><code>--xml_no_location</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1396"><code>--xml_spr_chr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1397"><code>--xml_spr_nmr</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1398">separator</indexterm></cindex>
<para><command>ncks</command> provides additional options to configure <acronym><acronymword>NcML</acronymword></acronym>
output: <samp>--xml_no_location</samp>, <samp>--xml_spr_chr</samp>, and
<samp>--xml_spr_nmr</samp>.
@@ -14624,19 +14916,19 @@ variables of character-type and numeric-type, respectively.
Their default separators are "*" and " ":
</para><example endspaces=" ">
<verbatim xml:space="preserve">
-zender@@roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
+zender at roulee:~$ ncks --xml -d time,0,3 -v two_dmn_rec_var_sng in.nc
...
<values separator="*">abc*bcd*cde*def</values>
...
- zender@@roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
+ zender at roulee:~$ ncks --xml_spr_chr=', ' -v two_dmn_rec_var_sng in.nc
...
<values separator=", ">abc, bcd, cde, def, efg, fgh, ghi, hij, jkl, klm</values>
...
-zender@@roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml -v one_dmn_rec_var in.nc
...
<values>1 2 3 4 5 6 7 8 9 10</values>
...
-zender@@roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
+zender at roulee:~$ ncks --xml_spr_nmr=', ' -v one_dmn_rec_var in.nc
...
<values separator=", ">1, 2, 3, 4, 5, 6, 7, 8, 9, 10</values>
...
@@ -14682,25 +14974,25 @@ include an NcML formatting characters (e.g., commas, angles, quotes).
</unnumberedsubsec>
<node name="Filters-for-ncks" spaces=" "><nodename>Filters for <command>ncks</command></nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">ncks netCDF Kitchen Sink</nodeprev><nodeup spaces=" ">ncks netCDF Kitchen Sink</nodeup></node>
<subsection spaces=" "><sectiontitle>Filters for <command>ncks</command></sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1386"><acronym><acronymword>UNIX</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1387"><command>ncattget</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1388"><command>ncavg</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1389"><command>ncdmnsz</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1390"><command>nclist</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1391"><command>ncmax</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1392"><command>ncmdn</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1393"><command>ncmin</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1394"><command>ncrecsz</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1395"><command>ncrng</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1396"><command>ncunits</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1397"><file>.bashrc</file></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1398">filters</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1399">alias</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1400">shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1401">Bash shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1402">Csh shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1403">Sh shell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1404"><command>bash</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1399"><acronym><acronymword>UNIX</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1400"><command>ncattget</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1401"><command>ncavg</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1402"><command>ncdmnsz</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1403"><command>nclist</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1404"><command>ncmax</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1405"><command>ncmdn</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1406"><command>ncmin</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1407"><command>ncrecsz</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1408"><command>ncrng</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1409"><command>ncunits</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1410"><file>.bashrc</file></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1411">filters</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1412">alias</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1413">shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1414">Bash shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1415">Csh shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1416">Sh shell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1417"><command>bash</command></indexterm></cindex>
<para>We encourage the use of standard <acronym><acronymword>UNIX</acronymword></acronym> pipes and filters to
narrow the verbose output of <command>ncks</command> into more precise targets.
For example, to obtain an uncluttered listing of the variables in a file
@@ -14725,8 +15017,10 @@ In this example, <command>ncks -m -v z</command> is too verbose so a robust
procedure could be implemented as a shell command or function called,
say, <command>ncattget</command>
</para><example endspaces=" ">
-<pre xml:space="preserve">function ncattget { ncks -M -m ${3} | grep -E -i "^${2} attribute [0-9]+: ${1}" | cut -f 11- -d ' ' | sort ; }
-</pre></example>
+<verbatim xml:space="preserve">
+function ncattget { ncks -M -m ${3} | grep -E -i "^${2} attribute [0-9]+: ${1}" | cut -f 11- -d ' ' | sort ; }
+</verbatim>
+</example>
<para>The shell <command>ncattget</command> is invoked with three arugments that are,
in order, the names of the attribute, variable, and file to examine.
Global attributes are indicated by using a variable name of <code>global</code>.
@@ -14825,12 +15119,12 @@ conventions:
<para>Now the file <file>out.nc</file> contains all the data from <file>in.nc</file>.
There are, however, two differences between <file>in.nc</file> and
<file>out.nc</file>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1405"><code>history</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1418"><code>history</code></indexterm></cindex>
First, the <code>history</code> global attribute (<pxref label="History-Attribute"><xrefnodename>History Attribute</xrefnodename></pxref>)
will contain the command used to create <file>out.nc</file>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1406">alphabetize output</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1407">sort alphabetically</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1408"><code>-a</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1419">alphabetize output</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1420">sort alphabetically</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1421"><code>-a</code></indexterm></cindex>
Second, the variables in <file>out.nc</file> will be defined in alphabetical
order.
Of course the internal storage of variable in a netCDF file should be
@@ -14840,16 +15134,16 @@ is useful (see description of <code>-a</code> switch).
<html endspaces=" ">
<a name="xmp_att_glb_cpy"></a> <!&textndash; http://nco.sf.net/nco.html#xmp_att_glb_cpy &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1409">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1410">attributes, global</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1411">subsetting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1412">exclusion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1413">extraction</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1414"><code>-v <var>var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1415"><code>--variable <var>var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1416"><code>-x</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1417"><code>--exclude</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1418"><code>--xcl</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1422">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1423">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1424">subsetting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1425">exclusion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1426">extraction</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1427"><code>-v <var>var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1428"><code>--variable <var>var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1429"><code>-x</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1430"><code>--exclude</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1431"><code>--xcl</code></indexterm></cindex>
<para>Copy all global attributes (and no variables) from <file>in.nc</file> to
<file>out.nc</file>:
</para><example endspaces=" ">
@@ -14860,10 +15154,10 @@ list (<pxref label="Subsetting-Files"><xrefnodename>Subsetting Files</xrefnodena
Since no extraction list is explicitly specified (with <samp>-v</samp>),
the default is to extract all variables.
The complement of all variables is no variables.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1419"><code>-A</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1420"><code>--apn</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1421"><code>--append</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1422">appending to files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1432"><code>-A</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1433"><code>--apn</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1434"><code>--append</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1435">appending to files</indexterm></cindex>
Without any variables to extract, the append (<samp>-A</samp>) command
(<pxref label="Appending-Variables"><xrefnodename>Appending Variables</xrefnodename></pxref>) has only to extract and copy
(i.e., append) global attributes to the output file.
@@ -14891,9 +15185,9 @@ ncks -A -C -H -v one,three_dmn_rec_var ~/in2.nc ~/out.nc
<para>Variables in <file>out.nc</file> now contain data (not metadata) from
<file>in.nc</file> and metadata (not data) from <file>in2.nc</file>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1423"><code>printf()</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1424"><code>\n</code> (linefeed)</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1425"><code>\t</code> (horizontal tab)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1436"><code>printf()</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1437"><code>\n</code> (linefeed)</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1438"><code>\t</code> (horizontal tab)</indexterm></cindex>
<para>Print variable <code>three_dmn_var</code> from file <file>in.nc</file> with
default notations.
Next print <code>three_dmn_var</code> as an un-annotated text column.
@@ -14952,32 +15246,34 @@ multidimensional arrays of characters representing fixed length strings
<pre xml:space="preserve">ncks -s '%c' -v fl_nm_arr in.nc
</pre></example>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1426"><code>core dump</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1439"><code>core dump</code></indexterm></cindex>
<para>Using the <code>%s</code> format code on strings which are not NUL-terminated
(and thus not technically strings) is likely to result in a core dump.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1427">subsetting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1428">exclusion</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1429">extraction</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1440">subsetting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1441">exclusion</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1442">extraction</indexterm></cindex>
<para>Create netCDF <file>out.nc</file> containing all variables, and any associated
coordinates, except variable <code>time</code>, from netCDF <file>in.nc</file>:
</para><example endspaces=" ">
<pre xml:space="preserve">ncks -x -v time in.nc out.nc
</pre></example>
<para>As a special case of this, consider how to remove a
-<acronym><acronymword>CF</acronymword></acronym> Convention comliant <code>bounds</code> or <code>coordinates</code>
-variable (<pxref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></pxref>) such as <code>time_bounds</code>.
-<acronym><acronymword>NCO</acronymword></acronym> subsetting assumes the user wants all coordinates
-and bounds and axes associated with all extracted variables
+<acronym><acronymword>CF</acronymword></acronym> Convention comliant <code>ancillary_variables</code>,
+<code>bounds</code>, or <code>coordinates</code> variable (<pxref label="CF-Conventions"><xrefnodename>CF Conventions</xrefnodename></pxref>)
+such as <code>time_bounds</code>.
+<acronym><acronymword>NCO</acronymword></acronym> subsetting assumes the user wants all ancillary variables,
+axes, bounds and coordinates associated with all extracted variables
(<pxref label="Subsetting-Coordinate-Variables"><xrefnodename>Subsetting Coordinate Variables</xrefnodename></pxref>).
-Hence to exclude a <code>bounds</code> or <code>coordinates</code> variable while
-retaining the &textldquo;parent&textrdquo; variable (here <code>time</code>), one must use the
-<samp>-C</samp> switch:
+Hence to exclude a <code>ancillary_variables</code>, <code>bounds</code>, or
+<code>coordinates</code> variable while retaining the &textldquo;parent&textrdquo; variable
+(here <code>time</code>), one must use the <samp>-C</samp> switch:
</para><example endspaces=" ">
<pre xml:space="preserve">ncks -C -x -v time_bounds in.nc out.nc
</pre></example>
<para>The <samp>-C</samp> switch tells the operator <emph>NOT</emph> to necessarily
-include all the <acronym><acronymword>CF</acronymword></acronym> coordinates and bounds and axes.
+include all the <acronym><acronymword>CF</acronymword></acronym> ancillary variables, axes, bounds, and
+coordinates.
Hence the output file will contain <code>time</code> and not
<code>time_bounds</code>.
</para>
@@ -15015,7 +15311,7 @@ decimal point <xref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></
-d lev,1000.0 in.nc out.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1430">wrapped coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1443">wrapped coordinates</indexterm></cindex>
<para>Assume the domain of the monotonically increasing longitude coordinate
<code>lon</code> is <math>0 < <var>lon</var> < 360</math>.
Here, <code>lon</code> is an example of a wrapped coordinate.
@@ -15040,13 +15336,13 @@ the easternmost longitude as <var>max</var>, as follows:
<findex index="fn" spaces=" "><indexterm index="fn" number="35" mergedindex="cp">ncpdq</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="36" mergedindex="cp">ncpack</indexterm></findex>
<findex index="fn" spaces=" "><indexterm index="fn" number="37" mergedindex="cp">ncunpack</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1431">reshape variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1432">permute dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1433">reverse dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1434">re-order dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1435">re-dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1436">packing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1437">unpacking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1444">reshape variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1445">permute dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1446">reverse dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1447">re-order dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1448">re-dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1449">packing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1450">unpacking</indexterm></cindex>
<noindent></noindent>
<para>SYNTAX
@@ -15071,10 +15367,10 @@ fashion with a minimum of time and memory.
The <dfn>pdq</dfn> may stand for &textldquo;Permute Dimensions Quickly&textrdquo;,
&textldquo;Pack Data Quietly&textrdquo;, &textldquo;Pillory Dan Quayle&textrdquo;, or other silly uses.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1438"><code>add_offset</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1439"><code>scale_factor</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1440"><command>ncap2</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1441">packing policy</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1451"><code>add_offset</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1452"><code>scale_factor</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1453"><command>ncap2</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1454">packing policy</indexterm></cindex>
<unnumberedsubsec spaces=" "><sectiontitle>Packing and Unpacking Functions</sectiontitle>
<para>The <command>ncpdq</command> packing (and unpacking) algorithms are described
in <ref label="Methods-and-functions"><xrefnodename>Methods and functions</xrefnodename></ref>, and are also implemented in
@@ -15082,10 +15378,10 @@ in <ref label="Methods-and-functions"><xrefnodename>Methods and functions</xrefn
<command>ncpdq</command> extends the functionality of these algorithms by
providing high level control of the <dfn>packing policy</dfn> so that
users can consistently pack (and unpack) entire files with one command.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1442"><var>pck_plc</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1443"><code>-P <var>pck_plc</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1444"><code>--pck_plc <var>pck_plc</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1445"><code>--pack_policy <var>pck_plc</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1455"><var>pck_plc</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1456"><code>-P <var>pck_plc</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1457"><code>--pck_plc <var>pck_plc</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1458"><code>--pack_policy <var>pck_plc</var></code></indexterm></cindex>
The user specifies the desired packing policy with the <samp>-P</samp> switch
(or its long option equivalents, <samp>--pck_plc</samp> and
<samp>--pack_policy</samp>) and its <var>pck_plc</var> argument.
@@ -15150,9 +15446,9 @@ unlike <command>ncpdq</command>.
Similarly, <command>ncunpack</command> is a synonym for <command>ncpdq</command>
except that <command>ncpack</command> implicitly assumes a request to unpack,
i.e., <samp>-P pck_upk</samp>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1446"><code>-U</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1447"><code>--upk</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1448"><code>--unpack</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1459"><code>-U</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1460"><code>--upk</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1461"><code>--unpack</code></indexterm></cindex>
Finally, the <command>ncpdq</command> <samp>-U</samp> switch (or its long option
equivalents, <samp>--upk</samp> and <samp>--unpack</samp>) requires no argument.
It simply requests unpacking.
@@ -15167,20 +15463,20 @@ The following commands are equivalent for unpacking:
and <code>ncunpack</code>.
Equivalent commands for other packing policies, e.g., <samp>all_xst</samp>,
follow by analogy.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1449"><command>alias</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1450"><command>ln -s</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1451">symbolic links</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1462"><command>alias</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1463"><command>ln -s</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1464">symbolic links</indexterm></cindex>
Note that <command>ncpdq</command> synonyms are subject to the same constraints
and recommendations discussed in the secion on <command>ncbo</command> synonyms
(<pxref label="ncbo-netCDF-Binary-Operator"><xrefnodename>ncbo netCDF Binary Operator</xrefnodename></pxref>).
That is, symbolic links must exist from the synonym to <command>ncpdq</command>,
or else the user must define an <command>alias</command>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1452">packing map</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1453"><var>pck_map</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1454"><code>-M <var>pck_map</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1455"><code>--pck_map <var>pck_map</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1456"><code>--map <var>pck_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1465">packing map</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1466"><var>pck_map</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1467"><code>-M <var>pck_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1468"><code>--pck_map <var>pck_map</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1469"><code>--map <var>pck_map</var></code></indexterm></cindex>
<para>The <command>ncpdq</command> packing algorithms must know to which type
particular types of input variables are to be packed.
The correspondence between the input variable type and the output,
@@ -15189,22 +15485,22 @@ The user specifies the desired packing map with the <samp>-M</samp> switch
(or its long option equivalents, <samp>--pck_map</samp> and
<samp>--map</samp>) and its <var>pck_map</var> argument.
Five packing maps are currently implemented:&linebreak;
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1457"><samp>hgh_sht</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1458"><samp>hgh_byt</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1459"><samp>flt_sht</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1460"><samp>flt_byt</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1461"><samp>nxt_lsr</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1462"><code>NC_DOUBLE</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1463"><code>NC_FLOAT</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1464"><code>NC_INT64</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1465"><code>NC_UINT64</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1466"><code>NC_INT</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1467"><code>NC_UINT</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1468"><code>NC_SHORT</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1469"><code>NC_USHORT</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1470"><code>NC_CHAR</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1471"><code>NC_BYTE</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1472"><code>NC_UBYTE</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1470"><samp>hgh_sht</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1471"><samp>hgh_byt</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1472"><samp>flt_sht</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1473"><samp>flt_byt</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1474"><samp>nxt_lsr</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1475"><code>NC_DOUBLE</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1476"><code>NC_FLOAT</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1477"><code>NC_INT64</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1478"><code>NC_UINT64</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1479"><code>NC_INT</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1480"><code>NC_UINT</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1481"><code>NC_SHORT</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1482"><code>NC_USHORT</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1483"><code>NC_CHAR</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1484"><code>NC_BYTE</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1485"><code>NC_UBYTE</code></indexterm></cindex>
</para><table commandarg="dfn" spaces=" " endspaces=" ">
<tableentry><tableterm><item spaces=" "><itemformat command="dfn">Pack Floating Precisions to <code>NC_SHORT</code> [<emph>default</emph>]</itemformat></item>
</tableterm><tableitem><para>Definition: Pack floating precision types to <code>NC_SHORT</code>&linebreak;
@@ -15243,9 +15539,9 @@ file size by <w>about 50%.</w>
<samp>flt_byt</samp> packing reduces an <code>NC_DOUBLE</code>-dominated file by
<w>about 87%.</w>
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1473"><var>_FillValue</var></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1474"><code>_FillValue</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1475"><code>NUL</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1486"><var>_FillValue</var></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1487"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1488"><code>NUL</code></indexterm></cindex>
<para>The netCDF packing algorithm (<pxref label="Methods-and-functions"><xrefnodename>Methods and functions</xrefnodename></pxref>) is
lossy&textmdash;once packed, the exact original data cannot be recovered without
a full backup.
@@ -15283,16 +15579,16 @@ dimension list, e.g., <samp>-a -lat</samp>.
Re-ordering and reversal may be performed simultaneously, e.g.,
<samp>-a lon,-lat,time,-lev</samp>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1476">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1489">record dimension</indexterm></cindex>
<para>Users may specify any permutation of dimensions, including
permutations which change the record dimension identity.
The record dimension is re-ordered like any other dimension.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1477">concatenation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1478">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1490">concatenation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1491">record dimension</indexterm></cindex>
This unique <command>ncpdq</command> capability makes it possible to concatenate
files along any dimension.
See <ref label="Concatenation"><xrefnodename>Concatenation</xrefnodename></ref> for a detailed example.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1479">record variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1492">record variable</indexterm></cindex>
The record dimension is always the most slowly varying dimension in a
record variable (<pxref label="C-and-Fortran-Index-Conventions"><xrefnodename>C and Fortran Index Conventions</xrefnodename></pxref>).
The specified re-ordering fails if it requires creating more than
@@ -15307,7 +15603,7 @@ variable.
To do this, include all the variable&textrsquo;s dimensions in the dimension
re-order list in their original order, and prefix each dimension name
with the negative sign.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1480">transpose</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1493">transpose</indexterm></cindex>
Second, it may useful to transpose a variable&textrsquo;s storage order, e.g.,
<w>from C</w> to Fortran data storage order
(<pxref label="C-and-Fortran-Index-Conventions"><xrefnodename>C and Fortran Index Conventions</xrefnodename></pxref>).
@@ -15428,9 +15724,9 @@ and the packing policy <var>pck_plc</var> as <samp>all_xst</samp>:
</para><example endspaces=" ">
<pre xml:space="preserve">ncpdq -P all_xst -M hgh_byt in.nc out.nc
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1481">appending variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1482"><samp>-A</samp></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1483"><samp>-v</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1494">appending variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1495"><samp>-A</samp></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1496"><samp>-v</samp></indexterm></cindex>
<para>Many different packing maps may be used to construct a given file
by performing the packing on subsets of variables (e.g., with <samp>-v</samp>)
and using the append feature with <samp>-A</samp> (<pxref label="Appending-Variables"><xrefnodename>Appending Variables</xrefnodename></pxref>).
@@ -15438,8 +15734,8 @@ and using the append feature with <samp>-A</samp> (<pxref label="Appending-Varia
<para>Users may wish to unpack data packed with the <acronym><acronymword>HDF</acronymword></acronym> convention,
and then re-pack it with the netCDF convention so that all their
datasets use the same packing convention prior to intercomparison.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1484"><command>ncl_convert2nc</command></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1485"><acronym><acronymword>NCL</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1497"><command>ncl_convert2nc</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1498"><acronym><acronymword>NCL</acronymword></acronym></indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve"># One-step procedure: For NCO 4.4.0+, netCDF 4.3.1+
# 1. Convert, unpack, and repack HDF file into netCDF file
@@ -15497,7 +15793,7 @@ ncpdq -v three_dmn_var -a lon,lat in.nc out.nc
The second command extracts and re-orders only the variable
<code>three_dmn_var</code>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1486">reverse dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1499">reverse dimensions</indexterm></cindex>
<para>Suppose the dimension <code>lat</code> represents latitude and monotonically
increases increases from south to north.
Reversing the <code>lat</code> dimension means re-ordering the data so that
@@ -15515,8 +15811,8 @@ lat[1]=-90
<para>This operation reversed the latitude dimension of all variables.
Whitespace immediately preceding the negative sign that specifies
dimension reversal may be dangerous.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1487">long options</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1488">quotes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1500">long options</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1501">quotes</indexterm></cindex>
Quotes and long options can help protect negative signs that should
indicate dimension reversal from being interpreted by the shell as
dashes that indicate new command line switches.
@@ -15527,7 +15823,7 @@ ncpdq -a lon,-lat in.nc out.nc # OK. No whitespace before "-"
ncpdq --rdr=-lat in.nc out.nc # Preferred. Uses "=" not whitespace
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1489">reverse dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1502">reverse dimensions</indexterm></cindex>
<para>To create the mathematical transpose of a variable, place all its
dimensions in the dimension re-order list in reversed order.
This example creates the transpose of <code>three_dmn_var</code>:
@@ -15551,7 +15847,7 @@ lon[3]=270 lev[2]=1000 lat[0]=-90 three_dmn_var[22]=11
lon[3]=270 lev[2]=1000 lat[1]=90 three_dmn_var[23]=23
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1490">reverse data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1503">reverse data</indexterm></cindex>
<para>To completely reverse the storage order of a variable, include
all its dimensions in the re-order list, each prefixed by a negative
sign.
@@ -15586,7 +15882,7 @@ has no existing record dimension is simple with <command>ncecat</command>:
<pre xml:space="preserve">ncecat -O -u time in.nc out.nc # Create degenerate record dimension named "time"
</pre></example>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1491">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1504">record dimension</indexterm></cindex>
<para>Now consider a file with all dimensions, including <code>time</code>, fixed
(non-record).
Suppose the user wishes to convert <code>time</code> from a fixed dimension to
@@ -15605,7 +15901,7 @@ a record dimension required three separate commands,
The recommended method is now to use <samp>ncks --fix_rec_dmn</samp>, yet it
is still instructive to present the original procedure, as it shows how
multiple operators can achieve the same ends by different means:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1492">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1505">degenerate dimension</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncecat -O in.nc out.nc # Add degenerate record dimension named "record"
ncpdq -O -a time,record out.nc out.nc # Switch "record" and "time"
@@ -15635,10 +15931,10 @@ changing variable dimensionality, including the record dimension.
</section>
<node name="ncra-netCDF-Record-Averager" spaces=" "><nodename>ncra netCDF Record Averager</nodename><nodenext spaces=" ">ncrcat netCDF Record Concatenator</nodenext><nodeprev spaces=" ">ncpdq netCDF Permute Dimensions Quickly</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncra</command> netCDF Record Averager</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1493">averaging data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1494">record average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1495">record dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1496">running average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1506">averaging data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1507">record average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1508">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1509">running average</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="38" mergedindex="cp">ncra</indexterm></findex>
<noindent></noindent>
@@ -15659,15 +15955,15 @@ changing variable dimensionality, including the record dimension.
</para>
<para><command>ncra</command> averages record variables across an arbitrary number of
<var>input-files</var>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1497">degenerate dimension</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1498">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1510">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1511">record dimension</indexterm></cindex>
The record dimension is, by default, retained as a degenerate
<w>(size 1)</w> dimension in the output variables.
<xref label="Statistics-vs_002e-Concatenation"><xrefnodename>Statistics vs. Concatenation</xrefnodename></xref>, for a description of the
distinctions between the various statistics tools and concatenators.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1499">multi-file operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1500">standard input</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1501"><code>stdin</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1512">multi-file operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1513">standard input</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1514"><code>stdin</code></indexterm></cindex>
As a multi-file operator, <command>ncra</command> will read the list of
<var>input-files</var> from <code>stdin</code> if they are not specified
as positional arguments on the command line
@@ -15676,10 +15972,10 @@ as positional arguments on the command line
<para>Input files may vary in size, but each must have a record dimension.
The record coordinate, if any, should be monotonic (or else non-fatal
warnings may be generated).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1502">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1515">hyperslab</indexterm></cindex>
Hyperslabs of the record dimension which include more than one file
work correctly.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1503">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1516">stride</indexterm></cindex>
<command>ncra</command> supports the <var>stride</var> argument to the <samp>-d</samp>
hyperslab option (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>) for the record dimension only,
<var>stride</var> is not supported for non-record dimensions.
@@ -15689,7 +15985,7 @@ hyperslab option (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodena
<command>ncra</command> does not attempt to see if, say, the <code>time</code>
coordinate is irregularly spaced and thus would require a weighted
average in order to be a true time average.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1504">operation types</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1517">operation types</indexterm></cindex>
<command>ncra</command> <emph>always averages</emph> coordinate variables regardless of
the arithmetic operation type performed on the non-coordinate variables.
(<pxref label="Operation-Types"><xrefnodename>Operation Types</xrefnodename></pxref>).
@@ -15702,10 +15998,10 @@ the arithmetic operation type performed on the non-coordinate variables.
</para>
<para>Average files <file>85.nc</file>, <file>86.nc</file>, <w>&dots; <file>89.nc</file></w>
along the record dimension, and store the results in <file>8589.nc</file>:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1505">globbing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1506"><code>NINTAP</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1507">Processor</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1508"><acronym><acronymword>CCM</acronymword></acronym> Processor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1518">globbing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1519"><code>NINTAP</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1520">Processor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1521"><acronym><acronymword>CCM</acronymword></acronym> Processor</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncra 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncra 8[56789].nc 8589.nc
@@ -15715,7 +16011,7 @@ ncra -n 5,2,1 85.nc 8589.nc
<xref label="Specifying-Input-Files"><xrefnodename>Specifying Input Files</xrefnodename></xref>, for an explanation of the distinctions
between these methods.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1509">Fortran</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1522">Fortran</indexterm></cindex>
<para>Assume the files <file>85.nc</file>, <file>86.nc</file>, <w>&dots; <file>89.nc</file></w>
each contain a record coordinate <var>time</var> of length 12 defined such
that the third record in <file>86.nc</file> contains data from March 1986,
@@ -15729,7 +16025,7 @@ ncra -F -d time,12,14 85.nc 86.nc 87.nc 8512_8602.nc
<noindent></noindent>
<para>The file <file>87.nc</file> is superfluous, but does not cause an error.
The <samp>-F</samp> turns on the Fortran (1-based) indexing convention.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1510">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1523">stride</indexterm></cindex>
The following uses the <var>stride</var> option to average all the March
temperature data from multiple input files into a single output file
</para><example endspaces=" ">
@@ -15752,8 +16048,8 @@ averages June, 1985&textndash;June, 1989:
</section>
<node name="ncrcat-netCDF-Record-Concatenator" spaces=" "><nodename>ncrcat netCDF Record Concatenator</nodename><nodenext spaces=" ">ncrename netCDF Renamer</nodenext><nodeprev spaces=" ">ncra netCDF Record Averager</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncrcat</command> netCDF Record Concatenator</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1511">concatenation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1512">record concatenation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1524">concatenation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1525">record concatenation</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="39" mergedindex="cp">ncrcat</indexterm></findex>
<noindent></noindent>
@@ -15774,14 +16070,14 @@ averages June, 1985&textndash;June, 1989:
</para>
<para><command>ncrcat</command> concatenates record variables across an arbitrary
number of <var>input-files</var>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1513">record dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1526">record dimension</indexterm></cindex>
The final record dimension is by default the sum of the lengths of the
record dimensions in the input files.
<xref label="Statistics-vs_002e-Concatenation"><xrefnodename>Statistics vs. Concatenation</xrefnodename></xref>, for a description of the
distinctions between the various statistics tools and concatenators.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1514">multi-file operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1515">standard input</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1516"><code>stdin</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1527">multi-file operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1528">standard input</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1529"><code>stdin</code></indexterm></cindex>
As a multi-file operator, <command>ncrcat</command> will read the list of
<var>input-files</var> from <code>stdin</code> if they are not specified
as positional arguments on the command line
@@ -15790,19 +16086,19 @@ as positional arguments on the command line
<para>Input files may vary in size, but each must have a record dimension.
The record coordinate, if any, should be monotonic (or else non-fatal
warnings may be generated).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1517">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1530">hyperslab</indexterm></cindex>
Hyperslabs along the record dimension that span more than one file are
handled correctly.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1518">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1531">stride</indexterm></cindex>
<command>ncra</command> supports the <var>stride</var> argument to the <samp>-d</samp>
hyperslab option for the record dimension only, <var>stride</var> is not
supported for non-record dimensions.
</para>
<findex index="fn" spaces=" "><indexterm index="fn" number="40" mergedindex="cp">ncpdq</indexterm></findex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1519">packing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1520">unpacking</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1521"><code>add_offset</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1522"><code>scale_factor</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1532">packing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1533">unpacking</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1534"><code>add_offset</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1535"><code>scale_factor</code></indexterm></cindex>
<para>Concatenating a variable packed with different scales multiple datasets
is beyond the capabilities of <command>ncrcat</command> (and <command>ncecat</command>,
the other concatenator (<ref label="Concatenation"><xrefnodename>Concatenation</xrefnodename></ref>).
@@ -15819,7 +16115,7 @@ First, unpack the data using <command>ncpdq</command>.
Second, concatenate the unpacked data using <command>ncrcat</command>,
Third, re-pack the result with <command>ncpdq</command>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1523">ARM conventions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1536">ARM conventions</indexterm></cindex>
<para><command>ncrcat</command> applies special rules to <acronym><acronymword>ARM</acronymword></acronym> convention time
fields (e.g., <code>time_offset</code>).
See <ref label="ARM-Conventions"><xrefnodename>ARM Conventions</xrefnodename></ref> for a complete description.
@@ -15832,10 +16128,10 @@ See <ref label="ARM-Conventions"><xrefnodename>ARM Conventions</xrefnodename></r
</para>
<para>Concatenate files <file>85.nc</file>, <file>86.nc</file>, <w>&dots; <file>89.nc</file></w>
along the record dimension, and store the results in <file>8589.nc</file>:
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1524">globbing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1525"><code>NINTAP</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1526">Processor</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1527"><acronym><acronymword>CCM</acronymword></acronym> Processor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1537">globbing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1538"><code>NINTAP</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1539">Processor</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1540"><acronym><acronymword>CCM</acronymword></acronym> Processor</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncrcat 85.nc 86.nc 87.nc 88.nc 89.nc 8589.nc
ncrcat 8[56789].nc 8589.nc
@@ -15846,7 +16142,7 @@ ncrcat -n 5,2,1 85.nc 8589.nc
<xref label="Specifying-Input-Files"><xrefnodename>Specifying Input Files</xrefnodename></xref>, for an explanation of the distinctions
between these methods.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1528">Fortran</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1541">Fortran</indexterm></cindex>
<para>Assume the files <file>85.nc</file>, <file>86.nc</file>, <w>&dots; <file>89.nc</file></w>
each contain a record coordinate <var>time</var> of <w>length 12</w> defined
such that the third record in <file>86.nc</file> contains data from March
@@ -15863,7 +16159,7 @@ When <command>ncra</command> and <command>ncrcat</command> encounter a file whic
contain any records that meet the specified hyperslab criteria, they
disregard the file and proceed to the next file without failing.
The <samp>-F</samp> turns on the Fortran (1-based) indexing convention.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1529">stride</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1542">stride</indexterm></cindex>
</para>
<para>The following uses the <var>stride</var> option to concatenate all the March
temperature data from multiple input files into a single output file
@@ -15887,14 +16183,14 @@ concatenates June, 1985&textndash;June, 1989:
</section>
<node name="ncrename-netCDF-Renamer" spaces=" "><nodename>ncrename netCDF Renamer</nodename><nodenext spaces=" ">ncwa netCDF Weighted Averager</nodenext><nodeprev spaces=" ">ncrcat netCDF Record Concatenator</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncrename</command> netCDF Renamer</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1530">renaming variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1531">renaming groups</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1532">renaming dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1533">renaming attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1534">variable names</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1535">dimension names</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1536">attribute names</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1537">group names</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1543">renaming variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1544">renaming groups</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1545">renaming dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1546">renaming attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1547">variable names</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1548">dimension names</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1549">attribute names</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1550">group names</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="41" mergedindex="cp">ncrename</indexterm></findex>
<noindent></noindent>
@@ -15910,7 +16206,7 @@ concatenates June, 1985&textndash;June, 1989:
<noindent></noindent>
<para>DESCRIPTION
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1538"><kbd>.</kbd></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1551"><kbd>.</kbd></indexterm></cindex>
<para><command>ncrename</command> renames netCDF dimensions, variables, attributes, and
groups.
Each object that has a name in the list of old names is renamed using
@@ -15939,9 +16235,9 @@ The object name is the terminal path component of <var>new_name</var> and
this object must already exist in the group specified by the
<var>old_name</var> path.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1539">data safety</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1540">safeguards</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1541">temporary output files</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1552">data safety</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1553">safeguards</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1554">temporary output files</indexterm></cindex>
<para><command>ncrename</command> is an exception to the normal <acronym><acronymword>NCO</acronymword></acronym> rule that
the user will be interactively prompted before an existing file is
changed, and that a temporary copy of an output file is constructed
@@ -15961,10 +16257,10 @@ In this case, the named dependent variable must be one-dimensional and
should have no missing values.
Such a variable will become a coordinate variable.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1542">performance</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1543">operator speed</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1544">speed</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1545">execution time</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1555">performance</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1556">operator speed</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1557">speed</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1558">execution time</indexterm></cindex>
<para>According to the <cite>netCDF User Guide</cite>, renaming properties in
netCDF files does not incur the penalty of recopying the entire file
when the <var>new_name</var> is shorter than the <var>old_name</var>.
@@ -15978,9 +16274,9 @@ when the <var>new_name</var> is shorter than the <var>old_name</var>.
The old and new names of the attribute are specified with <samp>-a</samp>
(or <samp>--attribute</samp>) by the associated <var>old_name</var> and
<var>new_name</var> values.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1546"><code>global</code> attribute</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1547">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1548">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1559"><code>global</code> attribute</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1560">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1561">attributes, global</indexterm></cindex>
Global attributes are treated no differently than variable attributes.
This option may be specified more than once.
As mentioned above, all occurrences of the attribute of a given name
@@ -16041,8 +16337,10 @@ In this case <code>p</code> must exist in the input file (or
<para>Rename the attribute <code>long_name</code> to <code>largo_nombre</code> in the
variable <code>u</code>, and no other variables in netCDF <file>in.nc</file>.
</para><example endspaces=" ">
-<pre xml:space="preserve">ncrename -a u&arobase;long_name,largo_nombre in.nc
-</pre></example>
+<verbatim xml:space="preserve">
+ncrename -a u at long_name,largo_nombre in.nc
+</verbatim>
+</example>
<para>Rename the group <code>g8</code> to <code>g20</code> in netCDF4 file
<file>in_grp.nc</file>:
@@ -16060,7 +16358,7 @@ ncrename -v /g1/lon,/g1/longitude in_grp.nc # Alternate
<html endspaces=" ">
<a name="ncrename_crd"></a> <!&textndash; http://nco.sf.net/nco.html#ncrename_crd &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1549">coordinate variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1562">coordinate variables</indexterm></cindex>
<para><command>ncrename</command> does not automatically attach dimensions to variables of
the same name.
This is done to make renaming an easy way to change whether a variable
@@ -16095,10 +16393,10 @@ ncrename -O -d lat_T42,lat ~/foo.nc ~/foo2.nc # Also renames variable
version 4.3.1-rc5 or later, or convert the file to netCDF3 first,
then rename as intended, then convert back.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1550">global attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1551">attributes, global</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1552"><code>_FillValue</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1553"><code>missing_value</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1563">global attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1564">attributes, global</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1565"><code>_FillValue</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1566"><code>missing_value</code></indexterm></cindex>
<para>Create netCDF <file>out.nc</file> identical to <file>in.nc</file> except the
attribute <code>_FillValue</code> is changed to <code>missing_value</code>,
the attribute <code>units</code> is changed to <code>CGS_units</code> (but only in
@@ -16106,9 +16404,11 @@ those variables which possess it), the attribute <code>hieght</code> is
changed to <code>height</code> in the variable <code>tpt</code>, and in the
variable <code>prs_sfc</code>, if it exists.
</para><example endspaces=" ">
-<pre xml:space="preserve">ncrename -a _FillValue,missing_value -a .units,CGS_units \
- -a tpt&arobase;hieght,height -a prs_sfc&arobase;.hieght,height in.nc out.nc
-</pre></example>
+<verbatim xml:space="preserve">
+ncrename -a _FillValue,missing_value -a .units,CGS_units \
+ -a tpt at hieght,height -a prs_sfc at .hieght,height in.nc out.nc
+</verbatim>
+</example>
<para>The presence and absence of the <samp>.</samp> and <samp>&arobase;</samp> features
cause this command to execute successfully only if a number of
conditions are met.
@@ -16124,13 +16424,15 @@ The variable <code>prs_sfc</code> need not exist, and need not contain the
<para>Rename the global or group attribute <code>Convention</code> to
<code>Conventions</code>
</para><example endspaces=" ">
-<pre xml:space="preserve">ncrename -a Convention,Conventions in.nc # Variable and global atts.
+<verbatim xml:space="preserve">
+ncrename -a Convention,Conventions in.nc # Variable and global atts.
ncrename -a .Convention,Conventions in.nc # Variable and global atts.
-ncrename -a &arobase;Convention,Conventions in.nc # Global atts. only
-ncrename -a &arobase;.Convention,Conventions in.nc # Global atts. only
-ncrename -a global&arobase;Convention,Conventions in.nc # Global atts. only
-ncrename -a .global&arobase;.Convention,Conventions in.nc # Global atts. only
-</pre></example>
+ncrename -a @Convention,Conventions in.nc # Global atts. only
+ncrename -a @.Convention,Conventions in.nc # Global atts. only
+ncrename -a global at Convention,Conventions in.nc # Global atts. only
+ncrename -a .global at .Convention,Conventions in.nc # Global atts. only
+</verbatim>
+</example>
<para>The examples without the <code>&arobase;</code> character attempt to change the
attribute name in both Global or Group and variable attributes.
The examples with the <code>&arobase;</code> character attempt to change only
@@ -16151,10 +16453,10 @@ Variables not prefixed with a period (<code>global</code>) must be present.
</section>
<node name="ncwa-netCDF-Weighted-Averager" spaces=" "><nodename>ncwa netCDF Weighted Averager</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">ncrename netCDF Renamer</nodeprev><nodeup spaces=" ">Operator Reference Manual</nodeup></node>
<section spaces=" "><sectiontitle><command>ncwa</command> netCDF Weighted Averager</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1554">averaging data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1555">weighted average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1556">masked average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1557">broadcasting variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1567">averaging data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1568">weighted average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1569">masked average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1570">broadcasting variables</indexterm></cindex>
<findex index="fn" spaces=" "><indexterm index="fn" number="42" mergedindex="cp">ncwa</indexterm></findex>
<noindent></noindent>
@@ -16182,7 +16484,7 @@ The default behavior of <command>ncwa</command> is to arithmetically average
every numerical variable over all dimensions and to produce a scalar
result for each.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1558">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1571">degenerate dimension</indexterm></cindex>
<para>Averaged dimensions are, by default, eliminated as dimensions.
Their corresponding coordinates, if any, are output as scalar
variables.
@@ -16196,9 +16498,9 @@ concatenation along the degenerate dimension.
<para>To average variables over only a subset of their dimensions, specify
these dimensions in a comma-separated list following <samp>-a</samp>, e.g.,
<samp>-a time,lat,lon</samp>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1559">arithmetic operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1560">hyperslab</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1561"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>]]</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1572">arithmetic operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1573">hyperslab</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1574"><code>-d <var>dim</var>,[<var>min</var>][,[<var>max</var>]]</code></indexterm></cindex>
As with all arithmetic operators, the operation may be restricted to
an arbitrary hypserslab by employing the <samp>-d</samp> option
(<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>).
@@ -16213,20 +16515,20 @@ With these options, <command>ncwa</command> can compute sophisticated averages
<a name="-w"></a> <!&textndash; http://nco.sf.net/nco.html#-w &textndash;>
<a name="wgt"></a> <!&textndash; http://nco.sf.net/nco.html#wgt &textndash;>
</html>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1562"><code>-w <var>weight</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1563"><code>--weight <var>weight</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1564"><code>--wgt_var <var>weight</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1565"><code>-m <var>mask_var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1566"><code>--mask-variable <var>mask_var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1567"><code>--mask_variable <var>mask_var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1568"><code>--msk_nm <var>mask_var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1569"><code>--msk_var <var>mask_var</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1570"><code>-B <var>mask_cond</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1571"><code>--msk_cnd <var>mask_cond</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1572"><code>--mask_condition <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1575"><code>-w <var>weight</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1576"><code>--weight <var>weight</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1577"><code>--wgt_var <var>weight</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1578"><code>-m <var>mask_var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1579"><code>--mask-variable <var>mask_var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1580"><code>--mask_variable <var>mask_var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1581"><code>--msk_nm <var>mask_var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1582"><code>--msk_var <var>mask_var</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1583"><code>-B <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1584"><code>--msk_cnd <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1585"><code>--mask_condition <var>mask_cond</var></code></indexterm></cindex>
<para><var>mask_var</var> and <var>weight</var>, if specified, are broadcast to conform
to the variables being averaged.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1573">rank</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1586">rank</indexterm></cindex>
The rank of variables is reduced by the number of dimensions which they
are averaged over.
Thus arrays which are one dimensional in the <var>input-file</var> and are
@@ -16261,8 +16563,8 @@ Since, by default <command>ncwa</command> weights coordinate variables, the
value of <code>latitude</code> in the <var>output-file</var> depends on the weights
in <var>lat_wgt</var> and is not likely to <w>be 45.0</w>, the midpoint latitude
of the hyperslab.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1574">coordinate variable</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1575"><code>-I</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1587">coordinate variable</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1588"><code>-I</code></indexterm></cindex>
Option <samp>-I</samp> overrides this default behavior and causes
<command>ncwa</command> not to weight or mask coordinate variables
<footnote><para>The default behavior of (<samp>-I</samp>) changed on
@@ -16280,8 +16582,8 @@ area-weighted mean latitude.
centroid of the hyperslab.
For the example given, this is about <w>30 degrees.</w></para></footnote>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1576">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1577">operation types</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1589">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1590">operation types</indexterm></cindex>
<para>As explained in <xref label="Operation-Types"><xrefnodename>Operation Types</xrefnodename></xref>, <command>ncwa</command>
<emph>always averages</emph> coordinate variables regardless of the arithmetic
operation type performed on the non-coordinate variables.
@@ -16301,8 +16603,8 @@ is given above (<pxref label="Operation-Types"><xrefnodename>Operation Types</xr
</html>
<node name="Mask-condition" spaces=" "><nodename>Mask condition</nodename><nodenext spaces=" ">Normalization and Integration</nodenext><nodeprev spaces=" ">ncwa netCDF Weighted Averager</nodeprev><nodeup spaces=" ">ncwa netCDF Weighted Averager</nodeup></node>
<subsection spaces=" "><sectiontitle>Mask condition</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1578">mask condition</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1579">truth condition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1591">mask condition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1592">truth condition</indexterm></cindex>
<tex endspaces=" ">
Each $\xxx_{\idx}$ also has an associated masking
weight~$\mskflg_{\idx}$ whose value is~0 or~1 (false or true).
@@ -16317,12 +16619,12 @@ As expected, $\mskflg_{\idx} = 1$ when the mask condition is
<dfn>true</dfn> and $\mskflg_{\idx} = 0$ otherwise.
</tex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1580"><code>--op_rlt <var>mask_comp</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1581"><code>--mask_comparator <var>mask_comp</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1582"><code>--msk_cmp_typ <var>mask_comp</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1583"><code>--msk_cnd_sng <var>mask_cond</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1584"><code>--mask_condition <var>mask_cond</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1585"><code>-B <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1593"><code>--op_rlt <var>mask_comp</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1594"><code>--mask_comparator <var>mask_comp</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1595"><code>--msk_cmp_typ <var>mask_comp</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1596"><code>--msk_cnd_sng <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1597"><code>--mask_condition <var>mask_cond</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1598"><code>-B <var>mask_cond</var></code></indexterm></cindex>
<para>The mask condition has the syntax <math><var>mask_var</var></math>
<math><var>mask_comp</var></math> <math><var>mask_val</var></math>.
The preferred method to specify the mask condition is in one string with
@@ -16337,7 +16639,7 @@ It is safest to write scripts using <samp>--mask_condition</samp>.</para></footn
The <var>mask_condition</var> string is automatically parsed into its three
constituents <var>mask_var</var>, <var>mask_comp</var>, and <var>mask_val</var>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1586">comparator</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1599">comparator</indexterm></cindex>
<para>Here <var>mask_var</var> is the name of the masking variable (specified with
<samp>-m</samp>, <samp>--mask-variable</samp>, <samp>--mask_variable</samp>,
<samp>--msk_nm</samp>, or <samp>--msk_var</samp>).
@@ -16356,9 +16658,9 @@ comparisons <math>==</math>, <math>!=</math>, <math>></math>, <math><</mat
<math><=</math>.
<clear name="flg" line=" flg"></clear>
The mask comparator defaults to <kbd>eq</kbd> (equality).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1587"><code>--mask-value <var>mask_val</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1588"><code>--mask_value <var>mask_val</var></code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1589"><code>--msk_val <var>mask_val</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1600"><code>--mask-value <var>mask_val</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1601"><code>--mask_value <var>mask_val</var></code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1602"><code>--msk_val <var>mask_val</var></code></indexterm></cindex>
The <var>mask_val</var> argument to <samp>-M</samp> (or <samp>--mask-value</samp>, or
<samp>--msk_val</samp>) is the right hand side of the
<dfn>mask condition</dfn>.
@@ -16411,11 +16713,11 @@ weight $\wgt_{\idx}=0.0$ as well).
</subsection>
<node name="Normalization-and-Integration" spaces=" "><nodename>Normalization and Integration</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Mask condition</nodeprev><nodeup spaces=" ">ncwa netCDF Weighted Averager</nodeup></node>
<subsection spaces=" "><sectiontitle>Normalization and Integration</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1590">normalization</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1591"><code>-N</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1592"><code>numerator</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1593">integration</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1594">dot product</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1603">normalization</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1604"><code>-N</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1605"><code>numerator</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1606">integration</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1607">dot product</indexterm></cindex>
<para><command>ncwa</command> has one switch which controls the normalization of the
averages appearing in the <var>output-file</var>.
Short option <samp>-N</samp> (or long options <samp>--nmr</samp> or
@@ -16440,7 +16742,7 @@ integrals (i.e., weighted sums) to be output.
For example, consider the variable
<code>lev</code> where <math><var>lev</var> = [100,500,1000]</math> weighted by
the weight <code>lev_wgt</code> where <math><var>lev_wgt</var> = [10,2,1]</math>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1595">dot product</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1608">dot product</indexterm></cindex>
The vertical integral of <code>lev</code>, weighted by <code>lev_wgt</code>,
is the dot product of <var>lev</var> and <var>lev_wgt</var>.
That this is <w>is 3000.0</w> can be seen by inspection and verified with
@@ -16484,7 +16786,8 @@ sophisticated averages (and integrals) from the command line.
</para>
<para>Given file <file>85_0112.nc</file>:
</para><example endspaces=" ">
-<pre xml:space="preserve">netcdf 85_0112 {
+<verbatim xml:space="preserve">
+netcdf 85_0112 {
dimensions:
lat = 64 ;
lev = 18 ;
@@ -16500,8 +16803,9 @@ variables:
float two_dmn_var(lat, lev) ;
float mask(lat, lon) ;
float gw(lat) ;
-}
-</pre></example>
+}
+</verbatim>
+</example>
<para>Average all variables in <file>in.nc</file> over all dimensions and store
results in <file>out.nc</file>:
@@ -16519,7 +16823,7 @@ specified (with <samp>-a</samp>).
ncwa -a lon -b in.nc out2.nc
</pre></example>
<noindent></noindent>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1596">degenerate dimension</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1609">degenerate dimension</indexterm></cindex>
<para>The first command turns <code>lon</code> into a scalar and the second retains
<code>lon</code> as a degenerate dimension in all variables.
</para><example endspaces=" ">
@@ -16531,9 +16835,9 @@ lon[0] = 135
<para>In either case the tally is simply the size of <code>lon</code>, i.e., 180
for the <file>85_0112.nc</file> file described by the sample header above.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1597"><code>gw</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1598">Gaussian weights</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1599">climate model</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1610"><code>gw</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1611">Gaussian weights</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1612">climate model</indexterm></cindex>
<para>Compute the meridional (latitudinal) mean, with values weighted by
the corresponding element of <var>gw</var>
<footnote><para><code>gw</code> stands for <dfn>Gaussian weight</dfn> in many
@@ -16559,8 +16863,8 @@ $64 \times 128 = 8192$.
64 times 128 = 8192.
<clear name="flg" line=" flg"></clear>
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1600"><code>ORO</code></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1601">climate model</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1613"><code>ORO</code></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1614">climate model</indexterm></cindex>
<para>Compute the area-mean over the globe using only points for which
<set name="flg" line=" flg"></set>
<tex endspaces=" ">
@@ -16615,20 +16919,22 @@ the variable <var>area</var> contains the area of each gridcell
Thus the <samp>-N</samp> switch, or, equivalently, the <samp>-y ttl</samp> switch,
correctly integrate the cell areas into a total regional area.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1602">mask condition</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1603">truth condition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1615">mask condition</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1616">truth condition</indexterm></cindex>
<para>Mask a file to contain <var>_FillValue</var> everywhere except where
<math><var>thr_min</var> <= <var>msk_var</var> <= <var>thr_max</var></math>:
</para><example endspaces=" ">
-<pre xml:space="preserve"># Set masking variable and its scalar thresholds
+<verbatim xml:space="preserve">
+# Set masking variable and its scalar thresholds
export msk_var='three_dmn_var_dbl' # Masking variable
export thr_max='20' # Maximum allowed value
export thr_min='10' # Minimum allowed value
ncecat -O in.nc out.nc # Wrap out.nc in degenerate "record" dimension
-ncwa -O -a record -B "${msk_var} <= ${thr_max}" out.nc out.nc
+ncwa -O -a record -B "${msk_var} <= ${thr_max}" out.nc out.nc
ncecat -O out.nc out.nc # Wrap out.nc in degenerate "record" dimension
-ncwa -O -a record -B "${msk_var} >= ${thr_min}" out.nc out.nc
-</pre></example>
+ncwa -O -a record -B "${msk_var} >= ${thr_min}" out.nc out.nc
+</verbatim>
+</example>
<para>After the first use of <command>ncwa</command>, <file>out.nc</file> contains
<var>_FillValue</var> where <code>${msk_var} >= ${thr_max}</code>.
The process is then repeated on the remaining data to filter out
@@ -16644,17 +16950,17 @@ where <math><var>thr_min</var> <= <var>msk_var</var> <= <var>thr_max</var>
</chapter>
<node name="Contributing" spaces=" "><nodename>Contributing</nodename><nodenext spaces=" ">Quick Start</nodenext><nodeprev spaces=" ">Operator Reference Manual</nodeprev><nodeup spaces=" ">Top</nodeup></node>
<chapter spaces=" "><sectiontitle>Contributing</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1604">contributing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1617">contributing</indexterm></cindex>
<para>We welcome contributions from anyone.
The project homepage at <uref><urefurl>https://sf.net/projects/nco</urefurl></uref>
contains more information on how to contribute.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1605">PayPal</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1618">PayPal</indexterm></cindex>
<para>Financial contributions to <acronym><acronymword>NCO</acronymword></acronym> development may be made through
<uref><urefurl>https://www.paypal.com/xclick/business=zender%40uci.edu&item_name=NCO+development&item_number=nco_dnt_dvl&no_note=1&tax=0¤cy_code=USD</urefurl><urefdesc spaces=" ">PayPal</urefdesc></uref>.
<acronym><acronymword>NCO</acronymword></acronym> has been shared for over <w>10 years</w> yet only two
users have contributed any money to the developers
-<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="1606">chocolate</indexterm></cindex>
+<footnote spaces="\n"><cindex index="cp" spaces=" "><indexterm index="cp" number="1619">chocolate</indexterm></cindex>
<para>Happy users have sent me a few gifts, though.
This includes a box of imported chocolate.
Mmm.
@@ -16672,21 +16978,22 @@ So you could be the third!
</html>
<menu endspaces=" ">
<menuentry leadingtext="* "><menunode separator="::">Contributors</menunode><menudescription><pre xml:space="preserve">
+</pre></menudescription></menuentry><menuentry leadingtext="* "><menunode separator="::">Citation</menunode><menudescription><pre xml:space="preserve">
</pre></menudescription></menuentry><menuentry leadingtext="* "><menunode separator="::">Proposals for Institutional Funding</menunode><menudescription><pre xml:space="preserve">
</pre></menudescription></menuentry></menu>
-<node name="Contributors" spaces=" "><nodename>Contributors</nodename><nodenext spaces=" ">Proposals for Institutional Funding</nodenext><nodeprev spaces=" ">Contributing</nodeprev><nodeup spaces=" ">Contributing</nodeup></node>
+<node name="Contributors" spaces=" "><nodename>Contributors</nodename><nodenext spaces=" ">Citation</nodenext><nodeprev spaces=" ">Contributing</nodeprev><nodeup spaces=" ">Contributing</nodeup></node>
<section spaces=" "><sectiontitle>Contributors</sectiontitle>
<para><acronym><acronymword>NCO</acronymword></acronym> would not exist without the dedicated efforts of the
remarkable software engineers who conceive, develop, and
maintain netCDF, UDUnits, and OPeNDAP.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1607">Russ Rew</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1608">John Caron</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1609">Glenn Davis</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1610">Steve Emmerson</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1611">James Gallagher</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1612">Ed Hartnett</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1613">Dennis Heimbigner</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1620">Russ Rew</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1621">John Caron</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1622">Glenn Davis</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1623">Steve Emmerson</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1624">James Gallagher</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1625">Ed Hartnett</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1626">Dennis Heimbigner</indexterm></cindex>
Since 1995 <acronym><acronymword>NCO</acronymword></acronym> has received support from, I believe, the
entire staff of all these projects, including
Russ Rew,
@@ -16701,10 +17008,10 @@ In addition to their roles in maintaining the software stack on which
or contributed to <acronym><acronymword>NCO</acronymword></acronym> specifically. That support is
acknowledged separately below.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1614">contributors</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1627">contributors</indexterm></cindex>
<para>The primary contributors to <acronym><acronymword>NCO</acronymword></acronym> development have been:
</para><table commandarg="asis" spaces=" " endspaces=" ">
-<beforefirstitem><cindex index="cp" spaces=" "><indexterm index="cp" number="1615">Charlie Zender</indexterm></cindex>
+<beforefirstitem><cindex index="cp" spaces=" "><indexterm index="cp" number="1628">Charlie Zender</indexterm></cindex>
</beforefirstitem><tableentry><tableterm><item spaces=" "><itemformat command="asis">Charlie Zender</itemformat></item>
</tableterm><tableitem><para>All concept, design and implementation from 1995&textndash;2000.
Since then autotools, bug-squashing, <acronym><acronymword>CDL</acronymword></acronym>, chunking,
@@ -16713,131 +17020,160 @@ documentation, anchoring, recursion, <acronym><acronymword>GPE</acronymword></ac
<command>ncbo</command>, <command>ncpdq</command>, SMP threading and MPI parallelization,
netCDF4 integration, external funding, project management, science
research, releases.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1616">Henry Butowsky</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1629">Henry Butowsky</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Henry Butowsky</itemformat></item>
</tableterm><tableitem><para>Non-linear operations and <code>min()</code>, <code>max()</code>, <code>total()</code>
support in <command>ncra</command> and <command>ncwa</command>.
Type conversion for arithmetic.
-Migration to netCDF3 API.
+Migration to netCDF3 <acronym><acronymword>API</acronymword></acronym>.
<command>ncap2</command> parser, lexer, <acronym><acronymword>GSL</acronymword></acronym>-support, <w>and I/O</w>.
Multislabbing algorithm.
Variable wildcarding.
Numerous hacks.
<command>ncap2</command> language.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1617">Rorik Peterson</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1630">Rorik Peterson</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Rorik Peterson</itemformat></item>
-</tableterm><tableitem><para>Original autotool build support.
+</tableterm><tableitem><para>Original autotools build support.
Long command-line options.
Original UDUnits support.
Debianization.
Numerous bug-fixes.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1618">Joe Hamman</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1631">Joe Hamman</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Joe Hamman</itemformat></item>
</tableterm><tableitem><para>Python bindings (NCOpy).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1619">Daniel Wang</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1632">Daniel Wang</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Daniel Wang</itemformat></item>
</tableterm><tableitem><para>Script Workflow Analysis for MultiProcessing (<acronym><acronymword>SWAMP</acronymword></acronym>).
<acronym><acronymword>RPM</acronymword></acronym> support.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1620">Harry Mangalam</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1633">Harry Mangalam</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Harry Mangalam</itemformat></item>
</tableterm><tableitem><para>Benchmarking.
OPeNDAP configuration.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1621">Pedro Vicente</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1634">Pedro Vicente</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Pedro Vicente</itemformat></item>
</tableterm><tableitem><para>Windows Visual Studio support.
netCDF4 groups.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1622">Russ Rew</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1635">Russ Rew</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Russ Rew</itemformat></item>
-</tableterm><tableitem><para>Advice on NCO structural algorithms
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1623">Brian Mays</indexterm></cindex>
+</tableterm><tableitem><para>Advice on <acronym><acronymword>NCO</acronymword></acronym> structural algorithms
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1636">Brian Mays</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Brian Mays</itemformat></item>
</tableterm><tableitem><para>Original packaging for Debian <acronym><acronymword>GNU</acronymword></acronym>/Linux, <command>nroff</command> man pages.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1624">George Shapovalov</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1637">George Shapovalov</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">George Shapovalov</itemformat></item>
</tableterm><tableitem><para>Packaging for Gentoo <acronym><acronymword>GNU</acronymword></acronym>/Linux.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1625">Bill Kocik</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1638">Bill Kocik</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Bill Kocik</itemformat></item>
</tableterm><tableitem><para>Memory management.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1626">Len Makin</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1639">Len Makin</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Len Makin</itemformat></item>
</tableterm><tableitem><para>NEC SX architecture support.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1627">Jim Edwards</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1640">Jim Edwards</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Jim Edwards</itemformat></item>
</tableterm><tableitem><para>AIX architecture support.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1628">Juliana Rew</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1641">Juliana Rew</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Juliana Rew</itemformat></item>
</tableterm><tableitem><para>Compatibility with large <acronym><acronymword>PID</acronymword></acronym>s.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1629">Karen Schuchardt</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1642">Karen Schuchardt</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Karen Schuchardt</itemformat></item>
</tableterm><tableitem><para>Auxiliary coordinate support.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1630">Gayathri Venkitachalam</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1643">Gayathri Venkitachalam</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Gayathri Venkitachalam</itemformat></item>
</tableterm><tableitem><para><acronym><acronymword>MPI</acronymword></acronym> implementation.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1631">Scott Capps</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1644">Scott Capps</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Scott Capps</itemformat></item>
</tableterm><tableitem><para>Large work-load testing
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1632">Peter Campbell</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1633">Martin Dix</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1634">Mark Flanner</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1635">Markus Liebig</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1636">Keith Lindsay</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1637">Stu Muller</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1638">Mike Page</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1639">Martin Schmidt</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1640">Lori Sentman</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1641">Michael Schulz</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1642">Gary Strand</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1643">Andrew Wittenberg</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1644">George White</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1645">Remik Ziemlinski</indexterm></cindex>
-</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski</itemformat></item>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1645">Peter Campbell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1646">Martin Dix</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1647">Mark Flanner</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1648">Markus Liebig</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1649">Keith Lindsay</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1650">Stu Muller</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1651">Mike Page</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1652">Martin Schmidt</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1653">Lori Sentman</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1654">Michael Schulz</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1655">Rich Signell</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1656">Gary Strand</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1657">Andrew Wittenberg</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1658">George White</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1659">Remik Ziemlinski</indexterm></cindex>
+</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Peter Campbell, Martin Dix, Mark Flanner, Markus Liebig, Keith Lindsay, Mike Page, Martin Schmidt, Michael Schulz, Lori Sentman, Rich Signell, Gary Strand, George White Andrew Wittenberg, Remik Ziemlinski</itemformat></item>
</tableterm><tableitem><para>Excellent bug reports and feature requests.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1646">Daniel Baumann</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1647">Nick Bower</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1648">Luk Claes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1649">Barry deFreese</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1650">Aleksandar Jelenak</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1651">Francesco Lovergine</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1652">Matej Vela</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1660">Daniel Baumann</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1661">Nick Bower</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1662">Luk Claes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1663">Barry deFreese</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1664">Aleksandar Jelenak</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1665">Francesco Lovergine</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1666">Matej Vela</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Daniel Baumann, Nick Bower, Luk Claebs, Barry deFreese, Aleksandar Jelenak, Francesco Lovergine, Matej Vela</itemformat></item>
</tableterm><tableitem><para>Debian packaging
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1653">Patrice Dumas</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1654">Ed Hill</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1655">Orion Powlawski</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1667">Patrice Dumas</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1668">Ed Hill</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1669">Orion Powlawski</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Patrice Dumas, Ed Hill, Orion Poplawski</itemformat></item>
</tableterm><tableitem><para>RedHat packaging
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1656">George Shapavalov</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1657">Patrick Kursawe</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1670">George Shapavalov</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1671">Patrick Kursawe</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">George Shapavalov, Patrick Kursawe</itemformat></item>
</tableterm><tableitem><para>Gentoo packaging
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1658">Filipe Fernandes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1672">Filipe Fernandes</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Filipe Fernandes</itemformat></item>
</tableterm><tableitem><para>OpenSuse packaging
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1659">Alexander Hansen</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1660">Takeshi Enomoto</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1673">Alexander Hansen</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1674">Takeshi Enomoto</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Takeshi Enomoto, Alexander Hansen</itemformat></item>
</tableterm><tableitem><para>Mac OS packaging
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1661">Eric Blake</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1675">Eric Blake</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Eric Blake</itemformat></item>
</tableterm><tableitem><para>Autoconf/M4 help
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1662">Gavin Burris</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1663">Kyle Wilcox</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1676">Gavin Burris</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1677">Kyle Wilcox</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Gavin Burris, Kyle Wilcox</itemformat></item>
</tableterm><tableitem><para>RHEL and CentOS build scripts and bug reports.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1664">Andrea Cimatoribus</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1678">Andrea Cimatoribus</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Andrea Cimatoribus</itemformat></item>
</tableterm><tableitem><para><acronym><acronymword>NCO</acronymword></acronym> Spiral Logo
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1665">Martin Otte</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1666">Etienne Tourigny</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1679">Martin Otte</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1680">Etienne Tourigny</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Martin Otte, Etienne Tourigny</itemformat></item>
</tableterm><tableitem><para>Single bug reports and fixes
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1667">Wenshan Wang</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1681">Wenshan Wang</indexterm></cindex>
</para></tableitem></tableentry><tableentry><tableterm><item spaces=" "><itemformat command="asis">Wenshan Wang</itemformat></item>
</tableterm><tableitem><para><acronym><acronymword>CMIP5</acronymword></acronym> and <acronym><acronymword>MODIS</acronymword></acronym> processing documentation.
</para></tableitem></tableentry></table>
<para>Please let me know if your name was omitted!
</para>
<html endspaces=" ">
+<a name="ctt"></a> <!&textndash; http://nco.sf.net/nco.html#ctt &textndash;>
+</html>
+</section>
+<node name="Citation" spaces=" "><nodename>Citation</nodename><nodenext spaces=" ">Proposals for Institutional Funding</nodenext><nodeprev spaces=" ">Contributors</nodeprev><nodeup spaces=" ">Contributing</nodeup></node>
+<section spaces=" "><sectiontitle>Citation</sectiontitle>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1682">citation</indexterm></cindex>
+<para>The recommended citations for <acronym><acronymword>NCO</acronymword></acronym> software are
+</para><example endspaces=" ">
+<verbatim xml:space="preserve">
+Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience
+Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10),
+1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+
+Zender, C. S. (2014), netCDF Operator (NCO) User Guide, Version 4.4.3,
+http://nco.sf.net/nco.pdf.
+</verbatim>
+</example>
+<para>Use the former when referring to overall design, purpose, and
+optimization of <acronym><acronymword>NCO</acronymword></acronym>, and use the latter when referring to
+specific features and/or the User Guide itself.
+</para>
+<para>Additional information on citing <acronym><acronymword>NCO</acronymword></acronym> is in the User Guide at
+<url><urefurl>http://nco.sf.net#ctt</urefurl></url>.
+A complete list of <acronym><acronymword>NCO</acronymword></acronym> publications and presentations is at
+<url><urefurl>http://nco.sf.net#pub</urefurl></url>.
+This list links to the full papers and seminars themselves.
+</para>
+<html endspaces=" ">
<a name="prp"></a> <!&textndash; http://nco.sf.net/nco.html#prp &textndash;>
<a name="prp_sei"></a> <!&textndash; http://nco.sf.net/nco.html#prp_sei &textndash;>
<a name="fnd"></a> <!&textndash; http://nco.sf.net/nco.html#fnd &textndash;>
@@ -16847,29 +17183,29 @@ netCDF4 groups.
</pre></menudescription></menuentry></menu>
</section>
-<node name="Proposals-for-Institutional-Funding" spaces=" "><nodename>Proposals for Institutional Funding</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Contributors</nodeprev><nodeup spaces=" ">Contributing</nodeup></node>
+<node name="Proposals-for-Institutional-Funding" spaces=" "><nodename>Proposals for Institutional Funding</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Citation</nodeprev><nodeup spaces=" ">Contributing</nodeup></node>
<section spaces=" "><sectiontitle>Proposals for Institutional Funding</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1668">funding</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1669">proposals</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1670"><acronym><acronymword>NSF</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1671">server-side processing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1672">Distributed Data Reduction & Analysis</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1673">Scientific Data Operators</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1674"><acronym><acronymword>DDRA</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1675">Server-Side Distributed Data Reduction & Analysis</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1676"><acronym><acronymword>SSDDRA</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1677"><acronym><acronymword>CCSM</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1678"><acronym><acronymword>IPCC</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1679"><acronym><acronymword>NSF</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1680"><acronym><acronymword>SDO</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1681"><acronym><acronymword>SEIII</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1682">OptIPuter</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1683">funding</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1684">proposals</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1685"><acronym><acronymword>NSF</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1686">server-side processing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1687">Distributed Data Reduction & Analysis</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1688">Scientific Data Operators</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1689"><acronym><acronymword>DDRA</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1690">Server-Side Distributed Data Reduction & Analysis</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1691"><acronym><acronymword>SSDDRA</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1692"><acronym><acronymword>CCSM</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1693"><acronym><acronymword>IPCC</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1694"><acronym><acronymword>NSF</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1695"><acronym><acronymword>SDO</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1696"><acronym><acronymword>SEIII</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1697">OptIPuter</indexterm></cindex>
<para><acronym><acronymword>NSF</acronymword></acronym> has funded a
<uref><urefurl>http://nco.sf.net#prp_sei</urefurl><urefdesc spaces=" ">project</urefdesc></uref>
to improve Distributed Data Reduction & Analysis (<acronym><acronymword>DDRA</acronymword></acronym>) by
evolving <acronym><acronymword>NCO</acronymword></acronym> into a suite of Scientific Data Operators called
<acronym><acronymword>SDO</acronymword></acronym>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1683">parallelism</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1698">parallelism</indexterm></cindex>
The two main components of this project are <acronym><acronymword>NCO</acronymword></acronym> parallelism
(OpenMP, <acronym><acronymword>MPI</acronymword></acronym>) and Server-Side <acronym><acronymword>DDRA</acronymword></acronym>
(<acronym><acronymword>SSDDRA</acronymword></acronym>) implemented through extensions to <acronym><acronymword>OPeNDAP</acronymword></acronym>
@@ -16877,9 +17213,9 @@ and netCDF4.
This project will dramatically reduce bandwidth usage for <acronym><acronymword>NCO</acronymword></acronym>
<acronym><acronymword>DDRA</acronymword></acronym>.
</para>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1684"><acronym><acronymword>NASA</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1685"><acronym><acronymword>NRA</acronymword></acronym></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1686"><acronym><acronymword>HDF</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1699"><acronym><acronymword>NASA</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1700"><acronym><acronymword>NRA</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1701"><acronym><acronymword>HDF</acronymword></acronym></indexterm></cindex>
<para>With this first <acronym><acronymword>NCO</acronymword></acronym> proposal funded, the content of the
next <acronym><acronymword>NCO</acronymword></acronym> proposal is clear.
We are interested in obtaining <acronym><acronymword>NASA</acronymword></acronym> support for
@@ -16899,7 +17235,7 @@ Comments on the proposals and letters of support are also very welcome.
</chapter>
<node name="Quick-Start" spaces=" "><nodename>Quick Start</nodename><nodenext spaces=" ">CMIP5 Example</nodenext><nodeprev spaces=" ">Contributing</nodeprev><nodeup spaces=" ">Top</nodeup></node>
<chapter spaces=" "><sectiontitle>Quick Start</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1687">Quick Start</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1702">Quick Start</indexterm></cindex>
<para>Simple examples in Bash shell scripts showing how to average data with
different file structures.
Here we include monthly, seasonal and annual average with daily or
@@ -16914,43 +17250,47 @@ monthly data in either one file or multiple files.
<node name="Daily-data-in-one-file" spaces=" "><nodename>Daily data in one file</nodename><nodenext spaces=" ">Monthly data in one file</nodenext><nodeprev spaces=" ">Quick Start</nodeprev><nodeup spaces=" ">Quick Start</nodeup></node>
<section spaces=" "><sectiontitle>Daily data in one file</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1688">daily data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1703">daily data</indexterm></cindex>
<para>Suppose we have daily data from Jan 1st, 1990 to Dec. 31, 2005 in the
file of <file>in.nc</file> with the record dimension as <code>time</code>.
</para>
<noindent></noindent>
<para><strong>Monthly average:</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1689">monthly average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1690">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1691">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1704">monthly average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1705">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1706">time-averaging</indexterm></cindex>
</para><example endspaces=" ">
-<pre xml:space="preserve">for yyyy in {1990..2005}; do # Loop over years
- for moy in {1..12}; do # Loop over months
- mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
+<verbatim xml:space="preserve">
+for yyyy in {1990..2005}; do # Loop over years
+ for moy in {1..12}; do # Loop over months
+ mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
# Average specific month yyyy-mm
- ncra -O -d time,"${yyyy}-${mm}-01","${yyyy}-${mm}-31" \
- in.nc in_${yyyy}${mm}.nc
+ ncra -O -d time,"${yyyy}-${mm}-01","${yyyy}-${mm}-31" \
+ in.nc in_${yyyy}${mm}.nc
done
done
# Concatenate monthly files together
ncrcat -O in_??????.nc out.nc
-</pre></example>
+</verbatim>
+</example>
<noindent></noindent>
<para><strong>Annual average:</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1692">annual average from daily data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1693">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1694">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1707">annual average from daily data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1708">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1709">time-averaging</indexterm></cindex>
</para><example endspaces=" ">
-<pre xml:space="preserve">for yyyy in {1990..2005}; do # Loop over years
- ncra -O -d time,"${yyyy}-01-01","${yyyy}-12-31" in.nc in_${yyyy}.nc
+<verbatim xml:space="preserve">
+for yyyy in {1990..2005}; do # Loop over years
+ ncra -O -d time,"${yyyy}-01-01","${yyyy}-12-31" in.nc in_${yyyy}.nc
done
# Concatenate annual files together
ncrcat -O in_????.nc out.nc
-</pre></example>
+</verbatim>
+</example>
<para>The <option>-O</option> switch means to overwrite the pre-existing files (<pxref label="Batch-Mode"><xrefnodename>Batch Mode</xrefnodename></pxref>).
The <option>-d</option> option is to specify the range of hyperslabs (<pxref label="Hyperslabs"><xrefnodename>Hyperslabs</xrefnodename></pxref>).
There are detailed instructions on <command>ncra</command> (<pxref label="ncra-netCDF-Record-Averager"><xrefnodename>ncra netCDF Record Averager</xrefnodename></pxref> and <command>ncrcat</command> (<pxref label="ncrcat-netCDF-Record-Concatenator"><xrefnodename>ncrcat netCDF Record Concatenator</xrefnodename></pxref>).
@@ -16959,23 +17299,23 @@ There are detailed instructions on <command>ncra</command> (<pxref label="ncra-n
</section>
<node name="Monthly-data-in-one-file" spaces=" "><nodename>Monthly data in one file</nodename><nodenext spaces=" ">One time point one file</nodenext><nodeprev spaces=" ">Daily data in one file</nodeprev><nodeup spaces=" ">Quick Start</nodeup></node>
<section spaces=" "><sectiontitle>Monthly data in one file</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1695">monthly data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1710">monthly data</indexterm></cindex>
<para>Inside the input file <file>in.nc</file>, the record dimension <code>time</code> is from Jan 1990 to Dec 2005.
</para>
<noindent></noindent>
<para><strong>Seasonal average (e.g., DJF):</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1696">seasonal average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1697">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1698">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1711">seasonal average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1712">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1713">time-averaging</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncra -O --mro -d time,"1990-12-01",,12,3 in.nc out.nc
</pre></example>
<noindent></noindent>
<para><strong>Annual average:</strong>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1699">annual average from monthly data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1700">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1701">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1714">annual average from monthly data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1715">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1716">time-averaging</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve">ncra -O --mro -d time,,,12,12 in.nc out.nc
</pre></example>
@@ -17000,10 +17340,10 @@ you can leave it blank if you want to include the minimum or the maximum of the
</section>
<node name="One-time-point-one-file" spaces=" "><nodename>One time point one file</nodename><nodenext spaces=" ">Multiple files with multiple time points</nodenext><nodeprev spaces=" ">Monthly data in one file</nodeprev><nodeup spaces=" ">Quick Start</nodeup></node>
<section spaces=" "><sectiontitle>One time point one file</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1702">daily data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1703">monthly data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1704">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1705">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1717">daily data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1718">monthly data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1719">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1720">time-averaging</indexterm></cindex>
<para>This means if you have daily data of 30 days, there will be 30 data files.
Or if you have monthly data of 12 months, there will be 12 data files.
Dealing with this kind of files, you need to specify the file names in shell scripts and pass them to NCO operators.
@@ -17014,18 +17354,20 @@ If you want to know the monthly average of Jan 1990, you can write like,
</pre></example>
<para>You might want to use loop if you need the average of each month.
</para><example endspaces=" ">
-<pre xml:space="preserve">for moy in {1..12}; do # Loop over months
- mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
+<verbatim xml:space="preserve">
+for moy in {1..12}; do # Loop over months
+ mm=$( printf "%02d" ${moy} ) # Change to 2-digit format
- ncra -O snd_????${mm}??.nc out_${mm}.nc
+ ncra -O snd_????${mm}??.nc out_${mm}.nc
done
-</pre></example>
+</verbatim>
+</example>
</section>
<node name="Multiple-files-with-multiple-time-points" spaces=" "><nodename>Multiple files with multiple time points</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">One time point one file</nodeprev><nodeup spaces=" ">Quick Start</nodeup></node>
<section spaces=" "><sectiontitle>Multiple files with multiple time points</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1706">daily data</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1707">monthly data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1721">daily data</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1722">monthly data</indexterm></cindex>
<para>Similar as the last one, it&textrsquo;s more about shell scripts.
Suppose you have daily data with one month of them in one data file.
The monthly average is simply to apply <command>ncra</command> on the specific data file.
@@ -17033,12 +17375,14 @@ And for seasonal averages, you can specify the three months by shell scripts.
</para>
<html endspaces=" ">
<a name="cmip5"></a> <!&textndash; http://nco.sf.net/nco.html#cmip5 &textndash;>
+<a name="godad"></a> <!&textndash; http://nco.sf.net/nco.html#godad &textndash;>
</html>
</section>
</chapter>
<node name="CMIP5-Example" spaces=" "><nodename>CMIP5 Example</nodename><nodenext spaces=" ">Parallel</nodenext><nodeprev spaces=" ">Quick Start</nodeprev><nodeup spaces=" ">Top</nodeup></node>
<chapter spaces=" "><sectiontitle><acronym><acronymword>CMIP5</acronymword></acronym> Example</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1708"><acronym><acronymword>CMIP5</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1723"><acronym><acronymword>CMIP5</acronymword></acronym></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1724"><acronym><acronymword>GODAD</acronymword></acronym></indexterm></cindex>
<ignore>
This @uref{http://nco.sf.net/xmp_cesm.html,Wonderful CMIP5 Documentation}
shows complete processing of the @acronym{CMIP5} dataset.
@@ -17051,11 +17395,37 @@ responses of climate models from around the world.
However, it is a tremendous workload to retrieve a single climate
statistic from all these models, each of which includes several ensemble
members.
-Not only that, it is too often a repetitive process which impedes new
+Not only that, it is too often a tedious process that impedes new
research and hypothesis testing.
-Our <acronym><acronymword>NASA</acronymword></acronym> <acronym><acronymword>ACCESS</acronymword></acronym> project is designed to simplify and
-accelerate this process.
-To begin, we document below a prototypical example of <acronym><acronymword>CMIP5</acronymword></acronym>
+Our <acronym><acronymword>NASA</acronymword></acronym> <acronym><acronymword>ACCESS</acronymword></acronym> 2011 project simplified and
+accelerated this process.
+</para>
+<para>Traditional geoscience data analysis requires users to work with
+numerous flat (data in one level or namespace) files.
+In that paradigm instruments or models produce, and then repositories
+archive and distribute, and then researchers request and analyze,
+collections of flat files.
+<acronym><acronymword>NCO</acronymword></acronym> works well with that paradigm, yet it also embodies the
+necessary algorithms to transition geoscience data analysis from relying
+solely on traditional (or &textldquo;flat&textrdquo;) datasets to allowing newer
+hierarchical (or &textldquo;nested&textrdquo;) datasets.
+</para>
+<para>Hierarchical datasets support and enable combining all datastreams that
+meet user-specified criteria into a single or small number of files that
+hold <emph>all</emph> the science-relevant data.
+<acronym><acronymword>NCO</acronymword></acronym> (and no other software to our knowledge) exploits this
+capability now.
+Data and metadata may be aggregated into and analyzed in hierarchical
+structures.
+We call the resulting data storage, distribution, and analysis
+paradigm Group-Oriented Data Analysis and Distribution
+(<acronym><acronymword>GODAD</acronymword></acronym>).
+<acronym><acronymword>GODAD</acronymword></acronym> lets the scientific question organize the data, not the
+<emph>ad hoc</emph> granularity of all relevant datasets.
+This chapter illustrates <acronym><acronymword>GODAD</acronymword></acronym> techniques applied to
+analysis of the <acronym><acronymword>CMIP5</acronymword></acronym> dataset.
+</para>
+<para>To begin, we document below a prototypical example of <acronym><acronymword>CMIP5</acronymword></acronym>
analysis and evaluation using traditional <acronym><acronymword>NCO</acronymword></acronym> commands on
netCDF3-format model and <acronym><acronymword>HDF-EOS</acronymword></acronym> format observational
(<acronym><acronymword>NASA</acronymword></acronym> <acronym><acronymword>MODIS</acronymword></acronym> satellite instrument) datasets.
@@ -17087,11 +17457,11 @@ group-based processing as well.
<node name="Combine-Files" spaces=" "><nodename>Combine Files</nodename><nodenext spaces=" ">Global Distribution of Long-term Average</nodenext><nodeprev spaces=" ">CMIP5 Example</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Combine Files</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1709">file combination</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1725">file combination</indexterm></cindex>
<para>Sometimes, the data of one ensemble member will be stored in several
files to reduce single file size.
-But it is not convenient to process in a batch mode.
-The following script illustrates how to concatenate these files into one.
+It is more convenient to concatenate these files into a single
+timeseries, and the following script illustrates how.
Key steps include:
</para><enumerate first="1" endspaces=" ">
<listitem spaces=" "><para>Obtain number and names (or partial names) of files in a directory
@@ -17102,24 +17472,24 @@ Key steps include:
<verbatiminclude file="xmp/cmb_fl.sh" spaces=" ">xmp/cmb_fl.sh</verbatiminclude>
</example>
-<para>Right now, <acronym><acronymword>CMIP5</acronymword></acronym> model data downloaded from Earth System Grid
+<para><acronym><acronymword>CMIP5</acronymword></acronym> model data downloaded from the Earth System Grid
Federation (<uref><urefurl>http://pcmdi9.llnl.gov/esgf-web-fe/</urefurl><urefdesc spaces=" "><acronym><acronymword>ESGF</acronymword></acronym></urefdesc></uref>)
-will not contain <key>group</key> features yet.
-Therefore users can aggregate the flat files into groups themselves.
-The following script shows how to aggregate models to one file.
+does not contain group features yet.
+Therefore users must aggregate flat files into hierarchical ones themselves.
+The following script shows how.
Each dataset becomes a group in the output file.
There can be several levels of groups.
-In this example, we employ two experiments as the top-level.
-The second-level comprises different models.
-Some models have more than one ensemble member.
-These ensemble members are on the third level.
-In each sub-group of ensemble members, we appended two variables,
-<var>snc</var> and <var>snd</var> (these stand for snow cover and snow depth, by
-the way).
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1710"><option>--gag</option></indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1711">aggregation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1712">group aggregation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1713">groups, creating</indexterm></cindex>
+In this example, we employ two experiments (&textldquo;scenarios&textrdquo;) as the top-level.
+The second-level comprises different models (e.g., CCSM4, CESM1-BGC).
+Many models are run multiple times with slight perturbed initial
+conditions to produce an ensemble of realizations.
+These ensemble members comprise the third level of the hierarchy.
+The script selects two variables, <var>snc</var> and <var>snd</var> (snow cover
+and snow depth).
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1726"><option>--gag</option></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1727">aggregation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1728">group aggregation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1729">groups, creating</indexterm></cindex>
</para><example endspaces=" ">
<verbatiminclude file="xmp/cmb_fl_grp.sh" spaces=" ">xmp/cmb_fl_grp.sh</verbatiminclude>
</example>
@@ -17127,10 +17497,10 @@ the way).
</section>
<node name="Global-Distribution-of-Long_002dterm-Average" spaces=" "><nodename>Global Distribution of Long-term Average</nodename><nodenext spaces=" ">Annual Average over Regions</nodenext><nodeprev spaces=" ">Combine Files</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Global Distribution of Long-term Average</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1714">spatial distribution</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1715">long-term average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1716">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1717">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1730">spatial distribution</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1731">long-term average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1732">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1733">time-averaging</indexterm></cindex>
<float name="fgr_003aglb" type="Figure" number="7.1" spaces=" " endspaces=" "><floattype>Figure</floattype><floatname>fgr:glb</floatname>
<image><imagefile>xmp/fgr1</imagefile><imagewidth>3.5in</imagewidth></image>
<caption><para>Global Distribution of Long-term Average.</para></caption>
@@ -17151,7 +17521,7 @@ Key steps include:
</example>
<para>With the use of <key>group</key>, the above script will be shortened to <w>ONE LINE</w>.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1718">groups, averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1734">groups, averaging</indexterm></cindex>
</para><example endspaces=" ">
<pre xml:space="preserve"># Data from cmb_fl_grp.sh
# ensemble averaging
@@ -17175,20 +17545,20 @@ ensembles with only one ensemble member will be left untouched.
</section>
<node name="Annual-Average-over-Regions" spaces=" "><nodename>Annual Average over Regions</nodename><nodenext spaces=" ">Monthly Cycle</nodenext><nodeprev spaces=" ">Global Distribution of Long-term Average</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Annual Average over Regions</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1719">annual average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1720">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1721">time-averaging</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1722">area-averaging</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1723">dimension order</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1724">anomalies</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1725">standard deviation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1726">renaming variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1727">attributes, editing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1728">attributes, modifying</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1729">attributes, overwriting</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1730">regression</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1731">nco script file</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1732">variables, appending</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1735">annual average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1736">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1737">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1738">area-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1739">dimension order</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1740">anomalies</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1741">standard deviation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1742">renaming variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1743">attributes, editing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1744">attributes, modifying</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1745">attributes, overwriting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1746">regression</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1747">nco script file</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1748">variables, appending</indexterm></cindex>
<float name="fgr_003aanl" type="Figure" number="7.2" spaces=" " endspaces=" "><floattype>Figure</floattype><floatname>fgr:anl</floatname>
<image><imagefile>xmp/fgr2</imagefile><imagewidth>4in</imagewidth></image>
<caption><para>Annual Average over Regions.</para></caption>
@@ -17223,12 +17593,12 @@ all the loops over experiments, models and ensemble members can be omitted.
As we are working on implementing <key>group</key> feature in all <acronym><acronymword>NCO</acronymword></acronym> operators,
some functions (e.g., regression and standard deviation over ensemble members)
may have to wait until the new versions.
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1733">group, spatial averaging</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1734">group, temporal averaging</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1735">group, anomaly</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1736">group, standard deviation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1737">group, aggregation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1738">group, dimension permutation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1749">group, spatial averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1750">group, temporal averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1751">group, anomaly</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1752">group, standard deviation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1753">group, aggregation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1754">group, dimension permutation</indexterm></cindex>
</para><example endspaces=" ">
<verbatiminclude file="xmp/ann_avg_grp.sh" spaces=" ">xmp/ann_avg_grp.sh</verbatiminclude>
</example>
@@ -17236,12 +17606,12 @@ may have to wait until the new versions.
</section>
<node name="Monthly-Cycle" spaces=" "><nodename>Monthly Cycle</nodename><nodenext spaces=" ">Regrid MODIS Data</nodenext><nodeprev spaces=" ">Annual Average over Regions</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Monthly Cycle</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1739">monthly average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1740">average</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1741">time-averaging</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1742">anomalies</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1743">geographical weight</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1744">weighted average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1755">monthly average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1756">average</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1757">time-averaging</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1758">anomalies</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1759">geographical weight</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1760">weighted average</indexterm></cindex>
<float name="fgr_003amon" type="Figure" number="7.3" spaces=" " endspaces=" "><floattype>Figure</floattype><floatname>fgr:mon</floatname>
<image><imagefile>xmp/fgr3</imagefile><imagewidth>4in</imagewidth></image>
<caption><para>Monthly Cycle.</para></caption>
@@ -17267,16 +17637,16 @@ the script will be shortened.
</section>
<node name="Regrid-MODIS-Data" spaces=" "><nodename>Regrid MODIS Data</nodename><nodenext spaces=" ">Add Coordinates to MODIS Data</nodenext><nodeprev spaces=" ">Monthly Cycle</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Regrid <acronym><acronymword>MODIS</acronymword></acronym> Data</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1745">regrid</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1746">MODIS</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1747">bilinear interpolation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1748">interpolation</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1749">renaming variables</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1750">renaming attributes</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1751">renaming dimensions</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1752">attributes, editing</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1753">attributes, modifying</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1754">attributes, overwriting</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1761">regrid</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1762">MODIS</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1763">bilinear interpolation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1764">interpolation</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1765">renaming variables</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1766">renaming attributes</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1767">renaming dimensions</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1768">attributes, editing</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1769">attributes, modifying</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1770">attributes, overwriting</indexterm></cindex>
<para>In order to compare the results between <acronym><acronymword>MODIS</acronymword></acronym> and
<acronym><acronymword>CMIP5</acronymword></acronym> models, one usually regrids one or both datasets so
that the spatial resolutions match.
@@ -17298,8 +17668,8 @@ Key steps include:
</section>
<node name="Add-Coordinates-to-MODIS-Data" spaces=" "><nodename>Add Coordinates to MODIS Data</nodename><nodenext spaces=" ">Permute MODIS Coordinates</nodenext><nodeprev spaces=" ">Regrid MODIS Data</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Add Coordinates to <acronym><acronymword>MODIS</acronymword></acronym> Data</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1755">MODIS</indexterm></cindex>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1756">coordinates</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1771">MODIS</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1772">coordinates</indexterm></cindex>
<para><strong>Main Script</strong>
</para><example endspaces=" ">
<verbatiminclude file="xmp/add_crd.sh" spaces=" ">xmp/add_crd.sh</verbatiminclude>
@@ -17312,7 +17682,7 @@ Key steps include:
</section>
<node name="Permute-MODIS-Coordinates" spaces=" "><nodename>Permute MODIS Coordinates</nodename><nodenext spaces=" "></nodenext><nodeprev spaces=" ">Add Coordinates to MODIS Data</nodeprev><nodeup spaces=" ">CMIP5 Example</nodeup></node>
<section spaces=" "><sectiontitle>Permute <acronym><acronymword>MODIS</acronymword></acronym> Coordinates</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1757">coordinates, modifying</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1773">coordinates, modifying</indexterm></cindex>
<!-- c NB: 20140130: @textdegree is in TeXInfo 4.12 but Mac OS X 10.8 ships with 4.8 -->
<para><acronym><acronymword>MODIS</acronymword></acronym> orders latitude data from 90°N to
-90°N, and longitude from -180°E to
@@ -17359,12 +17729,14 @@ Here is an example showing:
</chapter>
<node name="Parallel" spaces=" "><nodename>Parallel</nodename><nodenext spaces=" ">CCSM Example</nodenext><nodeprev spaces=" ">CMIP5 Example</nodeprev><nodeup spaces=" ">Top</nodeup></node>
<chapter spaces=" "><sectiontitle>Parallel</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1758"><command>parallel</command></indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1774"><command>parallel</command></indexterm></cindex>
<para>This section will describe scripting strategies, including the use of
<acronym><acronymword>GNU</acronymword></acronym> Parallel, to <acronym><acronymword>NCO</acronymword></acronym>.
</para><example endspaces=" ">
-<pre xml:space="preserve">ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" {} 50y/{}
-</pre></example>
+<verbatim xml:space="preserve">
+ls *historical*.nc | parallel ncks -O -d time,"1950-01-01","2000-01-01" {} 50y/{}
+</verbatim>
+</example>
<html endspaces=" ">
<a name="ccsm"></a> <!&textndash; http://nco.sf.net/nco.html#ccsm &textndash;>
@@ -17372,14 +17744,15 @@ Here is an example showing:
</chapter>
<node name="CCSM-Example" spaces=" "><nodename>CCSM Example</nodename><nodenext spaces=" ">mybibnode</nodenext><nodeprev spaces=" ">Parallel</nodeprev><nodeup spaces=" ">Top</nodeup></node>
<chapter spaces=" "><sectiontitle>CCSM Example</sectiontitle>
-<cindex index="cp" spaces=" "><indexterm index="cp" number="1759">CCSM</indexterm></cindex>
+<cindex index="cp" spaces=" "><indexterm index="cp" number="1775">CCSM</indexterm></cindex>
<para>This chapter illustrates how to use <acronym><acronymword>NCO</acronymword></acronym> to
process and analyze the results of a <acronym><acronymword>CCSM</acronymword></acronym> climate simulation.
</para><example endspaces=" ">
-<pre xml:space="preserve">************************************************************************
-Task 0: Finding input files
+<verbatim xml:space="preserve">
************************************************************************
+Task 0: Finding input files
+x************************************************************************
The CCSM model outputs files to a local directory like:
/ptmp/zender/archive/T42x1_40
@@ -17421,44 +17794,44 @@ Each month in the output file is the mean of 100 input files.
Normally, we store the "reduced" data in a smaller, local directory.
caseid='T42x1_40'
-#drc_in="${DATA}/archive/${caseid}/atm"
-drc_in="${DATA}/${caseid}"
-drc_out="${DATA}/${caseid}"
-mkdir -p ${drc_out}
-cd ${drc_out}
+#drc_in="${DATA}/archive/${caseid}/atm"
+drc_in="${DATA}/${caseid}"
+drc_out="${DATA}/${caseid}"
+mkdir -p ${drc_out}
+cd ${drc_out}
Method 1: Assume all data in directory applies
-for mth in {1..12}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
- ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
- ${drc_in}/${caseid}.cam2.h0.*-${mm}.nc
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.*-${mm}.nc
done # end loop over mth
Method 2: Use shell 'globbing' to construct input filenames
-for mth in {1..12}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
- ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
- ${drc_in}/${caseid}.cam2.h0.00??-${mm}.nc \
- ${drc_in}/${caseid}.cam2.h0.0100-${mm}.nc
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.00??-${mm}.nc \
+ ${drc_in}/${caseid}.cam2.h0.0100-${mm}.nc
done # end loop over mth
Method 3: Construct input filename list explicitly
-for mth in {1..12}; do
+for mth in {1..12}; do
mm=`printf "%02d" $mth`
fl_lst_in=''
- for yr in {1..100}; do
+ for yr in {1..100}; do
yyyy=`printf "%04d" $yr`
- fl_in=${caseid}.cam2.h0.${yyyy}-${mm}.nc
- fl_lst_in="${fl_lst_in} ${caseid}.cam2.h0.${yyyy}-${mm}.nc"
+ fl_in=${caseid}.cam2.h0.${yyyy}-${mm}.nc
+ fl_lst_in="${fl_lst_in} ${caseid}.cam2.h0.${yyyy}-${mm}.nc"
done # end loop over yr
- ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc -p ${drc_in} \
- ${fl_lst_in}
+ ncra -O -D 1 -o ${drc_out}/${caseid}_clm${mm}.nc -p ${drc_in} \
+ ${fl_lst_in}
done # end loop over mth
Make sure the output file averages correct input files!
ncks -M prints global metadata:
- ncks -M ${drc_out}/${caseid}_clm01.nc
+ ncks -M ${drc_out}/${caseid}_clm01.nc
The input files ncra used to create the climatological monthly mean
will appear in the global attribute named 'history'.
@@ -17466,23 +17839,23 @@ will appear in the global attribute named 'history'.
Use ncrcat to aggregate the climatological monthly means
ncrcat -O -D 1 \
- ${drc_out}/${caseid}_clm??.nc ${drc_out}/${caseid}_clm_0112.nc
+ ${drc_out}/${caseid}_clm??.nc ${drc_out}/${caseid}_clm_0112.nc
Finally, create climatological means for reference.
The climatological time-mean:
ncra -O -D 1 \
- ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm.nc
+ ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm.nc
The climatological zonal-mean:
ncwa -O -D 1 -a lon \
- ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_x.nc
+ ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_x.nc
The climatological time- and spatial-mean:
ncwa -O -D 1 -a lon,lat,time -w gw \
- ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_xyt.nc
+ ${drc_out}/${caseid}_clm.nc ${drc_out}/${caseid}_clm_xyt.nc
This file contains only scalars, e.g., "global mean temperature",
used for summarizing global results of a climate experiment.
@@ -17491,8 +17864,8 @@ Climatological monthly anomalies = Annual Cycle:
Subtract climatological mean from climatological monthly means.
Result is annual cycle, i.e., climate-mean has been removed.
- ncbo -O -D 1 -o ${drc_out}/${caseid}_clm_0112_anm.nc \
- ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm_xyt.nc
+ ncbo -O -D 1 -o ${drc_out}/${caseid}_clm_0112_anm.nc \
+ ${drc_out}/${caseid}_clm_0112.nc ${drc_out}/${caseid}_clm_xyt.nc
************************************************************************
Task 2: Correcting monthly averages
@@ -17508,29 +17881,29 @@ declare -a dpm
dpm=(0 31 28.25 31 30 31 30 31 31 30 31 30 31) # Allows 1-based indexing
Method 1: Create dpm directly in climatological monthly means
-for mth in {1..12}; do
- mm=`printf "%02d" ${mth}`
- ncap2 -O -s "dpm=0.0*date+${dpm[${mth}]}" \
- ${drc_out}/${caseid}_clm${mm}.nc ${drc_out}/${caseid}_clm${mm}.nc
+for mth in {1..12}; do
+ mm=`printf "%02d" ${mth}`
+ ncap2 -O -s "dpm=0.0*date+${dpm[${mth}]}" \
+ ${drc_out}/${caseid}_clm${mm}.nc ${drc_out}/${caseid}_clm${mm}.nc
done # end loop over mth
Method 2: Create dpm by aggregating small files
-for mth in {1..12}; do
- mm=`printf "%02d" ${mth}`
- ncap2 -O -v -s "dpm=${dpm[${mth}]}" ~/nco/data/in.nc \
- ${drc_out}/foo_${mm}.nc
+for mth in {1..12}; do
+ mm=`printf "%02d" ${mth}`
+ ncap2 -O -v -s "dpm=${dpm[${mth}]}" ~/nco/data/in.nc \
+ ${drc_out}/foo_${mm}.nc
done # end loop over mth
-ncecat -O -D 1 -p ${drc_out} -n 12,2,2 foo_${mm}.nc foo.nc
-ncrename -O -D 1 -d record,time ${drc_out}/foo.nc
+ncecat -O -D 1 -p ${drc_out} -n 12,2,2 foo_${mm}.nc foo.nc
+ncrename -O -D 1 -d record,time ${drc_out}/foo.nc
ncatted -O -h \
-a long_name,dpm,o,c,"Days per month" \
-a units,dpm,o,c,"days" \
- ${drc_out}/${caseid}_clm_0112.nc
-ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
+ ${drc_out}/${caseid}_clm_0112.nc
+ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
Method 3: Create small netCDF file using ncgen
cat > foo.cdl << 'EOF'
-netcdf foo {
+netcdf foo {
dimensions:
time=unlimited;
variables:
@@ -17539,10 +17912,10 @@ variables:
dpm:units="days";
data:
dpm=31,28.25,31,30,31,30,31,31,30,31,30,31;
-}
+}
EOF
ncgen -b -o foo.nc foo.cdl
-ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
+ncks -A -v dpm ${drc_out}/foo.nc ${drc_out}/${caseid}_clm_0112.nc
Another way to get correct monthly weighting is to average daily
output files, if available.
@@ -17554,8 +17927,8 @@ Let's say you are interested in examining the California region.
Hyperslab your dataset to isolate the appropriate latitude/longitudes.
ncks -O -D 1 -d lat,30.0,37.0 -d lon,240.0,270.0 \
- ${drc_out}/${caseid}_clm_0112.nc \
- ${drc_out}/${caseid}_clm_0112_Cal.nc
+ ${drc_out}/${caseid}_clm_0112.nc \
+ ${drc_out}/${caseid}_clm_0112_Cal.nc
The dataset is now much smaller!
To examine particular metrics.
@@ -17583,7 +17956,7 @@ http://www.esrl.noaa.gov/psd/thredds/dodsC/Datasets/ncep.reanalysis.dailyavgs/su
pres.sfc.1969.nc ~/foo.nc
LLNL PCMDI IPCC OPeNDAP Data Portal:
-ncks -M -p http://username:password&arobase;esgcet.llnl.gov/cgi-bin/dap-cgi.py/ipcc4/sresa1b/ncar_ccsm3_0 pcmdi.ipcc4.ncar_ccsm3_0.sresa1b.run1.atm.mo.xml
+ncks -M -p http://username:password@esgcet.llnl.gov/cgi-bin/dap-cgi.py/ipcc4/sresa1b/ncar_ccsm3_0 pcmdi.ipcc4.ncar_ccsm3_0.sresa1b.run1.atm.mo.xml
Earth System Grid (ESG): http://www.earthsystemgrid.org
@@ -17611,7 +17984,7 @@ iap_fgoals1_0_g inmcm3_0 ipsl_cm4 miroc3_2_hires miroc3_2_medres \
miub_echo_g mpi_echam5 mri_cgcm2_3_2a ncar_ccsm3_0 ncar_pcm1 \
ukmo_hadcm3 ukmo_hadgem1'; do
for run in '1'; do
- ncks -R -O -D 3 -p ftp://climate.llnl.gov/${scn}/atm/mo/${var}/${mdl}/run${run} -l ${DATA}/${scn}/atm/mo/${var}/${mdl}/run${run} '*' ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
+ ncks -R -O -D 3 -p ftp://climate.llnl.gov/${scn}/atm/mo/${var}/${mdl}/run${run} -l ${DATA}/${scn}/atm/mo/${var}/${mdl}/run${run} '*' ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
done # end loop over run
done # end loop over mdl
done # end loop over scn
@@ -17619,31 +17992,31 @@ done # end loop over var
cd sresa1b/atm/mo/tas/ukmo_hadcm3/run1/
ncks -H -m -v lat,lon,lat_bnds,lon_bnds -M tas_A1.nc | m
-bds -x 096 -y 073 -m 33 -o ${DATA}/data/dst_3.75x2.5.nc # ukmo_hadcm3
-ncview ${DATA}/data/dst_3.75x2.5.nc
+bds -x 096 -y 073 -m 33 -o ${DATA}/data/dst_3.75x2.5.nc # ukmo_hadcm3
+ncview ${DATA}/data/dst_3.75x2.5.nc
# msk_rgn is California mask on ukmo_hadcm3 grid
# area is correct area weight on ukmo_hadcm3 grid
-ncks -A -v area,msk_rgn ${DATA}/data/dst_3.75x2.5.nc \
-${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/area_msk_ukmo_hadcm3.nc
+ncks -A -v area,msk_rgn ${DATA}/data/dst_3.75x2.5.nc \
+${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/area_msk_ukmo_hadcm3.nc
Template for standardized data:
-${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
+${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
e.g., raw data
-${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/tas_A1.nc
+${DATA}/sresa1b/atm/mo/tas/ukmo_hadcm3/run1/tas_A1.nc
becomes standardized data
Level 0: raw from IPCC site--no changes except for name
Make symbolic link name match raw data
-Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
+Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
ln -s -f tas_A1.nc sresa1b_ukmo_hadcm3_run1_tas_200101_209911.nc
area_msk_ukmo_hadcm3.nc
Level I: Add all variables (not standardized in time)
to file containing msk_rgn and area
-Template: ${scn}_${mdl}_${run}_${yyyymm}_${yyyymm}.nc
+Template: ${scn}_${mdl}_${run}_${yyyymm}_${yyyymm}.nc
/bin/cp area_msk_ukmo_hadcm3.nc sresa1b_ukmo_hadcm3_run1_200101_209911.nc
ncks -A -v tas sresa1b_ukmo_hadcm3_run1_tas_200101_209911.nc \
@@ -17657,7 +18030,7 @@ mv sresa1b_ukmo_hadcm3_run1_200101_209911.nc foo.nc
ncks -A -v tas,pr foo.nc sresa1b_ukmo_hadcm3_run1_200101_209911.nc
Level II: Correct # years, months
-Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
+Template: ${scn}_${mdl}_${run}_${var}_${yyyymm}_${yyyymm}.nc
ncks -d time,....... file1.nc file2.nc
ncrcat file2.nc file3.nc sresa1b_ukmo_hadcm3_run1_200001_209912.nc
@@ -17673,7 +18046,8 @@ Level III: Many derived products from level II, e.g.,
ncwa -m msk_rgn -w area -a lat,lon \
sresa1b_ukmo_hadcm3_run1_200001_209912.nc \
sresa1b_ukmo_hadcm3_run1_200001_209912_xy_Cal.nc
-</pre></example>
+</verbatim>
+</example>
<html endspaces=" ">
<a name="bibliography"></a> <!&textndash; http://nco.sf.net/nco.html#bibliography &textndash;>
diff --git a/doc/nco_news.shtml b/doc/nco_news.shtml
index d38c4dd..959a1f0 100644
--- a/doc/nco_news.shtml
+++ b/doc/nco_news.shtml
@@ -1,4 +1,4 @@
-<!-- $Header: /cvsroot/nco/nco/doc/nco_news.shtml,v 1.22 2012/06/14 20:20:14 zender Exp $
+<!-- $Header: /cvsroot/nco/nco/doc/nco_news.shtml,v 1.23 2014/06/13 19:43:51 zender Exp $
Purpose: NCO news archive
@@ -23,11 +23,7 @@ scp -p ~/nco/doc/nco_news.shtml nco.sf.net:/home/project-web/nco/htdocs/nco_news
<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
<dt><a name="News"></a></dt>
-<h2>NCO News</h2>
-
-<ul>
-<li><a href="./nco_news.shtml">Past NCO News \& Announcements</a></li>
-</ul>
+<h2>NCO News and Announcements from 20030624 (version 2.8.3) and earlier</h2>
<a name="20030624"></a>
<p>2003/06/24: A potpurri of old news which is no longer needed on the homepage
diff --git a/doc/problems_old.shtml b/doc/problems_old.shtml
new file mode 100644
index 0000000..61f3ac0
--- /dev/null
+++ b/doc/problems_old.shtml
@@ -0,0 +1,440 @@
+<!-- $Header: /cvsroot/nco/nco/doc/problems_old.shtml,v 1.2 2014/06/15 16:45:40 zender Exp $
+
+Purpose: Problems archive
+
+URL:
+http://nco.sf.net/problems_old.shtml
+http://dust.ess.uci.edu/nco/problems_old.shtml
+file:///home/zender/nco/doc/problems_old.shtml
+
+Usage:
+/usr/bin/scp ~/nco/doc/problems_old.shtml zender,nco at web.sf.net:/home/project-web/nco/htdocs
+scp -p ~/nco/doc/problems_old.shtml dust.ess.uci.edu:/var/www/html/nco
+-->
+
+<!doctype html public "-//W3C//DTD HTML 3.2//EN">
+<html>
+<head>
+ <title>NCO Homepage</title>
+ <meta name="GENERATOR" content="Mozilla/3.04Gold (X11; I; Linux 2.0.0 i686) [Netscape]">
+ <meta name="Author" content="Charles S. Zender">
+ <meta name="Keywords" content="NCO Homepage, netCDF, netCDF operator, GCM, HDF, scientific data">
+</head>
+<body bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#008080" alink="#FF0000">
+
+<dt><a name="News"></a></dt>
+<h2>Known Problems through 2012 (version 4.2.3)</h2>
+
+<ul><b>Older Generic Run-time Problems:</b>
+
+<!-- http://nco.sf.net#bug_mm3 -->
+<a name="bug_mm3"></a>
+<li><i><tt>MM3</tt> slowdown:</i>
+A longstanding “feature” of netCDF3 was identified in
+March, 2012, and is now known by the tag MM3.
+The MM3 issue can lead to unusually slow performance.
+The problem is triggered by an aggregate pattern of file access so the
+workaround must be implemented in the application software (e.g., NCO)
+rather than in the netCDF library itself.
+The name MM3 fits because the problem is normally encountered on
+Multi-record Multi-variable netCDF3 files.
+And we call our “solution” the MM3-workaround.
+If you encounter unusually slow NCO performance while using NCO to
+analyze MM3 files on a large blocksize filesystem,
+chances are you are encountering an MM3-induced slowdown.
+NCO release 4.1.0 implements the MM3-workaround for <tt>ncks</tt>.
+It speeds-up common ncks sub-setting on NCAR's GLADE by 10-50x.
+MM3-induced slowdowns are present in other NCO operators and we are
+prioritizing our MM3-patches to those encountered most often.
+Thanks to Gary Strand for reporting this problem, and to Russ Rew for
+creating the workaround algorithm, which is also now in <tt>nccopy</tt>.
+</li>
+
+<!-- http://nco.sf.net#bug_nofill -->
+<a name="bug_nofill"></a>
+<li><i><tt>NOFILL</tt> bug:</i>
+All netCDF versions prior to 4.1.3 may create corrupt netCDF3 files
+when linked to any version of NCO except 4.0.8.
+The solution is to install netCDF version 4.1.3 or later.
+The corruption occurs silently (without warning or error messages).
+The problem has been seen "in the wild" only on filesystems with
+large block sizes (e.g., Lustre), although it may be more widespread.
+It is caused by a netCDF bug that NCO triggers by invoking
+NOFILL mode for faster writes. Hence it is called the NOFILL bug.
+The bug is hard to trigger, it depends on a rare interaction of
+filesystem block-size, hyperslab size, and order-of-variable writing.
+The bug exists in all versions of netCDF through 4.1.2.
+
+If you have a large block filesystem and cannot upgrade your netCDF
+library, then use NCO version 4.0.8, which disables NOFILL mode (and
+thus writes files more slowly).
+NCO 4.0.8 and will workaround the NOFILL bug on all versions of netCDF
+(i.e., 4.1.2 and earlier).
+Hence NCO 4.0.8 will always correctly write netCDF3 files.
+Other temporary workarounds include creating only netCDF4 files
+(e.g., <tt>ncks -4 ...</tt>) instead of netCDF3 files.
+The NOFILL patch included in NCO 4.0.8 was subsequently removed
+in NCO 4.0.9, which assumes that netCDF 4.1.3 or later is installed.
+</li>
+
+<!-- http://nco.sf.net#bug_hyp_dgn -->
+<a name="bug_hyp_dgn"></a>
+<li><i>Degenerate hyperslabbing bug:</i>
+Versions ???—4.0.6 could return incorrect hyperslabs when
+user-specified hyperslabs did not include at least one point.
+In such cases, instead of returning no data, hyperslabs could return all data.
+To determine whether your NCO is affected by this bug, run these commands:
+<tt>ncks -O -v lat -d lat,20.,20.001 ~/nco/data/in.nc ~/foo.nc;ncks -H ~/foo.nc</tt>
+If the returned hyperslab contains any data, then your NCO is buggy
+(because that hyperslab should be empty).
+This can lead to incorrect answers for hyperslabs that should be empty.
+Analogous problems would occur with empty auxiliary coordinate bounding boxes.
+Although most users do not specify empty hyperslabs, we urge all users
+to upgrade to NCO 4.0.7+ just to be safe.
+</li>
+
+<!-- http://nco.sf.net#bug_thr_msa -->
+<a name="bug_thr_msa"></a>
+<li><i>Threading problems with MSA:</i>
+NCO version 3.9.5 has a nasty bug that causes threaded arithmetic
+operators, e.g., <tt>nces</tt> to produce incorrect results under some
+conditions.
+The problem may occur whenever OpenMP is enabled and the operators
+run on a multi-core CPU with more than one thread.
+These incorrect answers, if generated, are relatively easy to notice.
+The number of threads used to generate a file is, by default, recorded
+in the global attribute <tt>nco_openmp_thread_number</tt> which may
+be examined with <tt>ncks -M foo.nc | grep nco_openmp_thread_number</tt>.
+The only action that will correct a file that you think (or know)
+contains corrupted data because of this NCO bug is to re-process the
+file with a non-buggy NCO version.
+<i>Version 3.9.5 is buggy and should be upgraded ASAP</i>.
+Be careful with data processed using this NCO version on multi-core CPUs.
+The (one-line!) patch to fix this bug in 3.9.5 is
+<a href="http://sf.net/forum/message.php?msg_id=6217274">here</a>.
+</li>
+
+<!-- http://nco.sf.net#bug_idx_hyp -->
+<a name="bug_idx_hyp"></a>
+<li><i>Index-based hyperslab problems:</i>
+NCO versions 2.7.3—2.8.3 have a nasty bug that causes
+index-based hyperslabs, e.g., <tt>-d lat,1,</tt> to
+behave like value-based hyperslabs, e.g., <tt>-d lat,1.0</tt> under
+some conditions.
+Unfortunately, the incorrect answers generated may be hard to notice!
+This problem was most often enountered by users trying to assemble
+monthly averages using the stride feature of <tt>ncrcat</tt>.
+One common symptom is that the time-offset of the output file is
+incorrect.
+<i>Versions 2.7.3—2.8.3 are buggy and should be upgraded ASAP</i>.
+Re-do any data-processing that used index-based hyperslabbing with
+these versions of NCO.
+</li>
+</ul>
+
+<ul><b>Older Operator-specific Run-time Problems:</b>
+
+<!-- http://nco.sf.net#bug_ncks_aux -->
+<a name="bug_ncks_aux"></a>
+<li><i><tt>ncks</tt> bug with auxiliary coordinates:</i>
+Versions 4.2.x–4.3.1 of <tt>ncks</tt> did not correctly
+support auxiliary coordinates (specified with <tt>-X</tt>).
+Auxiliary coordinates continued to work with the other hyperslabbing
+NCO operators. Auxiliary coordinates once again work in all
+hyperslabbing operators, including on netCDF4 group files in operators
+that support them.
+Fixed in version 4.3.2.
+</li>
+
+<!-- http://nco.sf.net#bug_ncatted_strcmp -->
+<a name="bug_ncatted_strcmp"></a>
+<li><i><tt>ncatted</tt> bug on implicit attribute names:</i>
+Versions 4.2.x–4.3.0 of <tt>ncatted</tt> could segfault when
+processing attributes specified implicitly (i.e., by leaving the
+attribute field blank in the <tt>-a</tt> specification.
+Fixed in version 4.3.1.
+</li>
+
+<!-- http://nco.sf.net#bug_ncbo_ccm_ccsm_cf -->
+<a name="bug_ncbo_ccm_ccsm_cf"></a>
+<li><i><tt>ncbo</tt> bug handling certain special variables:</i>
+Version 4.3.0 of <tt>ncbo</tt> inadvertently always turns off
+certain <a href="http://nco.sf.net/nco.html#prc_xcp">exceptions</a>
+to variable list processing.
+This may cause some grid-related variables (e.g., <tt>ntrm</tt> and <tt>nbdate</tt>)
+and some non-grid variables (e.g., <tt>ORO</tt> and <tt>gw</tt>) to be
+arithmetically processed (e.g., subtracted) even when that makes no
+sense in most climate model datasets.
+Fixed in version 4.3.1.
+</li>
+
+<!-- http://nco.sf.net#bug_ncks_mtd -->
+<a name="bug_ncks_mtd"></a>
+<li><i><tt>ncks</tt> bug copying metadata:</i>
+Version 4.2.6 of <tt>ncks</tt> does not copy variable metadata by default.
+Thus output files appear stripped of metadata.
+One can work around this problem in 4.2.6 by specifying the <tt>-m</tt> option.
+Otherwise an upgrade is recommended.
+Fixed in version 4.3.0.
+</li>
+
+<!-- http://nco.sf.net#bug_ncks_sbs -->
+<a name="bug_ncks_sbs"></a>
+<li><i><tt>ncks</tt> bug subsetting variables:</i>
+Version 4.2.4 of <tt>ncks</tt> sometimes dumps core
+when subsetting variables with <tt>-v var</tt>.
+Fixed in version 4.2.5.
+</li>
+
+<!-- http://nco.sf.net#bug_ncks_mk_rec_dmn -->
+<a name="bug_ncks_mk_rec_dmn"></a>
+<li><i><tt>ncks</tt> bug with altering record dimensions:</i>
+Version 4.2.4 of <tt>ncks</tt> ignored both the
+<tt>--mk_rec_dmn</tt> and the <tt>--fix_rec_dmn</tt> switches.
+It exited successfully without altering the record variable.
+Fixed in version 4.2.5.
+</li>
+
+<!-- http://nco.sf.net#bug_nces_rec_var -->
+<a name="bug_nces_rec_var"></a>
+<li><i><tt>nces</tt> bug with non-record files:</i>
+Versions 4.2.1—4.2.3 of <tt>nces</tt> incorrectly referenced
+the record variable on files which do not contain it.
+This caused a segmentation violation and core dump.
+</li>
+
+<!-- http://nco.sf.net#bug_ncra_flg_bfr_nrm -->
+<a name="bug_ncra_flg_bfr_nrm"></a>
+<li><i><tt>ncra</tt> bug when last file(s) is/are superfluous:</i>
+Versions 4.2.1—4.2.3 of <tt>ncra</tt> incorrectly skipped
+writing the results of the final normalization when trailing files
+were superfluous (not used).
+In the most common case, all values are zeros in the output file.
+Upgrade if you call <tt>ncra</tt> with trailing superfluous files.
+</li>
+
+<!-- http://nco.sf.net#bug_ncecat_nintap -->
+<a name="bug_ncecat_nintap"></a>
+<li><i><tt>ncecat</tt> bug when files generated with <tt>-n</tt>:</i>
+Version 4.2.2 of <tt>ncecat</tt> could incorrectly skip the first
+input file in the default mode (RECORD_AGGREGATE) when
+the <tt>-n NINTAP</tt> switch is used to automate filename generation.
+Upgrade if you use <tt>ncecat -n</tt>.
+</li>
+
+<!-- http://nco.sf.net#bug_ncra_cf_crd_rec_crd -->
+<a name="bug_ncra_cf_crd_rec_crd"></a>
+<li><i><tt>ncra</tt> bug handling CF <tt>coordinates</tt> attributes
+that contain the name of the record coordinate:</i>
+Versions 4.0.3—4.0.4 of <tt>ncra</tt> incorrectly treat the
+record variable (usually <tt>time</tt>) as a fixed variable if it
+is specified in the <tt>coordinates</tt> attribute of any variable in
+a file processed with CCM/CCSM/CF metadata conventions.
+This bug caused core dumps, and even weirder behavior like
+creating imaginary time slices in the ouput.
+Upgrade recommended if you work with NCAR CCSM/CESM model output.
+
+One workaround that does not require NCO upgrades is to remove the
+record coordinate name (usually <tt>time</tt>) from
+the <tt>coordinates</tt> attribute of all variables in CF-compliant
+files before processing the file with <tt>ncra</tt>.
+</li>
+
+<!-- http://nco.sf.net#bug_ncra_cf_YYYYMMDD_date -->
+<a name="bug_ncra_cf_YYYYMMDD_date"></a>
+<li><i><tt>ncra</tt> bug averaging YYYYMMDD-format <tt>date</tt>
+variables in CCSM/CF-compliant files:</i>
+Versions ???—4.0.5 of <tt>ncra</tt> contain a bug which
+produces an incorrect average (usually zero) of the <tt>date</tt>
+variable which many CCSM/CF-compliant files use to track model dates
+in the human-readable YYYYMMDD-format.
+Averaging YYYYMMDD-format integers is intrinsically difficult, since
+such dates have calendar assumptions built-in.
+NCO attempts this in CCSM/CF-compliant files by using the
+<tt>nbdate</tt> (beginning date) and <tt>time</tt> (days
+since <tt>nbdate</tt>) variables to find the average date,
+converting that to YYYYMMDD, and writing that as the average value
+of <tt>date</tt>.
+</li>
+
+<!-- http://nco.sf.net#bug_ncks_nc4_nc4_hyp_fix -->
+<a name="bug_ncks_nc4_nc4_hyp_fix"></a>
+<li><i><tt>ncks</tt> bug hyperslabbinging fixed netCDF4 dimensions:</i>
+Versions 4.0.3—4.0.4 of <tt>ncks</tt> contain a bug which
+triggers a core-dump when hyperslabbing (along a non-record
+dimension) a netCDF4-format input file into a netCDF4-format output
+file, e.g., <tt>ncks -d 0,1,lat in4.nc out4.nc</tt>.
+Three workarounds that do not require NCO upgrades (or downgrades) are
+to explicitly specify chunking with, e.g.,
+<tt>ncks --cnk_plc=all -d 0,1,lat in4.nc out4.nc</tt>, or, to use
+<tt>nces</tt> instead of <tt>ncks</tt> for hyperslabbing, e.g.,
+<tt>nces -d 0,1,lat in4.nc out4.nc</tt> (<tt>nces</tt> does a no-op
+when there is only one input file), or to write to a netCDF3 file,
+<tt>ncks -3 -d 0,1,lat in4.nc out3.nc</tt>.
+</li>
+
+<!-- http://nco.sf.net#bug_ncks_m -->
+<a name="bug_ncks_m"></a>
+<li><i>Core dump with <tt>ncks</tt>:</i>
+Printing variables to screen with <tt>ncks</tt> can trigger a segfault
+in NCO 3.9.9—4.0.3.
+Users may upgrade, downgrade, or apply this one-line patch to 3.9.9 sources:
+Remove this line
+“<tt>*cnk_sz=(size_t)NULL;</tt>”
+—near line 751 of <tt>nco/src/nco/nco_netcdf.c</tt>—
+should fix the problem.
+The problem in later NCO versions is due to a different bug and this
+patch will not work.
+</li>
+
+<!-- http://nco.sf.net#bug_ncrename_dot -->
+<a name="bug_ncrename_dot"></a>
+<li><i><tt>ncrename</tt> erroneous error exit:</i>
+Versions 4.0.1—4.0.3 of <tt>ncrename</tt> contain a bug where
+commands like <tt>ncrename -a .old_nm,new_nm in.nc out.nc</tt>
+would, if <tt>old_nm</tt> did not exist, write the correct file and
+then exit with an error message although no error had occurred.
+The files written were fine, and the error message can be safely
+ignored. This was due to not clearing an extraneous return code.
+
+<!-- http://nco.sf.net#bug_ncbo_rfr -->
+<a name="bug_ncbo_rfr"></a>
+<li><i><tt>ncbo</tt> segmentation fault:</i>
+<tt>ncbo</tt> versions 4.0.0—4.0.2 incorrectly refreshed
+internal metadata, leading to segmentation faults and core dumps with
+some exacting compilers, notably xlC on AIX.
+
+<!-- http://nco.sf.net#bug_ncra_date -->
+<a name="bug_ncra_date"></a>
+<li><i><tt>ncra</tt> segmentation fault:</i>
+<tt>ncra</tt> versions 4.0.0—4.0.1 mishandled some CF-compliant
+dates, leading to segmentation faults and core dumps.
+
+<!-- http://nco.sf.net#bug_ncap_cmt -->
+<a name="bug_ncap_cmt"></a>
+<li><i>Arithmetic problems with <tt>ncap</tt> division, modulo, and exponentiation:</i>
+<tt>ncap</tt> versions < 3.0.1 incorrectly exponentiate
+variables to variable powers (<tt>V^V</tt>).
+We recommend that all <tt>ncap</tt> users upgrade.<br>
+
+<tt>ncap</tt> versions up to 2.9.1 incorrectly handle division,
+modulo, and exponentiation operations of the form <tt>S/V</tt>,
+<tt>S%V</tt>, and <tt>S^V</tt> where first operand (<tt>S</tt>) is
+scalar (i.e., either typed directly in the <tt>ncap</tt> script or
+converted from an attribute) and the second operand (<tt>V</tt>) is
+a full variable (i.e., stored in a file or computed by <tt>ncap</tt>).
+Instead of the requested quantity, <tt>ncap</tt> returned
+<tt>V/S</tt>, <tt>V%S</tt>, and <tt>V^S</tt>.
+In other words <tt>ncap</tt> treated some non-commutative operations
+as commutative. This is now fixed.
+The
+<tt>V/V</tt>, <tt>V%V</tt>, <tt>V^V</tt>,
+<tt>V/S</tt>, <tt>V%S</tt>, <tt>V^S</tt>,
+<tt>S/S</tt>, <tt>S%S</tt>, and <tt>S^S</tt> operations were never
+affected.
+We recommend that all <tt>ncap</tt> users upgrade.
+</li>
+
+<!-- http://nco.sf.net#bug_ncbo_pck -->
+<a name="bug_ncbo_pck"></a>
+<li><i>Incorrect <tt>ncbo</tt> output for packed input:</i>
+<tt>ncbo</tt> versions ???—3.2.0 incorrectly write differences
+of packed input. This only affects packed variables.
+
+<!-- http://nco.sf.net#bug_ncflint_mss_val -->
+<a name="bug_ncflint_mss_val"></a>
+<li><i>Problems with <tt>ncflint</tt> and <tt>missing_value</tt>s:</i>
+The algorithm <tt>ncflint</tt> used to perform interpolation in
+versions up to 2.9.4 was not commutative.
+It returned the weighted valid datum when the other datum was
+<tt>missing_value</tt>, or it returned <tt>missing_value</tt>,
+depending on the order the input files were specified.
+As of version 2.9.5, <tt>ncflint</tt> always returns
+<tt>missing_value</tt> when either input datum is
+<tt>missing_value</tt>.
+Possible future implementations are discussed
+<a href="http://nco.sf.net/nco.html#ncflint">here</a>.
+
+<!-- http://nco.sf.net#bug_mss_val_zro_ncra -->
+<a name="bug_mss_val_zro_ncra"></a>
+<li><i>Problems with <tt>ncra</tt> and <tt>nces</tt> when <tt>missing_value</tt> = 0.0:</i>
+The algorithm <tt>ncra</tt> and <tt>nces</tt> used to perform
+arithmetic in versions up to 2.9.2 breaks if <tt>missing_value</tt>
+is 0.0.
+Why, you ask?
+Running average (or total, etc.) algorithms must initialize the answer
+to 0.0.
+This is done since the sum accumulates in place as <tt>ncra</tt> and
+<tt>nces</tt> proceeds across records and files.
+(Normalizing this accumulation by the total number of records is the
+last step).
+The old algorithm compared both the current running average and the
+new record to the <tt>missing_value</tt>.
+If either comparison matched, then nothing accumulated for that
+record.
+This zero-initialization led to a state where it was impossible
+to ever recognize valid data.
+As a result nothing accumulated and the answer was always zero.
+The record and ensemble averages would also fail (in a non-obvious)
+way whenever an intermediate sum equalled <tt>missing_value</tt>.
+The chances of the latter event ever happening are exceedingly
+remote.
+The new algorithm compares only the new record to the
+<tt>missing_value</tt>.
+This fixes both problems and is faster, too.
+
+<!-- http://nco.sf.net#bug_pck_ncwa -->
+<a name="bug_pck_ncwa"></a>
+<li><i>Packing problems with <tt>ncwa</tt>:</i>
+NCO versions ???—2.9.0 have a bug that causes <tt>ncwa</tt>
+to fail (produce garbage answers) when processing packed
+<tt>NC_FLOAT</tt> data. Version 2.9.1 fixes this problem.
+This problem may have been noticed most by
+<a href="http://opendap.org">OPeNDAP</a> users since many
+netCDF climate datasets served by
+<a href="http://opendap.org">OPeNDAP</a> are packed
+<tt>NC_FLOAT</tt>s.
+Upgrade to 2.9.1 if you use <tt>ncwa</tt> on packed data.
+</li>
+
+<!-- http://nco.sf.net#bug_pck -->
+<a name="bug_pck"></a>
+<li><i>Packing problems with <tt>ncap</tt>:</i>
+NCO versions 2.8.4—2.8.6 have a bug that causes the <tt>ncap</tt>
+intrinsic packing function <tt>pack()</tt> to fail.
+Version 2.8.7 fixes this problem.
+</li>
+</ul>
+
+<ul><b>Older Platform-specific Run-time Problems:</b>
+<a name="bug_ncap_flt_fnc_aix"></a>
+<li><i>Float-valued intrinsic arithmetic functions in <tt>ncap</tt> on AIX:</i>
+<tt>ncap</tt> versions through 4.0.4 have a bug that causes all float-valued
+intrinsic math functions to fail under AIX.
+Float-valued math functions are the ISO C99 functions, e.g.,
+<tt>cosf()</tt>, <tt>fabsf()</tt>, <tt>logf()</tt>.
+The user does not invoke these functions directly—
+the user always specifies the <i>generic function name</i>, e.g.,
+<tt>cos()</tt>, <tt>abs()</tt>, <tt>log()</tt>.
+NCO automatically calls the native single precision (i.e.,
+float-valued) math functions when the generic function argument
+is a native float (e.g., naked constants like <tt>1.0f</tt> or
+variables stored as <tt>NC_FLOAT</tt>).
+Double precision arguments cause NCO to invoke the standard
+(double-valued) form of the generic function, e.g., <tt>cos()</tt>,
+<tt>fabs()</tt>, <tt>log()</tt>.
+<!-- Whevnever this bug is fixed, here is some text
+Version info:
+<tt>ncap</tt> float functions work in AIX (<a href="#bug_ncap_flt_fnc_aix">long-time bug</a>, upgrade will be required for AIX ncap users)
+ANNOUNCE info:
+First, AIX NCO installations should upgrade to this version to get the
+AIX-specific ncap bug-fix.
+Bug-fixes:
+1. fxm: AIX uses NCO-supplied float-valued functions (e.g., cosf())
+-->
+</li>
+</ul>
+<hr></p>
+
+</body>
+</html>
diff --git a/doc/surfit_2014.txt b/doc/surfit_2014.txt
index e160fd3..7af37f6 100644
--- a/doc/surfit_2014.txt
+++ b/doc/surfit_2014.txt
@@ -2,6 +2,7 @@
# (Summer Undergraduate Research Fellowships in Information Technologies)
# 20140416: Submitted to Brittany Gray <grayb at uci.edu>
+cat > ${HOME}/sdn_ugr_03_adv.txt << 'EOF'
Optimized Storage Shapes for Multi-dimensional Gridded Datasets
PI: Prof. Charlie Zender
@@ -28,11 +29,15 @@ Recommended Web sites and publications:
4. netCDF Operators http://nco.sf.net
5. Zender, C. S., and H. J. Mangalam (2007), Scaling Properties of Common Statistical Operators for Gridded Datasets, Int. J. High Perform. Comput. Appl., 21(4), 485-498, doi:10.1177/1094342007083802.
6. Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10), 1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+EOF
+scp ${HOME}/sdn_ugr_03_adv.txt dust.ess.uci.edu:/var/www/html/hire
+URL: http://dust.ess.uci.edu/hire/sdn_ugr_03_adv.txt
************************************************************************
NB: Following project not "researchy" enough, maybe next year
************************************************************************
+cat > ${HOME}/sdn_ugr_02_adv.txt << 'EOF'
Next Generation Parser for Structured Data Analysis
PI: Prof. Charlie Zender
@@ -61,4 +66,7 @@ Recommended Web sites and publications:
2. netCDF Operators http://nco.sf.net
3. Zender, C. S., and H. J. Mangalam (2007), Scaling Properties of Common Statistical Operators for Gridded Datasets, Int. J. High Perform. Comput. Appl., 21(4), 485-498, doi:10.1177/1094342007083802.
4. Zender, C. S. (2008), Analysis of Self-describing Gridded Geoscience Data with netCDF Operators (NCO), Environ. Modell. Softw., 23(10), 1338-1342, doi:10.1016/j.envsoft.2008.03.004.
+EOF
+scp ${HOME}/sdn_ugr_02_adv.txt dust.ess.uci.edu:/var/www/html/hire
+URL: http://dust.ess.uci.edu/hire/sdn_ugr_02_adv.txt
diff --git a/doc/xmp/cmb_fl_grp.sh b/doc/xmp/cmb_fl_grp.sh
index e5603d9..6a1a13d 100644
--- a/doc/xmp/cmb_fl_grp.sh
+++ b/doc/xmp/cmb_fl_grp.sh
@@ -5,7 +5,7 @@
#
# Method:
# - Create files with groups by ncecat --gag
-# - Append groups level by level using ncks
+# - Append groups level by level using ncks
#
# Input files like:
# snc_LImon_CCSM4_historical_r1i1p1_199001-200512.nc
@@ -25,7 +25,7 @@ drc_out='../data/grp/'
# Constants
rlm='LImon' # Realm: LandIce; Time frequency: monthly
-tms='200001-200512' # Timeseris
+tms='200001-200512' # Timeseries
flt='nc' # File Type
# Geographical weights
diff --git a/man/ncks.1 b/man/ncks.1
index 233c036..dbdfdcb 100644
--- a/man/ncks.1
+++ b/man/ncks.1
@@ -1,4 +1,4 @@
-.\" $Header: /cvsroot/nco/nco/man/ncks.1,v 1.46 2014/05/29 18:00:26 zender Exp $ -*-nroff-*-
+.\" $Header: /cvsroot/nco/nco/man/ncks.1,v 1.47 2014/06/11 17:28:22 zender Exp $ -*-nroff-*-
.\" Purpose: ROFF man page for ncks
.\" Usage:
.\" nroff -man ~/nco/man/ncks.1 | less
@@ -32,6 +32,7 @@ dbg_lvl]
.IR gpe_dsc ]
[\-g
.IR grp [,...]]
+[\-\-grp_xtr_var_xcl]
[\-H] [\-h] [\-\-hdn]
[\-\-hdr_pad
.IR sz ]
@@ -590,7 +591,7 @@ ncks \-d lon,260.,45. in.nc out.nc
.RE
.\" NB: Append man_end.txt here
-.\" $Header: /cvsroot/nco/nco/man/ncks.1,v 1.46 2014/05/29 18:00:26 zender Exp $ -*-nroff-*-
+.\" $Header: /cvsroot/nco/nco/man/ncks.1,v 1.47 2014/06/11 17:28:22 zender Exp $ -*-nroff-*-
.\" Purpose: Trailer file for common ending to NCO man pages
.\" Usage:
.\" Append this file to end of NCO man pages immediately after marker
diff --git a/man/ncrcat.1 b/man/ncrcat.1
index 1995404..3c64ed1 100644
--- a/man/ncrcat.1
+++ b/man/ncrcat.1
@@ -1,4 +1,4 @@
-.\" $Header: /cvsroot/nco/nco/man/ncrcat.1,v 1.31 2014/05/29 18:00:26 zender Exp $ -*-nroff-*-
+.\" $Header: /cvsroot/nco/nco/man/ncrcat.1,v 1.32 2014/07/15 18:48:54 zender Exp $ -*-nroff-*-
.\" Purpose: ROFF man page for ncrcat
.\" Usage:
.\" nroff -man ~/nco/man/ncrcat.1 | less
@@ -136,8 +136,34 @@ concatenates June, 1985--June, 1989:
ncrcat \-d time,6.,54. ??.nc 8506_8906.nc
.RE
+.SH CAVEAT
+
+.B ncrcat
+does not re-scale packed data (i.e., data stored using the
+.B scale_factor
+and
+.B add_offset
+attributes recommended by the Unidat and CF conventions.
+.B ncrcat
+just copies the data directly from the input files.
+It copies the relevant metadata (i.e.,
+.B scale_factor
+and
+.B add_offset
+attributes) from the first file.
+Concatenating multiple datasets packed with different scales is beyond
+its capabilities (concatenating data packed with the same scales in
+multiple files works fine).
+The workaround for cases where the scales change among files is to
+first unpack the data in all the file using
+.B ncpdq,
+then to concatenate the unpacked data using
+.B ncrcat,
+and finally to repack the result using
+.B ncpdq.
+
.\" NB: Append man_end.txt here
-.\" $Header: /cvsroot/nco/nco/man/ncrcat.1,v 1.31 2014/05/29 18:00:26 zender Exp $ -*-nroff-*-
+.\" $Header: /cvsroot/nco/nco/man/ncrcat.1,v 1.32 2014/07/15 18:48:54 zender Exp $ -*-nroff-*-
.\" Purpose: Trailer file for common ending to NCO man pages
.\" Usage:
.\" Append this file to end of NCO man pages immediately after marker
diff --git a/po/es/nco.po b/po/es/nco.po
new file mode 100644
index 0000000..581a3a6
--- /dev/null
+++ b/po/es/nco.po
@@ -0,0 +1,42 @@
+# Portable Object Spanish translations for NCO, the netCDF Operators
+# Copyright (C) 1995-2014 Charlie Zender
+# This file is distributed under the same license as the NCO package
+
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: NCO 4.4.5\n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2014-06-17 13:16-0700\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: Charlie Zender <surname at uci.edu>\n"
+"Language-Team: Spanish <LL at li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=iso-8859-1\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../src/nco/ncra.c:539
+#, c-format
+msgid "%s: ERROR Incorrect abbreviation for file list\n"
+msgstr "%s: ERREUR Abreviatura incorrecta para lista de archivos\n"
+
+#: ../src/nco/ncra.c:616
+#, c-format
+msgid "%s: I18N Current charset = %s\n"
+msgstr "%s: I18N Corriente charset = %s\n"
+
+#: ../src/nco/ncra.c:796
+#, c-format
+msgid "%s: INFO Input file %d is %s"
+msgstr "%s: INFO archivo de entrada %d es %s"
+
+#: ../src/nco/ncra.c:799
+#, c-format
+msgid ", local file is %s"
+msgstr ", archivo local es %s"
+
+#: ../src/nco/ncks.c:717
+#, c-format
+msgid "%s: I18N This text may appear in a foreign language\n"
+msgstr "%s: I18N Este texto puede aparecer en un idioma extranjero\n"
diff --git a/po/fr/nco.po b/po/fr/nco.po
new file mode 100644
index 0000000..7577405
--- /dev/null
+++ b/po/fr/nco.po
@@ -0,0 +1,42 @@
+# Portable Object French translations for NCO, the netCDF Operators
+# Copyright (C) 1995-2014 Charlie Zender
+# This file is distributed under the same license as the NCO package
+
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: NCO 4.4.5\n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2014-06-17 13:16-0700\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: Charlie Zender <surname at uci.edu>\n"
+"Language-Team: French <LL at li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=iso-8859-1\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../src/nco/ncra.c:539
+#, c-format
+msgid "%s: ERROR Incorrect abbreviation for file list\n"
+msgstr "%s: ERREUR abr�viation incorrecte pour la liste de fichiers\n"
+
+#: ../src/nco/ncra.c:616
+#, c-format
+msgid "%s: I18N Current charset = %s\n"
+msgstr "%s: I18N Courant charset = %s\n"
+
+#: ../src/nco/ncra.c:796
+#, c-format
+msgid "%s: INFO Input file %d is %s"
+msgstr "%s: INFO Fichier d'entr�e %d est %s"
+
+#: ../src/nco/ncra.c:799
+#, c-format
+msgid ", local file is %s"
+msgstr ", fichier local est %s"
+
+#: ../src/nco/ncks.c:717
+#, c-format
+msgid "%s: I18N This text may appear in a foreign language\n"
+msgstr "%s: I18N Ce texte peut appara�tre dans une langue �trang�re\n"
diff --git a/po/nco.pot b/po/nco.pot
new file mode 100644
index 0000000..334f96c
--- /dev/null
+++ b/po/nco.pot
@@ -0,0 +1,37 @@
+# Portable Object Template file for NCO, the netCDF Operators
+# Copyright (C) 1995-2014 Charlie Zender
+# This file is distributed under the same license as the NCO package
+
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: NCO 4.4.5\n"
+"Report-Msgid-Bugs-To: \n"
+"POT-Creation-Date: 2014-06-17 13:16-0700\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: Charlie Zender <surname at uci.edu>\n"
+"Language-Team: LANGUAGE <LL at li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#: ../src/nco/ncra.c:539
+#, c-format
+msgid "%s: ERROR Incorrect abbreviation for file list\n"
+msgstr ""
+
+#: ../src/nco/ncra.c:616
+#, c-format
+msgid "%s: I18N Current charset = %s\n"
+msgstr ""
+
+#: ../src/nco/ncra.c:796
+#, c-format
+msgid "%s: INFO Input file %d is %s"
+msgstr ""
+
+#: ../src/nco/ncra.c:799
+#, c-format
+msgid ", local file is %s"
+msgstr ""
diff --git a/src/nco++/Makefile.am b/src/nco++/Makefile.am
index 3df55f7..94ea6c6 100644
--- a/src/nco++/Makefile.am
+++ b/src/nco++/Makefile.am
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/src/nco++/Makefile.am,v 1.27 2013/07/25 04:51:36 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/src/nco++/Makefile.am,v 1.28 2014/07/30 22:47:02 zender Exp $ -*-makefile-*-
# Purpose: Template builds for nco++ directory
# Process this file with automake to produce Makefile.in
@@ -37,6 +37,10 @@ ncap2_LDADD = -lnco -lantlr
# fxm: 20080515 Takeshi Enomoto reports that MACOSX needs
# ncap2_LDADD = ../nco/.libs/libnco.dylib -lantlr
+# fxm: 20140730 Ed Anderson reports that PGI- and GCC-compiled ncap2 need
+# -Xcompiler -shared added to ncap2_LINK which, apparently, would be done with
+# ncap2_LDFLAGS = -Xcompiler -shared
+
if ENABLE_GSL
GSL_LIB_ARG = $(shell gsl-config --libs)
GSL_INC_ARG = $(shell gsl-config --cflags)
diff --git a/src/nco++/Makefile.in b/src/nco++/Makefile.in
index 2d35c92..0084728 100644
--- a/src/nco++/Makefile.in
+++ b/src/nco++/Makefile.in
@@ -14,7 +14,7 @@
@SET_MAKE@
-# $Header: /cvsroot/nco/nco/src/nco++/Makefile.in,v 1.98 2014/04/02 05:40:24 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/src/nco++/Makefile.in,v 1.99 2014/08/03 23:49:17 zender Exp $ -*-makefile-*-
# Purpose: Template builds for nco++ directory
# Process this file with automake to produce Makefile.in
@@ -370,6 +370,10 @@ nco_gsl.c
ncap2_LDADD = -lnco -lantlr
# fxm: 20080515 Takeshi Enomoto reports that MACOSX needs
# ncap2_LDADD = ../nco/.libs/libnco.dylib -lantlr
+
+# fxm: 20140730 Ed Anderson reports that PGI- and GCC-compiled ncap2 need
+# -Xcompiler -shared added to ncap2_LINK which, apparently, would be done with
+# ncap2_LDFLAGS = -Xcompiler -shared
@ENABLE_GSL_TRUE at GSL_LIB_ARG = $(shell gsl-config --libs)
@ENABLE_GSL_TRUE at GSL_INC_ARG = $(shell gsl-config --cflags)
@ENABLE_GSL_FALSE at ncap2_LDFLAGS = -L../nco
diff --git a/src/nco++/Makefile.old b/src/nco++/Makefile.old
index 05aa267..9f5f0c5 100644
--- a/src/nco++/Makefile.old
+++ b/src/nco++/Makefile.old
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/src/nco++/Makefile.old,v 1.125 2014/05/04 05:39:01 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/src/nco++/Makefile.old,v 1.132 2014/07/07 06:04:23 zender Exp $ -*-makefile-*-
# Purpose: Makefile for NCO C++ directory nco++
# Requires GNU Make---AT&T Make chokes on GNU syntax
@@ -15,25 +15,25 @@
# Usage:
# cd ~/nco/src/nco++;make -f Makefile.old dpn_cln cln all
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D UDUNITS2=Y all # givre, neige
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D UDUNITS2=Y lib_cln cln ncap2 # givre, neige
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS2=Y all # virga
-# cd ~/nco/src/nco++;SZ_LIB=/sopt/lib make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D SZ=Y UDUNITS2=N all # greenplanet intel
-# cd ~/nco/src/nco++;ANTLR_ROOT=/sopt/gfortran_g++ NETCDF_ROOT=/sopt/gfortran_g++ SZ_LIB=/sopt/lib make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D SZ=Y UDUNITS2=N all # greenplanet gcc
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=N OPTS=D UDUNITS2=Y all # ashes, elnino
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS2=N all # esmf
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS2=N all # silt
-# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=N OPTS=D UDUNITS2=N all # sand, clay, tephra
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D UDUNITS=Y all # givre, neige
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D UDUNITS=Y lib_cln cln ncap2 # givre, neige
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS=Y all # virga
+# cd ~/nco/src/nco++;SZ_LIB=/sopt/lib make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D SZ=Y UDUNITS=N all # greenplanet intel
+# cd ~/nco/src/nco++;ANTLR_ROOT=/sopt/gfortran_g++ NETCDF_ROOT=/sopt/gfortran_g++ SZ_LIB=/sopt/lib make -f Makefile.old NETCDF4=Y OMP=Y OPTS=D SZ=Y UDUNITS=N all # greenplanet gcc
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=Y OMP=N OPTS=D UDUNITS=Y all # ashes, elnino
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS=N all # esmf
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=Y OPTS=D UDUNITS=N all # silt
+# cd ~/nco/src/nco++;make -f Makefile.old NETCDF4=N OMP=N OPTS=D UDUNITS=N all # sand, clay, tephra
# 64-bit ABI on UCI MPC systems:
# cd ${HOME}/nco/src/nco++;env ANTLR='/software/antlr/bin/antlr' ANTLR_ROOT='/software/antlr' UDUNITS_INC='/software/udunits/include' UDUNITS_LIB='/software/udunits/lib' make -f Makefile.old --jobs=1 ABI=64 all;cd -
# cd ${HOME}/nco/src/nco++;env ANTLR='/usr/local/pgi/bin/antlr' ANTLR_ROOT='/usr/local/pgi' make -f Makefile.old --jobs=1 ABI=64 all;cd -
# 64-bit ABI netCDF3 on NCAR AIX systems (bluefire):
-# cd ${HOME}/nco/src/nco++;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' NETCDF_LIB='/usr/local/lib64/r4i4' UDUNITS_INC='/contrib/udunits-1.12.9/include' UDUNITS_LIB='/contrib/udunits-1.12.9/lib' make -f Makefile.old --jobs=1 ABI=64 OPTS=D NETCDF4=N UDUNITS2=N all;cd -
+# cd ${HOME}/nco/src/nco++;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' NETCDF_LIB='/usr/local/lib64/r4i4' UDUNITS_INC='/contrib/udunits-1.12.9/include' UDUNITS_LIB='/contrib/udunits-1.12.9/lib' make -f Makefile.old --jobs=1 ABI=64 OPTS=D NETCDF4=N UDUNITS=N all;cd -
# 64-bit ABI netCDF4 on NCAR AIX systems (bluefire):
# cd ${HOME}/nco/src/nco++;ANTLR='/contrib/antlr-2.7.7/bin/antlr' ANTLR_ROOT='/contrib/antlr-2.7.7' CURL_LIB='/contrib/curl/7.21.2/lib' GSL_INC='/contrib/gsl-1.12/include' GSL_LIB='/contrib/gsl-1.12/lib' GSL_MINOR_VERSION='12' HDF5_ROOT='/contrib/hdf5-1.8.7_seq' LDFLAGS='-lnetcdf -lhdf5_hl -lhdf5 -lz' NETCDF_ROOT='/contrib/netcdf/4.1.3_seq' SZ_LIB='/contrib/szip/lib' UDUNITS_LIB='/contrib/zlib/lib' make -f Makefile.old --jobs=1 ABI=64 OPTS=D SZ=Y all;cd -
#
# Cygwin on Windows Vista systems:
-# cd ~/nco/src/nco++;ANTLR='antlr' make -f Makefile.old GSL=Y OPTS=D NETCDF4=Y UDUNITS2=Y all;cd -
+# cd ~/nco/src/nco++;ANTLR='antlr' make -f Makefile.old GSL=Y OPTS=D NETCDF4=Y UDUNITS=Y all;cd -
# NB: ncap2 requires ANTLR headers and library
# http://www.antlr.org
@@ -105,11 +105,17 @@ endif # endif ANTLR
ifndef ANTLR_ROOT
ANTLR_ROOT := /usr/local
endif
-ifndef ANTLR_INC
- ANTLR_INC := ${ANTLR_ROOT}/include # Directory containing AST.hpp
+ifdef ANTLR_INC
+# Directory containing AST.hpp
+ ANTLR_INC := -I${ANTLR_INC}
+else
+ ANTLR_INC := -I${ANTLR_ROOT}/include
endif
-ifndef ANTLR_LIB
- ANTLR_LIB := ${ANTLR_ROOT}/lib # Directory containing libantlr.a
+ifdef ANTLR_LIB
+# Directory containing libantlr.a
+ ANTLR_LIB := -L${ANTLR_LIB} -lantlr
+else
+ ANTLR_LIB := -L${ANTLR_ROOT}/lib -lantlr
endif
ifndef ${CCACHE}
CCACHE := N
@@ -118,12 +124,9 @@ ifndef CNK
# Use newer netCDF4.1 chunking API
CNK := Y
endif # endif CNK
-ifndef DAP_NETCDF
- DAP_NETCDF := Y
-endif # DAP_NETCDF
-ifndef DAP_OPENDAP
- DAP_OPENDAP := N
-endif # DAP_OPENDAP
+ifndef DAP
+ DAP := Y
+endif # DAP
ifndef ${DBG}
# Debugging token N=No (default) Y=Yes
DBG := N
@@ -195,11 +198,7 @@ ifndef SZ
endif
ifndef UDUNITS
# Use UDUnits functionality
- UDUNITS := N
-endif
-ifndef UDUNITS2
-# Use UDUnits2 functionality
- UDUNITS2 := Y
+ UDUNITS := Y
endif
ifndef UNAMES
UNAMES := $(shell uname -s)
@@ -262,53 +261,12 @@ ifeq (${PRC},D)
else
USR_TKN := -DPRC_FLT ${USR_TKN}
endif # endif PRC
+# Derived-tokens based on primary tokens
+# These tokens should not be altered by hand
# NB: CPP_TKN is recursively expanded variable, define only when components are ready
CPP_TKN = ${USR_TKN} -D${PVM_ARCH} -DNO_NETCDF_2 -DVERSION='${VRS_SNG}' -DHOSTNAME='${HOST}' -DUSER='${USER}' -DNCO_ABORT_ON_ERROR
-# Default NCO build: DAP_NETCDF, DAP_OPENDAP, NETCDF4, PNETCDF, and ZNETCDF clauses may overwrite this
-NC_LDFLAGS := -L${NETCDF_LIB}
-NC_LIBS := -lnetcdf
-
-ifeq (${DAP_NETCDF},Y)
-# Build NCO as DAP-enabled clients with netCDF-provided DAP
-ifndef DAP_NETCDF_ROOT
-# Directory containing libcurl.a
- DAP_NETCDF_ROOT := /usr
-endif # DAP_NETCDF_ROOT
- NC_LDFLAGS := -L${DAP_NETCDF_ROOT}/lib
-# netCDF 4.0.1+:
- NC_LIBS += -lcurl
-endif # end DAP_NETCDF
-
-ifeq (${DAP_OPENDAP},Y)
-# Build NCO as DAP-enabled clients with OPeNDAP
-# fxm: OPeNDAP bloats executables, should automagically enable stripping?
-# http://www.opendap.org/user/guide-html/guide_28.html
-ifndef DAP_OPENDAP_ROOT
-# Directory containing libdap.a, libnc-dap.a
- DAP_OPENDAP_ROOT := /usr/local
-endif # DAP_OPENDAP_ROOT
- NC_LDFLAGS := -L${DAP_OPENDAP_ROOT}/lib
-# NB: nc-dods, dap++ prior to version 3.5.X must be linked twice!
-# Required libraries for
-# DODS 3.3-:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lwww -lz -lrx
-# DODS 3.4.X:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lxml2 -lcurl -lpthread -ldl -lz
-# OPeNDAP 3.5.0-3.5.1:
-# NC_LIBS := -lnc-dap -ldap++ -lxml2 -lcurl
-# OPeNDAP 3.5+:
- NC_LIBS := -lnc-dap -ldap -lxml2 -lcurl
-# In addition, AIX OPeNDAP requires these libraries...
-ifneq (${null},$(findstring AIX,${PVM_ARCH}))
- NC_LIBS += -lcrypto -liconv -lssl -lz
-endif # end AIX
-# Get netCDF from OPeNDAP version
- NETCDF_INC=${DAP_OPENDAP_ROOT}/include/libnc-dap
- NETCDF_LIB=${DAP_OPENDAP_ROOT}/lib
-endif # end DAP_OPENDAP
-
# Internationalize NCO with i18n features
ifeq (${I18N},Y)
MY_SHR_DIR := ${HOME}/share
@@ -316,11 +274,6 @@ ifeq (${I18N},Y)
MY_FR_DIR := ${MY_SHR_DIR}/locale/fr/LC_MESSAGES
endif
-ifeq (${NETCDF4},Y)
- CPPFLAGS += -DENABLE_NETCDF4 -DHAVE_NETCDF4_H
-endif
-# endif NETCDF4
-
# Message Passing Interface (MPI)
ifeq (${MPI_FAKE},Y)
# MPI_FAKE instructs make to compile mpnc*.c operators without defining ENABLE_MPI
@@ -338,122 +291,61 @@ else # !MPI_PRC
MPI_PRC_SNG :=
endif # !MPI_PRC
-ifeq (${NETCDF4},Y)
-# Enable netCDF4 functionality
-ifndef HDF5_ROOT
- HDF5_ROOT := ${NETCDF4_ROOT}
-endif
-ifndef HDF5_INC
- HDF5_INC := ${HDF5_ROOT}/include # Directory containing hdf5.h
-endif
-ifndef HDF5_LIB
- HDF5_LIB := ${HDF5_ROOT}/lib # Directory containing libhdf5.a
-endif
-# fxm: Temporary kludge: Machines with MPI_ROOT set are assumed to have parallel filesystems for NCO builds
-ifdef MPI_ROOT
- HDF5_INC += -I${MPI_ROOT}/include # Directory containing mpi.h
- HDF5_LIB += ${MPI_ROOT}/lib64 # Directory containing libmpi.a
-endif # !MPI_ROOT
- NETCDF_INC := ${NETCDF4_ROOT}/include
- NETCDF_LIB := ${NETCDF4_ROOT}/lib
- NC_LDFLAGS := -L${NETCDF_LIB} $(addprefix -L,${HDF5_LIB})
-# NC_LIBS := -lnetcdf -lhdf5_hl -lhdf5 -lz ${NC_LIBS}
- NC_LIBS := $(shell nc-config --libs) ${NC_LIBS}
-ifdef MPI_ROOT
- NC_LIBS += -lmpi
-endif # !MPI_ROOT
-ifdef CURL_LIB
- NC_LDFLAGS += -L${CURL_LIB}
-endif # end
-ifeq (${SZ},Y)
-ifndef SZ_LIB
- SZ_LIB := /usr/lib # Directory containing libsz.a
-endif
- NC_LDFLAGS += -L${SZ_LIB}
- NC_LIBS += -lsz
-endif # !SZ
-ifneq (${HDF5_INC},${NETCDF_INC})
- NETCDF_INC += -I${HDF5_INC}
-endif # end
-endif # endif NETCDF4
-
-ifeq (${PNETCDF},Y)
-# Enable pnetCDF functionality
- NC_LDFLAGS := -L${NETCDF_LIB}
- NC_LIBS += -lpnetcdf
-endif # endif PNETCDF
-
ifeq (${GSL},Y)
# Build GSL-enabled NCO
-# Place GSL block after DAP block for both to work together
+# Place GSL block after DAP blocks for both to work together
ifdef GSL_INC
GSL_INC := -I${GSL_INC}
else
GSL_INC := $(shell gsl-config --cflags)
endif # endif GSL_INC
ifdef GSL_LIB
- GSL_LIB := -L${GSL_LIB}
+ GSL_LIB := -L${GSL_LIB} -lgsl
else
GSL_LIB := $(shell gsl-config --libs)
endif # endif GSL_LIB
- NETCDF_INC += ${GSL_INC}
- NC_LDFLAGS += ${GSL_LIB}
- NC_LIBS += -lgsl
- # Assumes GSL version in form [1-9].[0-9]+
-ifndef GSL_MINOR_VERSION
- GSL_MINOR_VERSION := $(shell gsl-config --version | sed s/^[1-9]\.// )
- ifeq (${GSL_MINOR_VERSION},${null})
- GSL_MINOR_VERSION := 4
- endif # end if GSL_MINOR_VERSION
-endif # endif GSL_MINOR_VERSION
+ ifndef GSL_MINOR_VERSION
+ GSL_MINOR_VERSION := $(shell gsl-config --version | sed s/^[1-9]\.// )
+ ifeq (${GSL_MINOR_VERSION},${null})
+ GSL_MINOR_VERSION := 4
+ endif # end if GSL_MINOR_VERSION
+ endif # endif GSL_MINOR_VERSION
endif # end if GSL
-ifeq (${UDUNITS2},Y)
- UDUNITS := Y
-endif # end if UDUNITS
ifeq (${UDUNITS},Y)
-# Build UDUnits-enabled NCO
-# Place UDUNITS block after DAP block for both to work together
-ifndef UDUNITS_INC
- UDUNITS_INC := /usr/local/include # Directory containing udunits.h
-endif
-ifndef UDUNITS_LIB
- UDUNITS_LIB := /usr/local/lib # Directory containing libudunits.a
-endif
-ifneq (${UDUNITS_INC},${NETCDF_INC})
- NETCDF_INC += -I${UDUNITS_INC}
-endif # end
-ifneq (${UDUNITS_LIB},${NETCDF_LIB})
- NC_LDFLAGS += -L${UDUNITS_LIB}
-endif # end if
-ifeq (${UDUNITS2},Y)
# 20130607: -lexpat needed on .deb systems, not on RPM systems
-UDUNITS_RPM_DRC := /usr/include/udunits2
-ifneq (${UDUNITS_INC},/usr/local/include)
-# UDUNITS_RPM_TST := $(shell ls ${UDUNITS_RPM_DRC}/udunits2.h)
- UDUNITS_RPM_TST := ${UDUNITS_RPM_DRC}/udunits2.h
+ifdef UDUNITS_INC
+ UDUNITS_INC := -I${UDUNITS_INC}
else
- UDUNITS_RPM_TST := /usr/include/udunits2.h
-endif # end if
-ifeq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NETCDF_INC += -I${UDUNITS_RPM_DRC}
-endif # end if
-ifneq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NC_LIBS += -ludunits2 -lexpat
-else # end if UDUNITS2 Fedora
- NC_LIBS += -ludunits2
-endif # end if UDUNITS2 Fedora
+ UDUNITS_INC := -I/usr/include/udunits2
+endif # endif UDUNITS_INC
+ifdef UDUNITS_LIB
+ UDUNITS_LIB := -L${UDUNITS_LIB} -ludunits2
else
- NC_LIBS += -ludunits
-endif # end if UDUNITS2
+ UDUNITS_LIB := -ludunits2
+endif # end if UDUNITS_LIB
endif # end if UDUNITS
-# TMP_* and NCO_* are required to play nicely with DAP flags
-NCO_LDFLAGS := -L${MY_LIB_DIR}
-# NCO_LIBS := -lnco++ -lnco -lnco_c++
-NCO_LIBS := -lnco++ -lnco
-TMP_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS} -L${ANTLR_LIB}
-TMP_LIBS := ${NCO_LIBS} ${NC_LIBS} -lantlr
+# At this point we change NETCDF_INC from a directory to a flag
+NC_CFLAGS := $(shell nc-config --cflags)
+NC_LDFLAGS := $(shell nc-config --libs)
+NCO_LDFLAGS := -L${MY_LIB_DIR} -lnco -lnco++
+
+ifeq (${PNETCDF},Y)
+# Enable pnetCDF functionality
+ NC_CFLAGS := $(shell /usr/local/parallel/bin/nc-config --cflags)
+ NC_LDFLAGS := $(shell /usr/local/parallel/bin/nc-config --libs)
+ MPI_CFLAGS := -I/usr/include/openmpi-x86_64
+ MPI_LDFLAGS := -L/usr/lib64/openmpi/lib -lmpi
+endif # endif PNETCDF
+
+ifdef LIB_NCAR
+ NC_LDFLAGS := ${LIB_NCAR} ${NC_LDFLAGS}
+endif
+
+OTHER_CFLAGS := ${NC_CFLAGS} ${MPI_CFLAGS} ${GSL_INC} ${UDUNITS_INC} ${ANTLR_INC}
+OTHER_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS} ${MPI_LDFLAGS} ${GSL_LIB} ${UDUNITS_LIB} ${ANTLR_LIB}
+
# sort removes duplicates but unfortunately changes precedence too
# fxm: use uniq instead
#TMP_LDFLAGS := $(sort ${TMP_LDFLAGS})
@@ -605,12 +497,9 @@ endif # AIX
ifeq (${CNK},Y)
CPP_TKN_OS += -DHAVE_NEW_CHUNKING_API
endif # !CNK
-ifeq (${DAP_NETCDF},Y)
- CPP_TKN_OS += -DENABLE_DAP
-endif # !DAP_NETCDF
-ifeq (${DAP_OPENDAP},Y)
+ifeq (${DAP},Y)
CPP_TKN_OS += -DENABLE_DAP
-endif # !DAP_OPENDAP
+endif # !DAP
ifeq (${GSL},Y)
CPP_TKN_OS += -DENABLE_GSL -DHAVE_GSL_H -DNCO_GSL_MINOR_VERSION='${GSL_MINOR_VERSION}'
endif # !GSL
@@ -620,10 +509,7 @@ ifneq (${MPI_FAKE},Y)
endif # MPI_FAKE
endif # !MPI
ifeq (${UDUNITS},Y)
- CPP_TKN_OS += -DENABLE_UDUNITS -DHAVE_UDUNITS_H
-ifeq (${UDUNITS2},Y)
- CPP_TKN_OS += -DHAVE_UDUNITS2_H
-endif # !UDUNITS2
+ CPP_TKN_OS += -DENABLE_UDUNITS -DHAVE_UDUNITS_H -DHAVE_UDUNITS2_H
endif # !UDUNITS
ifeq (${null},$(findstring SGI,${PVM_ARCH}))
CPP_TKN_OS += -DHAVE_CSTDLIB
@@ -643,10 +529,10 @@ ifneq (${null},$(findstring xl,${CC}))
CPP_TKN_OS += -I/usr/vacpp/include
endif # xlC compilers
# Add /usr/local/include for libintl.h explicitly until netCDF is moved there
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC} -I/usr/local/include
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS} -I/usr/local/include
FC := xlf95_r
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -760,13 +646,13 @@ CXX := cxx -std strict_ansi
CC := cc
CFLAGS := ${OMP_FLG}
# OSF1 is for CCM compatibility
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DOSF1 ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DOSF1 ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
FFLAGS := -c ${OMP_FLG} -automatic -fpe3
FIXEDFLAGS := -extend_source
FREEFLAGS := -DHIDE_SHR_MSG -free
LD := ld
-LDFLAGS += ${OMP_FLG} ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OMP_FLG} ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -797,10 +683,10 @@ ifeq (${PVM_ARCH},CRAY)
CXX := g++
CC := cc
CPP := cpp
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
LDFLAGS += -L/lib -lf
LEX := lex
LINT := lint
@@ -829,16 +715,19 @@ ${MY_OBJ_DIR}/%.o : %.f
endif
# endif CRAY
-# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD
-ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSD))
+# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD and MACOSX
+ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSDMACOSX))
CXX := ${LINUX_CXX}
CC := ${LINUX_CC}
CPP := ${CXX}
# HAVE_INLINE is GNU standard to activate inline functions (used by GSL)
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DHAVE_INLINE ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DHAVE_INLINE ${CPP_PTH} ${OTHER_CFLAGS}
FC := ${LINUX_FC}
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
+ifeq (${PVM_ARCH},MACOSX)
+ LDFLAGS += -lresolv
+endif # endif MACOSX
LEX := flex
LINT := lint
YACC := bison
@@ -860,8 +749,15 @@ ifeq (${OPTS},X)
endif
CXXFLAGS := ${CFLAGS}
endif # endif Comeau C Compiler
-# GNU Compiler Collection
-ifeq (${CXX},g++)
+# GNU Compiler Collection or LLVM
+# 20140204: gcc and clang should receive identical options
+ifeq (g++,$(firstword ${CXX}))
+ GCC_OR_CLANG := Y
+endif
+ifeq (clang,$(firstword ${CXX}))
+ GCC_OR_CLANG := Y
+endif
+ifeq (${GCC_OR_CLANG},Y)
CPPFLAGS += -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
CFLAGS := -Wno-unused-variable
# Compilation flags for numerical routines recommended by GSL 1.3 manual, p. 397
@@ -882,7 +778,7 @@ ifeq (${CXX},g++)
# -Wwrite-strings: Apply const-qualifier to string constants, die if overwritten
# -fno-common: Prevent global variables from being simultaneously defined in different files
# -g: Put debugging symbols in executable
-# -O4: Turn on optimization so unitialized variables are flagged
+# -O4: Turn on optimization so uninitialized variables are flagged
# Compilation flags recommended by GSL that I do not like and do not use:
# -ansi: Support only strict ANSI C. Equivalent to -std=c89, conflicts with -std=c99
# --no-alias? -fstrict-aliasing
@@ -894,10 +790,18 @@ ifeq (${CXX},g++)
# -Dinline=: inline is not an ANSI keyword, must undefine inline to work with -ansi
# -fshort-enums: Make enums as short as possible, ususally non-int. Do not ever invoke this! This breaks ABI and causes subtle problems
ifeq (${OMP},Y)
+ifneq (clang,$(firstword ${CXX}))
+# 20140526 clang does not recognize/utilize -fopenmp
OMP_FLG_C := -fopenmp
OMP_FLG_F := -fopenmp
LDFLAGS += -lgomp -lpthread
+endif # endif clang
endif # endif OMP
+ifeq (clang,$(firstword ${CXX}))
+# 20140531 avoid clang error that -O4 is ame as -O3
+ CFLAGS := $(subst -O4,-O3,${CFLAGS})
+ LDFLAGS += -lstdc++
+endif # endif clang
ifeq (${OPTS},O)
CFLAGS += -O -g ${GCC_RCH_ARG}
endif
@@ -918,7 +822,7 @@ ifeq (${ABI},64)
endif # endif ABI
endif # endif LINUXAMD64
CXXFLAGS := ${CFLAGS}
-endif # endif GNU Compiler Collection
+endif # endif GNU Compiler Collection or LLVM
# Intel (Kai) C++ Compiler
ifeq (icpc,$(firstword ${CXX}))
# -cxxlib-gcc: link using C++ run-time libraries provided with GCC (default) (generated code is binary compatible with g++)
@@ -1071,17 +975,17 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG_C} ${LDFLAGS}
endif # endif OMP
endif
-# endif LINUX
+# endif LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD and MACOSX
-ifeq (${PVM_ARCH},MACOSX)
+ifeq (${PVM_ARCH},MACOSXOLD)
CXX := c++
CC := cc
CFLAGS := -Wall
CPP := ${CC}
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lresolv -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lresolv -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1105,7 +1009,7 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG} ${LDFLAGS}
endif # endif OMP
endif
-# endif MACOSX
+# endif MACOSXOLD
ifeq (${PVM_ARCH},NECSX)
ifeq (${OMP},Y)
@@ -1116,10 +1020,10 @@ CXX := c++
CC := cc
CPP := c++ -E
#CPP := /usr/lib/cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
ifeq ($(USE_FORTRAN_ARITHMETIC),Y)
# LDFLAGS += -L/lib -lf
endif
@@ -1150,10 +1054,10 @@ ifeq (${PVM_ARCH},RS6K)
CXX := g++
CC := gcc -ansi
CPP := /lib/cpp -P
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${OTHER_CFLAGS}
FC := xlf
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
ifeq ($(USE_FORTRAN_ARITHMETIC),Y)
LDFLAGS += -lxlf90 -lxlf
endif
@@ -1187,10 +1091,10 @@ CC := cc -c99
# 20000302: -w suppresses warnings which will swamp linker
#CXX := g++ -w
#CC := gcc
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90 -cpp
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -1210,7 +1114,7 @@ else # ABI=32
endif # endif ABI
endif # endif SGI64, SGIMP64
ifeq (gcc,$(firstword ${CC}))
- LDFLAGS := $(GCC_LDFLAGS_SZ_SPC) ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS := $(GCC_LDFLAGS_SZ_SPC) ${OTHER_LDFLAGS} -lm
CFLAGS := ${GCC_ABI_FLG} -Wall
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1229,7 +1133,7 @@ endif
# endif CC=gcc
ifeq (CC,$(firstword ${CXX}))
# SGI Native C++ headers are in /usr/include/CC
- LDFLAGS := ${SGI_ABI_FLG} ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS := ${SGI_ABI_FLG} ${OTHER_LDFLAGS} -lm
CFLAGS := ${SGI_ABI_FLG}
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1271,12 +1175,12 @@ CXX := g++
CC := gcc
CFLAGS := -Wall
CPP := cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90 -DHIDE_SHR_MSG
#FFLAGS := -xs -stackvar -e -Qoption f90comp -r8const
FFLAGS := -xs -stackvar -e
LD := ld
-LDFLAGS := ${TMP_LDFLAGS} ${TMP_LIBS} -lsunmath -lsocket -lnsl
+LDFLAGS := ${OTHER_LDFLAGS} -lsunmath -lsocket -lnsl
#LDFLAGS += -lF77 -lM77 -lresolv
LEX := lex
LINT := lint
@@ -1321,10 +1225,10 @@ CC := gcc -ansi
CPP := cpp
# NB: nameser.h needs -Di386, but gcc sends -Di586 (on pentiums)
CPP_TKN_OS += -Di386 -DNEED_STRCASECMP -DNEED_STRDUP -I/usr/include
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I${ANTLR_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := g77
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1471,10 +1375,8 @@ dbg:
@printf "CURL_LIB = ${CURL_LIB}\n"
@printf "CXX = ${CXX}\n"
@printf "CXXFLAGS = ${CXXFLAGS}\n"
- @printf "DAP_NETCDF = ${DAP_NETCDF}\n"
- @printf "DAP_NETCDF_ROOT = ${DAP_NETCDF_ROOT}\n"
- @printf "DAP_OPENDAP = ${DAP_OPENDAP}\n"
- @printf "DAP_OPENDAP_ROOT = ${DAP_OPENDAP_ROOT}\n"
+ @printf "DAP = ${DAP}\n"
+ @printf "DAP_ROOT = ${DAP_ROOT}\n"
@printf "DBG = ${DBG}\n"
@printf "FC = ${FC}\n"
@printf "FFLAGS = ${FFLAGS}\n"
@@ -1537,7 +1439,6 @@ dbg:
@printf "TMP_LDFLAGS = ${TMP_LDFLAGS}\n"
@printf "TMP_LIBS = ${TMP_LIBS}\n"
@printf "UDUNITS = $(UDUNITS)\n"
- @printf "UDUNITS2 = $(UDUNITS2)\n"
@printf "UDUNITS_INC = $(UDUNITS_INC)\n"
@printf "UDUNITS_LIB = $(UDUNITS_LIB)\n"
@printf "UNAMES = ${UNAMES}\n"
diff --git a/src/nco++/fmc_all_cls.cc b/src/nco++/fmc_all_cls.cc
index b8cce0a..82e9e65 100644
--- a/src/nco++/fmc_all_cls.cc
+++ b/src/nco++/fmc_all_cls.cc
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/fmc_all_cls.cc,v 1.68 2014/04/10 10:45:49 hmb Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/fmc_all_cls.cc,v 1.70 2014/08/11 11:44:24 hmb Exp $ */
/* Purpose: netCDF arithmetic processor class methods: families of functions/methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "fmc_all_cls.hh"
@@ -2702,6 +2703,393 @@ double bil_cls::clc_lin_ipl(double x1,double x2, double x, double Q0,double Q1){
}
+
+//misc Functions /******************************************/
+// These fuctions are used to create and apply masks to 2D grid variables
+// mask_out=imask_make(var_in,lat,lon)
+//
+// var_in is a 2D var. mask_out is a 0/1 mask of grid points.
+// value is set to 1 if point in var_in is missing_value but has a neigbour with a non-missing value;
+//
+// var_out=imask_fill(var_in.mask_out,lat,lon)
+//
+// Points in var_in are filled if they are missing AND are specified in mask_out.
+// The fill value is an average from the nearest neigbours. nb if a neighbour has just been filled
+// in then this value is NOT used in the calculation of the average
+// Typically mask_out and var_in should be the same shape.
+// Howver its possible to specify multiple mask in mask_out - in this case each mask is iterativly applied to var_in
+// so the shape would be like mask_out(mask_size,lat,lon)
+//
+//
+//
+ misc_cls::misc_cls(bool flg_dbg){
+ //Populate only on first constructor call
+ if(fmc_vtr.empty()){
+ fmc_vtr.push_back( fmc_cls("imask",this,(int)PMISC1));
+ fmc_vtr.push_back( fmc_cls("imask_make",this,(int)PMISC2));
+ fmc_vtr.push_back( fmc_cls("imask_fill",this,(int)PMISC3));
+ }
+ }
+
+
+
+
+ var_sct *misc_cls::fnd(RefAST expr, RefAST fargs,fmc_cls &fmc_obj, ncoTree &walker){
+ const std::string fnc_nm("misc_cls::fnd");
+ int idx;
+ int fdx=fmc_obj.fdx(); //index
+ int nbr_args;
+ int in_nbr_args;
+ prs_cls* prs_arg=walker.prs_arg;
+ var_sct *var_arr[4];
+ var_sct *var_out;
+ RefAST tr;
+ nc_type in_typ;
+ std::string susg;
+ std::string serr;
+ std::string sfnm =fmc_obj.fnm(); //method name
+ std::vector<RefAST> vtr_args;
+ NcapVector<dmn_sct*> dmn_vtr;
+
+
+ if(expr)
+ vtr_args.push_back(expr);
+
+ if(tr=fargs->getFirstChild()) {
+ do
+ vtr_args.push_back(tr);
+ while(tr=tr->getNextSibling());
+ }
+
+
+ nbr_args=vtr_args.size();
+
+ switch(fdx){
+
+ case PMISC1:
+ in_nbr_args=nbr_args;
+ susg="usage: var_out="+sfnm+"(Data_2D, X_in, Y_in)";
+ break;
+
+ case PMISC2:
+ in_nbr_args=nbr_args;
+ susg="usage: var_out="+sfnm+"(data_2D, mask,X_in?, Y_in?)";
+ break;
+
+
+ case PMISC3:
+ in_nbr_args=nbr_args;
+ susg="usage: var_out="+sfnm+"(data_2D,mask, X_in, Y_in)";
+ break;
+
+
+ } // end switch
+
+
+ if(in_nbr_args <3 ){
+ serr="function requires at least two arguments. You have only supplied "+nbr2sng(in_nbr_args)+ " arguments\n";
+ err_prn(sfnm,serr+susg);
+ }
+
+
+
+ // process input args
+ for(idx=0 ; idx<in_nbr_args; idx++)
+ var_arr[idx]=walker.out(vtr_args[idx]);
+
+
+ // initial scan
+ if(prs_arg->ntl_scn){
+ for(idx=1 ; idx<in_nbr_args ; idx++)
+ nco_var_free(var_arr[idx]);
+
+ return var_arr[0];
+ }
+
+ // save inital type
+ in_typ=var_arr[0]->type;
+ // convert all args to type DOUBLE
+ for(idx=0;idx<in_nbr_args;idx++)
+ var_arr[idx]=nco_var_cnf_typ(NC_DOUBLE,var_arr[idx]);
+
+
+
+ if(fdx==PMISC1){
+ // recall input arguments in order
+ // 0 - input data
+ // 1 - input X co-ordinate var
+ // 2 - input Y co-ordinate var
+ long cnt=0l;
+ long ldx;
+ long idx;
+ long jdx;
+ long v_sz;
+ long iidx;
+ long jjdx;
+ long lldx;
+ long x_sz;
+ long y_sz;
+ double *dpi;
+ double *dpo;
+ double mss_dbl=9.999e20;;
+
+ var_out=nco_var_dpl(var_arr[0]);
+ (void)cast_void_nctype(NC_DOUBLE,&var_out->val);
+
+ for(idx=0;idx<in_nbr_args;idx++)
+ (void)cast_void_nctype(NC_DOUBLE,&var_arr[idx]->val);
+
+ // grab missing value;
+ if( var_arr[0]->has_mss_val ){
+ cast_void_nctype(NC_DOUBLE,&var_arr[0]->mss_val);
+ mss_dbl=*var_arr[0]->mss_val.dp;
+ cast_nctype_void(NC_DOUBLE,&var_arr[0]->mss_val);
+ }
+
+ dpi=var_arr[0]->val.dp;
+ dpo=var_out->val.dp;
+ v_sz=var_arr[0]->sz;
+ x_sz=var_arr[1]->sz;
+ y_sz=var_arr[2]->sz;
+
+
+
+ // set all values to zero
+ memset((void*)dpo,0, sizeof(double) *v_sz);
+
+ for(idx=2;idx<x_sz-2; idx++)
+ for(jdx=2;jdx<y_sz-2;jdx++ ){
+ ldx=idx*y_sz+jdx;
+ // set output to default missing vale;
+ dpo[ldx]=mss_dbl;
+ // mask either 1 or mss_dbl
+ if( dpi[ldx] !=1.0 ){
+ for(iidx=idx-2; iidx<idx+3;iidx++){
+ for(jjdx=jdx-2; jjdx<jdx+3;jjdx++){
+ lldx=iidx*y_sz+jjdx;
+ if(dpi[lldx]==1.0){
+ dpo[ldx]=1.0;
+ cnt++;
+ goto outer;
+ }
+ }
+ }
+ }
+ outer: ;
+ }
+
+ printf("misc_cls number of spots processed=%ld\n" ,cnt);
+
+ } // end fdx
+
+ if(fdx==PMISC2){
+ // recall input arguments in order
+ // 0 - input var -2D INPUT GRID
+ // 1 - input X co-ordinate var
+ // 2 - input Y co-ordinate var
+ long ldx;
+ long v_sz;
+ long x_sz;
+ long y_sz;
+ long mcnt=0l; // num missing values count
+ long vmcnt=0l; // num missing processed;
+ double mss_dbl=9.999e20;
+ double *dpi; // input pointer
+ double *dpo; //output pointer
+ double *dpm; // mask pointer;
+ // save in type;
+ ostringstream os;
+
+ // var_out is the output mask - same shape as input var
+ var_out=nco_var_dpl(var_arr[0]);
+ (void)cast_void_nctype(NC_DOUBLE,&var_out->val);
+
+ // cast all vars
+ for(idx=0;idx<in_nbr_args;idx++)
+ (void)cast_void_nctype(NC_DOUBLE,&var_arr[idx]->val);
+
+ v_sz=var_arr[0]->sz;
+ x_sz=var_arr[1]->sz;
+ y_sz=var_arr[2]->sz;
+
+
+ dpo=var_out->val.dp;
+ dpi=var_arr[0]->val.dp;
+ dpm=var_arr[1]->val.dp;
+
+ // grab missing value;
+ if( var_arr[0]->has_mss_val ){
+ cast_void_nctype(NC_DOUBLE,&var_arr[0]->mss_val);
+ mss_dbl=*var_arr[0]->mss_val.dp;
+ cast_nctype_void(NC_DOUBLE,&var_arr[0]->mss_val);
+ }
+
+ for(ldx=0; ldx<v_sz ; ldx++){
+ // set otuput to default -0.0
+ dpo[ldx]=0.0;
+
+ if(dpi[ldx]==mss_dbl ){
+ int cnt=0;
+ int jdx;
+ long iX=ldx/y_sz;
+ long iY= ldx -iX*y_sz;
+ double sum=0.0;
+ double Q[4]={mss_dbl,mss_dbl,mss_dbl,mss_dbl};
+ mcnt++;
+
+
+ if(iY >0 ) Q[0]=dpi[ldx-1];
+ if(iY+1<y_sz) Q[1]=dpi[ldx+1];
+ if(iX>0 ) Q[2]=dpi[ldx-y_sz];
+ if(iX+1 < x_sz) Q[3]=dpi[ldx+y_sz];
+
+ for(jdx=0 ; jdx<4 ;jdx++)
+ if(Q[jdx] !=mss_dbl) {
+ sum+=Q[jdx];
+ cnt++;
+ }
+
+ if(cnt){
+ dpo[ldx]=1.0;
+ vmcnt++;
+ }
+
+ } // end if
+
+ } // end for
+
+ if(nco_dbg_lvl_get() >= 2){
+ os<< sfnm<<": num missing="<<mcnt<<+" num valid="<<vmcnt;
+ dbg_prn(fnc_nm,os.str());
+ }
+
+ } // end fdx
+
+
+ if(fdx==PMISC3){
+ // recall input arguments in order
+ // 0 - input var -2D INPUT GRID
+ // 1 - input mask 2D GRID (VARMASK these are the places we want to fill a value)
+ // nb this mask may contain multiple masks. So size of mask is a multiple of the
+ // the input size grid i.e mask size = n * v_sz, When its a multiple we apply each mask
+ // i an iteration
+ // 2 - input X co-ordinate var
+ // 3 - input Y co-ordinate var
+ long ldx;
+ long mdx;
+ long v_sz;
+ long m_sz;
+ long x_sz;
+ long y_sz;
+ size_t m_offset=0ll;
+ double mss_dbl=9.999e20;
+ double *dpi; // input pointer
+ double *dpo; //output pointer
+ double *dpm; // mask pointer;
+
+ // save in type;
+
+
+
+ var_out=nco_var_dpl(var_arr[0]);
+ (void)cast_void_nctype(NC_DOUBLE,&var_out->val);
+
+ // cast all arguments
+ for(idx=0;idx<in_nbr_args;idx++)
+ (void)cast_void_nctype(NC_DOUBLE,&var_arr[idx]->val);
+
+ v_sz=var_arr[0]->sz;
+ m_sz=var_arr[1]->sz;
+ x_sz=var_arr[2]->sz;
+ y_sz=var_arr[3]->sz;
+
+
+ assert(v_sz==x_sz*y_sz);
+ // check mask size
+ assert(m_sz % v_sz ==0l);
+
+ dpo=var_out->val.dp;
+ dpi=var_arr[0]->val.dp;
+
+
+ // grab missing value;
+ if( var_arr[0]->has_mss_val ){
+ cast_void_nctype(NC_DOUBLE,&var_arr[0]->mss_val);
+ mss_dbl=*var_arr[0]->mss_val.dp;
+ cast_nctype_void(NC_DOUBLE,&var_arr[0]->mss_val);
+ }
+
+ for(mdx=0;mdx < m_sz/v_sz ; mdx++){
+ long mcnt=0l;
+ long vmcnt=0l;
+ ostringstream os;
+ dpm=var_arr[1]->val.dp+mdx*v_sz;
+
+ // copy new values into input pointer !!
+ // dont want dpi and dpo the same
+ if(mdx >0)
+ memcpy(dpi,dpo, v_sz* sizeof(double));
+
+ for(ldx=0; ldx<v_sz ; ldx++){
+ //check mask
+ // if(dpm[ldx]==1.0 && dpi[ldx]==mss_dbl){
+ // if( dpi[ldx]==mss_dbl) dpo[ldx]=0.0;
+ // if(dpm[ldx]==1.0 && dpi[ldx]==mss_dbl){
+ if(dpi[ldx]==mss_dbl && dpm[ldx]==1.0){
+ int cnt=0;
+ int jdx;
+ long iX=ldx/y_sz;
+ long iY= ldx -iX*y_sz;
+ double sum=0.0;
+ double Q[4]={mss_dbl,mss_dbl,mss_dbl,mss_dbl};
+ mcnt++;
+
+ if(iY >0 ) Q[0]=dpi[ldx-1];
+ if(iY+1<x_sz) Q[1]=dpi[ldx+1];
+ if(iX>0 ) Q[2]=dpi[ldx-y_sz];
+ if(iX+1 < x_sz) Q[3]=dpi[ldx+y_sz];
+
+ for(jdx=0 ; jdx<4 ;jdx++){
+ if(Q[jdx] !=mss_dbl) {
+ sum+=Q[jdx];
+ cnt++;
+ }
+ }
+ if(cnt){
+ dpo[ldx]=sum/cnt;
+ vmcnt++;
+ }
+
+ } // end if
+
+ } // end for ldx
+
+ if(nco_dbg_lvl_get() >= 2){
+ os<< sfnm<<" mask num="<<mdx<<" : num missing="<<mcnt<<+" num processed="<<vmcnt;
+ dbg_prn(fnc_nm,os.str());
+ }
+
+ } // end for mdx
+ }
+
+ // cast everything back to void,and free up
+ for(idx=0;idx<in_nbr_args;idx++){
+ (void)cast_nctype_void(NC_DOUBLE,&var_arr[idx]->val);
+ nco_var_free(var_arr[idx]);
+ }
+
+ (void)cast_nctype_void(NC_DOUBLE,&var_out->val);
+ // change back to input type
+ var_out=nco_var_cnf_typ(in_typ,var_out);
+
+
+ return var_out;
+
+
+ }// end
+
+
+
/*****************************************************************************************************************/
/* ncap2 functions and methods */
diff --git a/src/nco++/fmc_all_cls.hh b/src/nco++/fmc_all_cls.hh
index 4840fa0..3fe893a 100644
--- a/src/nco++/fmc_all_cls.hh
+++ b/src/nco++/fmc_all_cls.hh
@@ -1,8 +1,9 @@
/* Purpose: netCDF arithmetic processor class methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Standard C++ headers
#ifndef FMC_ALL_CLS_HH
@@ -202,6 +203,18 @@ public:
double clc_lin_ipl(double x1,double x2, double x, double Q0,double Q1);
};
+
+//Miscellaneous Function /****************************************/
+ class misc_cls: public vtl_cls {
+ private:
+ enum {PMISC1, PMISC2, PMISC3 };
+ bool _flg_dbg;
+ public:
+ misc_cls(bool flg_dbg);
+ var_sct *fnd(RefAST expr, RefAST fargs,fmc_cls &fmc_obj, ncoTree &walker);
+
+ };
+
// Co-ord class /*********************************************************/
class cod_cls: public vtl_cls {
private:
diff --git a/src/nco++/fmc_cls.hh b/src/nco++/fmc_cls.hh
index f1b7ae5..8daf511 100644
--- a/src/nco++/fmc_cls.hh
+++ b/src/nco++/fmc_cls.hh
@@ -1,8 +1,9 @@
/* Purpose: netCDF arithmetic processor class methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Standard C++ headers
#ifndef FMC_CLS_HH
diff --git a/src/nco++/fmc_gsl_cls.cc b/src/nco++/fmc_gsl_cls.cc
index 91338cc..5d29781 100644
--- a/src/nco++/fmc_gsl_cls.cc
+++ b/src/nco++/fmc_gsl_cls.cc
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/fmc_gsl_cls.cc,v 1.69 2014/02/17 23:12:39 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/fmc_gsl_cls.cc,v 1.70 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: netCDF arithmetic processor class methods for GSL */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "fmc_gsl_cls.hh"
#include "nco_gsl.h"
diff --git a/src/nco++/fmc_gsl_cls.hh b/src/nco++/fmc_gsl_cls.hh
index 0829c4e..2194642 100644
--- a/src/nco++/fmc_gsl_cls.hh
+++ b/src/nco++/fmc_gsl_cls.hh
@@ -1,8 +1,9 @@
/* Purpose: netCDF arithmetic processor class methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#ifndef FMC_GSL_CLS_HH // Contents have not yet been inserted in current source file
#define FMC_GSL_CLS_HH
diff --git a/src/nco++/libnco++.hh b/src/nco++/libnco++.hh
index 5002ac6..f04083a 100644
--- a/src/nco++/libnco++.hh
+++ b/src/nco++/libnco++.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco++/libnco++.hh,v 1.21 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco++/libnco++.hh,v 1.22 2014/06/15 21:06:24 zender Exp $
// Purpose: Prototypes, typedefs, and global variables for libnco++
-/* Copyright (C) 2006--2014 Charlie Zender
- You may copy, distribute, and/or modify this software under the terms of the GNU General Public License (GPL) Version 2
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* libnco++.hh headers depend on system headers and libnco.a headers
Thus libnco++.a requires libnco.a to function correctly
diff --git a/src/nco++/ncap2.cc b/src/nco++/ncap2.cc
index d2ea09a..b489834 100644
--- a/src/nco++/ncap2.cc
+++ b/src/nco++/ncap2.cc
@@ -1,21 +1,19 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/ncap2.cc,v 1.189 2014/03/25 14:19:36 hmb Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncap2.cc,v 1.194 2014/08/11 11:41:26 hmb Exp $ */
/* ncap2 -- netCDF arithmetic processor */
/* Purpose: Compute user-defined derived fields using forward algebraic notation applied to netCDF files */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -72,9 +70,8 @@
/* 3rd party vendors */
#ifdef ENABLE_GSL
-#include <gsl/gsl_errno.h>
-#include <gsl/gsl_rng.h>
-
+# include <gsl/gsl_errno.h>
+# include <gsl/gsl_rng.h>
#endif // !ENABLE_GSL
/* Personal headers */
@@ -125,6 +122,8 @@ main(int argc,char **argv)
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
+ aed_sct att_item; // Used to convert atts in vector to normal form
+
char **fl_lst_abb=NULL_CEWI; /* Option n */
char **fl_lst_in;
char **var_lst_in=NULL_CEWI;
@@ -145,8 +144,8 @@ main(int argc,char **argv)
char *spt_arg[NCAP_SPT_NBR_MAX]; /* fxm: Arbitrary size, should be dynamic */
char *spt_arg_cat=NULL_CEWI; /* [sng] User-specified script */
- const char * const CVS_Id="$Id: ncap2.cc,v 1.189 2014/03/25 14:19:36 hmb Exp $";
- const char * const CVS_Revision="$Revision: 1.189 $";
+ const char * const CVS_Id="$Id: ncap2.cc,v 1.194 2014/08/11 11:41:26 hmb Exp $";
+ const char * const CVS_Revision="$Revision: 1.194 $";
const char * const att_nm_tmp="eulaVlliF_"; /* For netCDF4 name hack */
const char * const opt_sht_lst="3467ACcD:FfhL:l:n:Oo:p:Rrs:S:t:vx-:"; /* [sng] Single letter command line options */
@@ -223,8 +222,6 @@ main(int argc,char **argv)
var_sct **var_prc;
var_sct **var_prc_out;
- aed_sct att_item; // Used to convert atts in vector to normal form
-
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -401,6 +398,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
@@ -521,8 +519,8 @@ main(int argc,char **argv)
bil_cls bil_obj(true);
// Co-ordinates functions
cod_cls cod_obj(true);
-
-
+ // misc functions
+ misc_cls misc_obj(true);
// Populate vector
(void)pop_fmc_vtr(fmc_vtr,&cnv_obj);
@@ -539,6 +537,7 @@ main(int argc,char **argv)
(void)pop_fmc_vtr(fmc_vtr,&arr_obj);
(void)pop_fmc_vtr(fmc_vtr,&bil_obj);
(void)pop_fmc_vtr(fmc_vtr,&cod_obj);
+ (void)pop_fmc_vtr(fmc_vtr,&misc_obj);
#ifdef ENABLE_GSL
#ifdef ENABLE_NCO_GSL
@@ -738,6 +737,7 @@ main(int argc,char **argv)
xtr_lst_a=nco_var_lst_mk(out_id,nbr_var_fl,(char**)NULL,False,False,&nbr_xtr);
for(idx=0;idx<nbr_var_fl;idx++){
var_tmp=prs_arg.ncap_var_init(xtr_lst_a[idx].nm,false);
+
Nvar=new NcapVar(var_tmp);
Nvar->flg_stt=2;
prs_arg.var_vtr.push(Nvar);
@@ -877,7 +877,7 @@ main(int argc,char **argv)
/* Define non-processed vars */
(void)nco_var_dfn(in_id,fl_out,out_id,var_out,xtr_nbr,(dmn_sct **)NULL,(int)0,nco_pck_plc_nil,nco_pck_map_nil,dfl_lvl);
- /* Write out new attributes possibly overwriting old ones */
+ /* Write new attributes possibly overwriting old ones */
for(idx=0;idx<var_vtr.size();idx++){
if(var_vtr[idx]->xpr_typ == ncap_var){
@@ -887,35 +887,34 @@ main(int argc,char **argv)
var_ref=var_vtr[idx]->var;
rcd=nco_inq_varid_flg(out_id,var_ref->nm,&var_id);
- /* filter out ram vars */
+ /* Filter-out RAM vars */
if(rcd!=NC_NOERR || !var_ref->has_mss_val) continue;
- /* see if missing value already present */
+ /* Is missing value already present? */
rcd_inq_att=nco_inq_att_flg(out_id,var_id,nco_mss_val_sng_get(),&att_item.type,&att_item.sz);
- /* type mismatch dont overwrite. This can occur when packed vars are in output from using the -A switch */
- if(rcd_inq_att==NC_NOERR && var_ref->type != att_item.type) continue;
+ /* Do not overwrite if type mismatch, e.g., packed variable are in output with -A switch */
+ if(rcd_inq_att == NC_NOERR && var_ref->type != att_item.type) continue;
- /* fill mode and att exists */
- if(prs_arg.NCAP4_FILL && rcd_inq_att==NC_NOERR){
+ /* Fill-mode and attribute exists */
+ if(prs_arg.NCAP4_FILL && rcd_inq_att == NC_NOERR){
(void)nco_rename_att(out_id,var_id,nco_mss_val_sng_get(),att_nm_tmp);
(void)nco_put_att(out_id,var_id,att_nm_tmp,var_ref->type,1,var_ref->mss_val.vp);
(void)nco_rename_att(out_id,var_id,att_nm_tmp,nco_mss_val_sng_get());
continue;
- }
+ } /* end if */
- /* fill mode and att doesn't exist */
- if(prs_arg.NCAP4_FILL && rcd_inq_att!=NC_NOERR){
+ /* Fill-mode and attribute does not exist */
+ if(prs_arg.NCAP4_FILL && rcd_inq_att != NC_NOERR){
(void)nco_put_att(out_id,var_id,att_nm_tmp,var_ref->type,1,var_ref->mss_val.vp);
(void)nco_rename_att(out_id,var_id,att_nm_tmp,nco_mss_val_sng_get());
continue;
- }
+ } /* end if */
- /* netcdf3 file just put att */
+ /* netCDF3 file so just put attribute */
(void)nco_put_att(out_id,var_id,nco_mss_val_sng_get(),var_ref->type,1,var_ref->mss_val.vp);
continue;
- }
-
+ } /* endif */
/* Write misssing value contained inside variable */
/* If missing value type is same as disk type */
@@ -958,15 +957,15 @@ main(int argc,char **argv)
/* NB: These attributes should probably be written prior to last data mode */
(void)nco_aed_prc(out_id,var_id,att_item);
- cln_up: ;
- att_item.var_nm=(char*)nco_free(att_item.var_nm);
- att_item.att_nm=(char*)nco_free(att_item.att_nm);
+ cln_up:
+ att_item.var_nm=(char*)nco_free(att_item.var_nm);
+ att_item.att_nm=(char*)nco_free(att_item.att_nm);
} /* end for */
/* Set chunksize parameters */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) (void)nco_cnk_sz_set(out_id,(lmt_msa_sct **)NULL_CEWI,(int)0,&cnk_map,&cnk_plc,cnk_sz_scl,cnk.cnk_dmn,cnk_nbr);
- /* Turn off default filling behavior to enhance efficiency */
+ /* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
diff --git a/src/nco++/ncap2_utl.cc b/src/nco++/ncap2_utl.cc
index 0cab060..e2c5804 100644
--- a/src/nco++/ncap2_utl.cc
+++ b/src/nco++/ncap2_utl.cc
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/ncap2_utl.cc,v 1.158 2014/05/27 16:51:56 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncap2_utl.cc,v 1.159 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: netCDF arithmetic processor */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "ncap2_utl.hh"
diff --git a/src/nco++/ncap2_utl.hh b/src/nco++/ncap2_utl.hh
index 891ded2..1af0ed8 100644
--- a/src/nco++/ncap2_utl.hh
+++ b/src/nco++/ncap2_utl.hh
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/ncap2_utl.hh,v 1.20 2013/04/16 21:53:24 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncap2_utl.hh,v 1.21 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: netCDF arithmetic processor definitions and function prototypes for ncap.c, ncap_utl.c, ncap_lex.l, and ncap_yacc.y */
-/* Copyright (C) 1995--2008 Charlie Zender
- You may copy, distribute, and/or modify this software under the terms of the GNU General Public License (GPL) Version 2
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "ncap.h" *//* netCDF arithmetic processor-specific definitions (symbol table, ...) */
diff --git a/src/nco++/ncoGrammer.g b/src/nco++/ncoGrammer.g
index 3a130bf..d76a84d 100644
--- a/src/nco++/ncoGrammer.g
+++ b/src/nco++/ncoGrammer.g
@@ -1,11 +1,12 @@
header {
-/* $Header: /cvsroot/nco/nco/src/nco++/ncoGrammer.g,v 1.206 2014/05/01 19:05:39 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncoGrammer.g,v 1.207 2014/06/15 21:06:25 zender Exp $ */
/* Purpose: ANTLR Grammar and support files for ncap2 */
-/* Copyright (C) 2005--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// C Standard Headers
#include <assert.h>
diff --git a/src/nco++/ncoLexer.cpp b/src/nco++/ncoLexer.cpp
index 733ac94..da50109 100644
--- a/src/nco++/ncoLexer.cpp
+++ b/src/nco++/ncoLexer.cpp
@@ -1324,7 +1324,7 @@ void ncoLexer::mBLASTOUT(bool _createToken) {
ANTLR_USE_NAMESPACE(std)string::size_type _saveIndex;
matchNot(EOF/*_CHAR*/);
-#line 435 "ncoGrammer.g"
+#line 436 "ncoGrammer.g"
// blast out of lexer & parser
// Can't use RecognitionException() as
@@ -1381,7 +1381,7 @@ void ncoLexer::mUNUSED_OPS(bool _createToken) {
}
}
}
-#line 451 "ncoGrammer.g"
+#line 452 "ncoGrammer.g"
ostringstream os;
@@ -1415,7 +1415,7 @@ void ncoLexer::mWS(bool _createToken) {
case 0x9 /* '\t' */ :
{
match('\t' /* charlit */ );
-#line 464 "ncoGrammer.g"
+#line 465 "ncoGrammer.g"
tab();
#line 1421 "ncoLexer.cpp"
break;
@@ -1428,7 +1428,7 @@ void ncoLexer::mWS(bool _createToken) {
case 0xa /* '\n' */ :
{
match('\n' /* charlit */ );
-#line 464 "ncoGrammer.g"
+#line 465 "ncoGrammer.g"
newline();
#line 1434 "ncoLexer.cpp"
break;
@@ -1439,7 +1439,7 @@ void ncoLexer::mWS(bool _createToken) {
}
}
}
-#line 465 "ncoGrammer.g"
+#line 466 "ncoGrammer.g"
_ttype = antlr::Token::SKIP;
#line 1445 "ncoLexer.cpp"
if ( _createToken && _token==ANTLR_USE_NAMESPACE(antlr)nullToken && _ttype!=ANTLR_USE_NAMESPACE(antlr)Token::SKIP ) {
@@ -1469,7 +1469,7 @@ void ncoLexer::mCXX_COMMENT(bool _createToken) {
_loop149:;
} // ( ... )*
match('\n' /* charlit */ );
-#line 470 "ncoGrammer.g"
+#line 471 "ncoGrammer.g"
_ttype = antlr::Token::SKIP; newline();
#line 1475 "ncoLexer.cpp"
if ( _createToken && _token==ANTLR_USE_NAMESPACE(antlr)nullToken && _ttype!=ANTLR_USE_NAMESPACE(antlr)Token::SKIP ) {
@@ -1510,7 +1510,7 @@ void ncoLexer::mC_COMMENT(bool _createToken) {
}
}
}
-#line 477 "ncoGrammer.g"
+#line 478 "ncoGrammer.g"
newline();
#line 1516 "ncoLexer.cpp"
}
@@ -1527,7 +1527,7 @@ void ncoLexer::mC_COMMENT(bool _createToken) {
_loop154:;
} // ( ... )*
match("*/");
-#line 481 "ncoGrammer.g"
+#line 482 "ncoGrammer.g"
_ttype = antlr::Token::SKIP;
#line 1533 "ncoLexer.cpp"
if ( _createToken && _token==ANTLR_USE_NAMESPACE(antlr)nullToken && _ttype!=ANTLR_USE_NAMESPACE(antlr)Token::SKIP ) {
@@ -1566,7 +1566,7 @@ void ncoLexer::mNUMBER_DOT(bool _createToken) {
}
}
-#line 488 "ncoGrammer.g"
+#line 489 "ncoGrammer.g"
_ttype = DOUBLE;
#line 1572 "ncoLexer.cpp"
{
@@ -1592,7 +1592,7 @@ void ncoLexer::mNUMBER_DOT(bool _createToken) {
}
}
}
-#line 489 "ncoGrammer.g"
+#line 490 "ncoGrammer.g"
_ttype = DOUBLE;
#line 1598 "ncoLexer.cpp"
break;
@@ -1618,7 +1618,7 @@ void ncoLexer::mNUMBER_DOT(bool _createToken) {
}
}
}
-#line 490 "ncoGrammer.g"
+#line 491 "ncoGrammer.g"
_ttype = FLOAT;
#line 1624 "ncoLexer.cpp"
break;
@@ -1644,7 +1644,7 @@ void ncoLexer::mNUMBER_DOT(bool _createToken) {
}
}
}
-#line 491 "ncoGrammer.g"
+#line 492 "ncoGrammer.g"
_ttype = DOUBLE;
#line 1650 "ncoLexer.cpp"
break;
@@ -1681,7 +1681,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
_loop165:;
} // ( ... )+
-#line 496 "ncoGrammer.g"
+#line 497 "ncoGrammer.g"
_ttype = INT;
#line 1687 "ncoLexer.cpp"
{
@@ -1736,7 +1736,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
-#line 497 "ncoGrammer.g"
+#line 498 "ncoGrammer.g"
_ttype = DOUBLE;
#line 1742 "ncoLexer.cpp"
break;
@@ -1747,7 +1747,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
{
mXPN(false);
}
-#line 498 "ncoGrammer.g"
+#line 499 "ncoGrammer.g"
_ttype = DOUBLE;
#line 1753 "ncoLexer.cpp"
break;
@@ -1773,7 +1773,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 500 "ncoGrammer.g"
+#line 501 "ncoGrammer.g"
_ttype = SHORT;
#line 1779 "ncoLexer.cpp"
break;
@@ -1799,7 +1799,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 501 "ncoGrammer.g"
+#line 502 "ncoGrammer.g"
_ttype = BYTE;
#line 1805 "ncoLexer.cpp"
break;
@@ -1824,7 +1824,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 506 "ncoGrammer.g"
+#line 507 "ncoGrammer.g"
_ttype = UINT64;
#line 1830 "ncoLexer.cpp"
}
@@ -1847,7 +1847,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 502 "ncoGrammer.g"
+#line 503 "ncoGrammer.g"
_ttype = UBYTE;
#line 1853 "ncoLexer.cpp"
}
@@ -1870,7 +1870,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 503 "ncoGrammer.g"
+#line 504 "ncoGrammer.g"
_ttype = USHORT;
#line 1876 "ncoLexer.cpp"
}
@@ -1893,7 +1893,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 505 "ncoGrammer.g"
+#line 506 "ncoGrammer.g"
_ttype = INT64;
#line 1899 "ncoLexer.cpp"
}
@@ -1916,7 +1916,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 499 "ncoGrammer.g"
+#line 500 "ncoGrammer.g"
_ttype = INT;
#line 1922 "ncoLexer.cpp"
}
@@ -1939,7 +1939,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
-#line 504 "ncoGrammer.g"
+#line 505 "ncoGrammer.g"
_ttype = UINT;
#line 1945 "ncoLexer.cpp"
}
@@ -1970,7 +1970,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 508 "ncoGrammer.g"
+#line 509 "ncoGrammer.g"
_ttype = FLOAT;
#line 1976 "ncoLexer.cpp"
break;
@@ -1996,7 +1996,7 @@ void ncoLexer::mNUMBER(bool _createToken) {
}
}
}
-#line 509 "ncoGrammer.g"
+#line 510 "ncoGrammer.g"
_ttype = DOUBLE;
#line 2002 "ncoLexer.cpp"
break;
@@ -2104,7 +2104,7 @@ void ncoLexer::mVAR_ATT(bool _createToken) {
}
_loop188:;
} // ( ... )*
-#line 516 "ncoGrammer.g"
+#line 517 "ncoGrammer.g"
// try to intelligently guess the type to avoid un-necessary function search
bool bDoSearch;
@@ -2226,7 +2226,7 @@ void ncoLexer::mVAR_ATT(bool _createToken) {
}
_loop192:;
} // ( ... )*
-#line 548 "ncoGrammer.g"
+#line 549 "ncoGrammer.g"
_ttype = ATT_ID;
#line 2232 "ncoLexer.cpp"
}
@@ -2254,7 +2254,7 @@ void ncoLexer::mVAR_ATT_QT(bool _createToken) {
text.erase(_saveIndex);
}
mVAR_NM_QT(false);
-#line 553 "ncoGrammer.g"
+#line 554 "ncoGrammer.g"
_ttype = VAR_ID;
#line 2260 "ncoLexer.cpp"
{
@@ -2263,7 +2263,7 @@ void ncoLexer::mVAR_ATT_QT(bool _createToken) {
{
match('@' /* charlit */ );
mVAR_NM_QT(false);
-#line 554 "ncoGrammer.g"
+#line 555 "ncoGrammer.g"
_ttype = ATT_ID;
#line 2269 "ncoLexer.cpp"
break;
@@ -2306,7 +2306,7 @@ void ncoLexer::mDIM_QT(bool _createToken) {
match('$' /* charlit */ );
text.erase(_saveIndex);
mVAR_NM_QT(false);
-#line 560 "ncoGrammer.g"
+#line 561 "ncoGrammer.g"
_ttype = DIM_ID;
#line 2312 "ncoLexer.cpp"
}
@@ -2320,7 +2320,7 @@ void ncoLexer::mDIM_QT(bool _createToken) {
_saveIndex = text.length();
match(".size");
text.erase(_saveIndex);
-#line 562 "ncoGrammer.g"
+#line 563 "ncoGrammer.g"
_ttype = DIM_ID_SIZE;
#line 2326 "ncoLexer.cpp"
}
@@ -2429,7 +2429,7 @@ void ncoLexer::mDIM_VAL(bool _createToken) {
}
_loop205:;
} // ( ... )*
-#line 567 "ncoGrammer.g"
+#line 568 "ncoGrammer.g"
_ttype = DIM_ID;
#line 2435 "ncoLexer.cpp"
{
@@ -2437,7 +2437,7 @@ void ncoLexer::mDIM_VAL(bool _createToken) {
_saveIndex = text.length();
match(".size");
text.erase(_saveIndex);
-#line 569 "ncoGrammer.g"
+#line 570 "ncoGrammer.g"
_ttype = DIM_ID_SIZE;
#line 2443 "ncoLexer.cpp"
}
@@ -2508,7 +2508,7 @@ void ncoLexer::mNSTRING(bool _createToken) {
_saveIndex = text.length();
match('\"' /* charlit */ );
text.erase(_saveIndex);
-#line 582 "ncoGrammer.g"
+#line 583 "ncoGrammer.g"
_ttype = NSTRING;
#line 2514 "ncoLexer.cpp"
{
@@ -2516,7 +2516,7 @@ void ncoLexer::mNSTRING(bool _createToken) {
_saveIndex = text.length();
match('s' /* charlit */ );
text.erase(_saveIndex);
-#line 583 "ncoGrammer.g"
+#line 584 "ncoGrammer.g"
_ttype = N4STRING;
#line 2522 "ncoLexer.cpp"
}
@@ -2561,7 +2561,7 @@ void ncoLexer::mINCLUDE(bool _createToken) {
}
mNSTRING(true);
f=_returnToken;
-#line 588 "ncoGrammer.g"
+#line 589 "ncoGrammer.g"
// ANTLR_USING_NAMESPACE(std)
// create lexer to handle include
diff --git a/src/nco++/ncoLexer.hpp b/src/nco++/ncoLexer.hpp
index 433654d..bfc9877 100644
--- a/src/nco++/ncoLexer.hpp
+++ b/src/nco++/ncoLexer.hpp
@@ -10,13 +10,14 @@
#include <antlr/CharScanner.hpp>
#line 1 "ncoGrammer.g"
-/* $Header: /cvsroot/nco/nco/src/nco++/ncoLexer.hpp,v 1.130 2014/05/02 03:08:27 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncoLexer.hpp,v 1.135 2014/06/16 23:04:51 zender Exp $ */
/* Purpose: ANTLR Grammar and support files for ncap2 */
-/* Copyright (C) 2005--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// C Standard Headers
#include <assert.h>
@@ -49,10 +50,10 @@
ANTLR_USING_NAMESPACE(std);
ANTLR_USING_NAMESPACE(antlr);
-#line 53 "ncoLexer.hpp"
+#line 54 "ncoLexer.hpp"
class CUSTOM_API ncoLexer : public ANTLR_USE_NAMESPACE(antlr)CharScanner, public ncoParserTokenTypes
{
-#line 322 "ncoGrammer.g"
+#line 323 "ncoGrammer.g"
private:
prs_cls *prs_arg;
@@ -81,7 +82,7 @@ public:
}
// else ANTLR_USE_NAMESPACE(std)cout << "Hit EOF of main file" << ANTLR_USE_NAMESPACE(std)endl;
}
-#line 57 "ncoLexer.hpp"
+#line 58 "ncoLexer.hpp"
private:
void initLiterals();
public:
diff --git a/src/nco++/ncoParser.cpp b/src/nco++/ncoParser.cpp
index 976adc0..8ccd33c 100644
--- a/src/nco++/ncoParser.cpp
+++ b/src/nco++/ncoParser.cpp
@@ -88,7 +88,7 @@ void ncoParser::statement() {
astFactory->addASTChild( currentAST, returnAST );
match(SEMI);
statement_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 93 "ncoGrammer.g"
+#line 94 "ncoGrammer.g"
if( ncap_fnc_srh(e1_AST))
statement_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(FEXPR,"FEXPR"))->add(statement_AST)));
@@ -171,7 +171,7 @@ void ncoParser::statement() {
{
match(SEMI);
statement_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 110 "ncoGrammer.g"
+#line 111 "ncoGrammer.g"
statement_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(1))->add(astFactory->create(NULL_NODE,"null_stmt"))));
#line 177 "ncoParser.cpp"
currentAST.root = statement_AST;
@@ -499,7 +499,7 @@ void ncoParser::block() {
} // ( ... )*
match(RCURL);
block_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 131 "ncoGrammer.g"
+#line 132 "ncoGrammer.g"
block_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(BLOCK,"block"))->add(block_AST)));
#line 505 "ncoParser.cpp"
currentAST.root = block_AST;
@@ -618,7 +618,7 @@ void ncoParser::lmt() {
_loop20:;
} // ( ... )*
lmt_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 144 "ncoGrammer.g"
+#line 145 "ncoGrammer.g"
lmt_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(LMT,"lmt"))->add(lmt_AST)));
#line 624 "ncoParser.cpp"
currentAST.root = lmt_AST;
@@ -656,7 +656,7 @@ void ncoParser::lmt_list() {
} // ( ... )*
match(RPAREN);
lmt_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 148 "ncoGrammer.g"
+#line 149 "ncoGrammer.g"
lmt_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(LMT_LIST,"lmt_list"))->add(lmt_list_AST)));
#line 662 "ncoParser.cpp"
currentAST.root = lmt_list_AST;
@@ -738,7 +738,7 @@ void ncoParser::dmn_list() {
} // ( ... )*
match(RSQUARE);
dmn_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 156 "ncoGrammer.g"
+#line 157 "ncoGrammer.g"
dmn_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(DMN_LIST,"dmn_list"))->add(dmn_list_AST)));
#line 744 "ncoParser.cpp"
currentAST.root = dmn_list_AST;
@@ -820,7 +820,7 @@ void ncoParser::dmn_arg_list() {
} // ( ... )*
match(DIVIDE);
dmn_arg_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 162 "ncoGrammer.g"
+#line 163 "ncoGrammer.g"
dmn_arg_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(DMN_ARG_LIST,"dmn_arg_list"))->add(dmn_arg_list_AST)));
#line 826 "ncoParser.cpp"
currentAST.root = dmn_arg_list_AST;
@@ -858,7 +858,7 @@ void ncoParser::value_list() {
} // ( ... )*
match(RCURL);
value_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 167 "ncoGrammer.g"
+#line 168 "ncoGrammer.g"
value_list_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(VALUE_LIST,"value_list"))->add(value_list_AST)));
#line 864 "ncoParser.cpp"
currentAST.root = value_list_AST;
@@ -1051,7 +1051,7 @@ void ncoParser::func_arg() {
} // ( ... )*
match(RPAREN);
func_arg_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(currentAST.root);
-#line 174 "ncoGrammer.g"
+#line 175 "ncoGrammer.g"
func_arg_AST = ANTLR_USE_NAMESPACE(antlr)RefAST(astFactory->make((new ANTLR_USE_NAMESPACE(antlr)ASTArray(2))->add(astFactory->create(FUNC_ARG,"func_arg"))->add(func_arg_AST)));
#line 1057 "ncoParser.cpp"
currentAST.root = func_arg_AST;
@@ -1362,7 +1362,7 @@ void ncoParser::unaryleft_exp() {
in_AST = astFactory->create(in);
astFactory->makeASTRoot(currentAST, in_AST);
match(INC);
-#line 191 "ncoGrammer.g"
+#line 192 "ncoGrammer.g"
in_AST->setType(POST_INC);
in_AST->setText("POST_INC");
#line 1369 "ncoParser.cpp"
@@ -1374,7 +1374,7 @@ void ncoParser::unaryleft_exp() {
de_AST = astFactory->create(de);
astFactory->makeASTRoot(currentAST, de_AST);
match(DEC);
-#line 193 "ncoGrammer.g"
+#line 194 "ncoGrammer.g"
de_AST->setType(POST_DEC);
de_AST->setText("POST_DEC");
#line 1381 "ncoParser.cpp"
@@ -1483,7 +1483,7 @@ void ncoParser::unary_exp() {
ur_AST = astFactory->create(ur);
astFactory->makeASTRoot(currentAST, ur_AST);
match(TIMES);
-#line 206 "ncoGrammer.g"
+#line 207 "ncoGrammer.g"
ur_AST->setType(UTIMES);ur_AST->setText("UTIMES");
#line 1489 "ncoParser.cpp"
break;
diff --git a/src/nco++/ncoParser.hpp b/src/nco++/ncoParser.hpp
index ef14240..699aba9 100644
--- a/src/nco++/ncoParser.hpp
+++ b/src/nco++/ncoParser.hpp
@@ -10,13 +10,14 @@
#line 1 "ncoGrammer.g"
-/* $Header: /cvsroot/nco/nco/src/nco++/ncoParser.hpp,v 1.127 2014/05/02 03:08:27 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncoParser.hpp,v 1.132 2014/06/16 23:04:51 zender Exp $ */
/* Purpose: ANTLR Grammar and support files for ncap2 */
-/* Copyright (C) 2005--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// C Standard Headers
#include <assert.h>
@@ -49,15 +50,15 @@
ANTLR_USING_NAMESPACE(std);
ANTLR_USING_NAMESPACE(antlr);
-#line 53 "ncoParser.hpp"
+#line 54 "ncoParser.hpp"
class CUSTOM_API ncoParser : public ANTLR_USE_NAMESPACE(antlr)LLkParser, public ncoParserTokenTypes
{
-#line 81 "ncoGrammer.g"
+#line 82 "ncoGrammer.g"
public:
std::vector<std::string> inc_vtr;
-#line 57 "ncoParser.hpp"
+#line 58 "ncoParser.hpp"
public:
void initializeASTFactory( ANTLR_USE_NAMESPACE(antlr)ASTFactory& factory );
protected:
diff --git a/src/nco++/ncoTree.cpp b/src/nco++/ncoTree.cpp
index 1c1621c..8329908 100644
--- a/src/nco++/ncoTree.cpp
+++ b/src/nco++/ncoTree.cpp
@@ -13,7 +13,7 @@ ncoTree::ncoTree()
}
int ncoTree::lmt_peek(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 956 "ncoGrammer.g"
+#line 957 "ncoGrammer.g"
int nbr_dmn=0;
#line 19 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST lmt_peek_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
@@ -24,7 +24,7 @@ int ncoTree::lmt_peek(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,LMT_LIST);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 958 "ncoGrammer.g"
+#line 959 "ncoGrammer.g"
RefAST aRef;
aRef=lmt->getFirstChild();
@@ -51,7 +51,7 @@ int ncoTree::lmt_peek(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
}
int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 969 "ncoGrammer.g"
+#line 970 "ncoGrammer.g"
int iret=0;
#line 57 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST statements_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
@@ -71,7 +71,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
ANTLR_USE_NAMESPACE(antlr)RefAST pvid = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST patt = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST pstr = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 969 "ncoGrammer.g"
+#line 970 "ncoGrammer.g"
var_sct *var;
const std::string fnc_nm("statements");
@@ -92,7 +92,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,BLOCK);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 978 "ncoGrammer.g"
+#line 979 "ncoGrammer.g"
//std::cout <<"Num of Children in block="<<blk->getNumberOfChildren()<<endl;
iret=run_exe(blk->getFirstChild(),lpp_vtr.size() );
@@ -114,7 +114,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t219;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 984 "ncoGrammer.g"
+#line 985 "ncoGrammer.g"
RefAST tr;
RefAST ntr;
@@ -151,7 +151,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t220;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1008 "ncoGrammer.g"
+#line 1009 "ncoGrammer.g"
var=out(fss);
@@ -177,7 +177,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t221;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1016 "ncoGrammer.g"
+#line 1017 "ncoGrammer.g"
//if can have only 3 or 4 parts , 1 node and 2 or 3 siblings
// IF LOGICAL_EXP STATEMENT1 STATEMENT2
@@ -225,7 +225,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t222;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1046 "ncoGrammer.g"
+#line 1047 "ncoGrammer.g"
// convert mask to short
RefAST tr;
@@ -288,7 +288,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t223;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1090 "ncoGrammer.g"
+#line 1091 "ncoGrammer.g"
bool br;
@@ -342,7 +342,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t224;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1119 "ncoGrammer.g"
+#line 1120 "ncoGrammer.g"
bool b1,b2,b3,br;
var_sct *var_f1;
@@ -403,7 +403,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,ELSE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1170 "ncoGrammer.g"
+#line 1171 "ncoGrammer.g"
iret=ELSE;
#line 409 "ncoTree.cpp"
}
@@ -415,7 +415,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,BREAK);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1171 "ncoGrammer.g"
+#line 1172 "ncoGrammer.g"
iret=BREAK;
#line 421 "ncoTree.cpp"
}
@@ -427,7 +427,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,CONTINUE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1172 "ncoGrammer.g"
+#line 1173 "ncoGrammer.g"
iret=CONTINUE;
#line 433 "ncoTree.cpp"
}
@@ -439,7 +439,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,NULL_NODE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1173 "ncoGrammer.g"
+#line 1174 "ncoGrammer.g"
iret=NULL_NODE;
#line 445 "ncoTree.cpp"
}
@@ -459,7 +459,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t225;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1175 "ncoGrammer.g"
+#line 1176 "ncoGrammer.g"
long sz;
@@ -513,7 +513,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t229;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1188 "ncoGrammer.g"
+#line 1189 "ncoGrammer.g"
int var_id;
@@ -601,7 +601,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t233;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1234 "ncoGrammer.g"
+#line 1235 "ncoGrammer.g"
int apsn;
@@ -697,7 +697,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t237;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1289 "ncoGrammer.g"
+#line 1290 "ncoGrammer.g"
char *prn_sng;
@@ -731,7 +731,7 @@ int ncoTree::statements(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
}
var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 1835 "ncoGrammer.g"
+#line 1836 "ncoGrammer.g"
var_sct *var;
#line 737 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST out_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
@@ -765,7 +765,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
ANTLR_USE_NAMESPACE(antlr)RefAST val_uint = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST val_int64 = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST val_uint64 = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 1835 "ncoGrammer.g"
+#line 1836 "ncoGrammer.g"
const std::string fnc_nm("out");
var_sct *var1;
@@ -791,7 +791,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t305;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1862 "ncoGrammer.g"
+#line 1863 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, TIMES );
#line 797 "ncoTree.cpp"
}
@@ -810,7 +810,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t306;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1865 "ncoGrammer.g"
+#line 1866 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, DIVIDE );
#line 816 "ncoTree.cpp"
}
@@ -829,7 +829,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t307;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1867 "ncoGrammer.g"
+#line 1868 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, MOD);
#line 835 "ncoTree.cpp"
}
@@ -848,7 +848,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t308;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1869 "ncoGrammer.g"
+#line 1870 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, CARET);
#line 854 "ncoTree.cpp"
}
@@ -865,7 +865,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t309;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1872 "ncoGrammer.g"
+#line 1873 "ncoGrammer.g"
var=ncap_var_var_op(var1,NULL_CEWI, LNOT );
#line 871 "ncoTree.cpp"
}
@@ -882,7 +882,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t312;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1878 "ncoGrammer.g"
+#line 1879 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,INC,false,prs_arg);
#line 888 "ncoTree.cpp"
}
@@ -899,7 +899,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t313;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1880 "ncoGrammer.g"
+#line 1881 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI, DEC,false,prs_arg );
#line 905 "ncoTree.cpp"
}
@@ -916,7 +916,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t314;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1882 "ncoGrammer.g"
+#line 1883 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,POST_INC,false,prs_arg);
@@ -935,7 +935,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t315;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1885 "ncoGrammer.g"
+#line 1886 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,POST_DEC,false,prs_arg);
@@ -956,7 +956,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t316;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1890 "ncoGrammer.g"
+#line 1891 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, LAND );
#line 962 "ncoTree.cpp"
}
@@ -975,7 +975,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t317;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1892 "ncoGrammer.g"
+#line 1893 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, LOR );
#line 981 "ncoTree.cpp"
}
@@ -994,7 +994,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t318;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1895 "ncoGrammer.g"
+#line 1896 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, LTHAN );
#line 1000 "ncoTree.cpp"
}
@@ -1013,7 +1013,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t319;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1897 "ncoGrammer.g"
+#line 1898 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, GTHAN );
#line 1019 "ncoTree.cpp"
}
@@ -1032,7 +1032,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t320;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1899 "ncoGrammer.g"
+#line 1900 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, GEQ );
#line 1038 "ncoTree.cpp"
}
@@ -1051,7 +1051,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t321;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1901 "ncoGrammer.g"
+#line 1902 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, LEQ );
#line 1057 "ncoTree.cpp"
}
@@ -1070,7 +1070,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t322;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1903 "ncoGrammer.g"
+#line 1904 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, EQ );
#line 1076 "ncoTree.cpp"
}
@@ -1089,7 +1089,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t323;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1905 "ncoGrammer.g"
+#line 1906 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, NEQ );
#line 1095 "ncoTree.cpp"
}
@@ -1108,7 +1108,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t324;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1908 "ncoGrammer.g"
+#line 1909 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, FLTHAN );
#line 1114 "ncoTree.cpp"
}
@@ -1127,7 +1127,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t325;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1910 "ncoGrammer.g"
+#line 1911 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, FGTHAN );
#line 1133 "ncoTree.cpp"
}
@@ -1147,7 +1147,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t326;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1912 "ncoGrammer.g"
+#line 1913 "ncoGrammer.g"
var1=out_asn(pls_asn);
var=ncap_var_var_inc(var1,var2, PLUS_ASSIGN ,(pls_asn->getType()==UTIMES), prs_arg);
@@ -1170,7 +1170,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t327;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1916 "ncoGrammer.g"
+#line 1917 "ncoGrammer.g"
var1=out_asn(min_asn);
var=ncap_var_var_inc(var1,var2, MINUS_ASSIGN ,(min_asn->getType()==UTIMES), prs_arg);
@@ -1193,7 +1193,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t328;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1920 "ncoGrammer.g"
+#line 1921 "ncoGrammer.g"
var1=out_asn(tim_asn);
var=ncap_var_var_inc(var1,var2, TIMES_ASSIGN ,(tim_asn->getType()==UTIMES), prs_arg);
@@ -1216,7 +1216,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t329;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1924 "ncoGrammer.g"
+#line 1925 "ncoGrammer.g"
var1=out_asn(div_asn);
var=ncap_var_var_inc(var1,var2, DIVIDE_ASSIGN ,(div_asn->getType()==UTIMES), prs_arg);
@@ -1237,7 +1237,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t330;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1930 "ncoGrammer.g"
+#line 1931 "ncoGrammer.g"
// Check for RAM variable - if present
// change tree - for example from:
@@ -1288,7 +1288,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t331;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1964 "ncoGrammer.g"
+#line 1965 "ncoGrammer.g"
@@ -1310,7 +1310,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t332;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1969 "ncoGrammer.g"
+#line 1970 "ncoGrammer.g"
bool br;
@@ -1343,7 +1343,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t333;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1987 "ncoGrammer.g"
+#line 1988 "ncoGrammer.g"
// The lexer has appended the index of the function to the function name m - (name#index)
// the index is into fmc_vtr
@@ -1375,7 +1375,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t334;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1998 "ncoGrammer.g"
+#line 1999 "ncoGrammer.g"
// The lexer has appended the index of the function to the function name m - (name#index)
// the index is into fmc_vtr
@@ -1394,7 +1394,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,DIM_ID_SIZE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2008 "ncoGrammer.g"
+#line 2009 "ncoGrammer.g"
string sDim=dval->getText();
dmn_sct *dmn_fd;
@@ -1444,7 +1444,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,ATT_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2080 "ncoGrammer.g"
+#line 2081 "ncoGrammer.g"
NcapVar *Nvar=NULL;
@@ -1484,7 +1484,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,VALUE_LIST);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2111 "ncoGrammer.g"
+#line 2112 "ncoGrammer.g"
var=value_list(vlst);
@@ -1498,7 +1498,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,NSTRING);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2116 "ncoGrammer.g"
+#line 2117 "ncoGrammer.g"
char *tsng;
@@ -1530,7 +1530,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,N4STRING);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2139 "ncoGrammer.g"
+#line 2140 "ncoGrammer.g"
char *tsng;
@@ -1568,7 +1568,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,FLOAT);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2169 "ncoGrammer.g"
+#line 2170 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~float"),(nc_type)NC_FLOAT,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~float"),static_cast<float>(std::strtod(val_float->getText().c_str(),(char **)NULL)));
#line 1574 "ncoTree.cpp"
}
@@ -1580,7 +1580,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,DOUBLE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2171 "ncoGrammer.g"
+#line 2172 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~double"),(nc_type)NC_DOUBLE,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~double"),strtod(val_double->getText().c_str(),(char **)NULL));
#line 1586 "ncoTree.cpp"
}
@@ -1592,7 +1592,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,INT);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2173 "ncoGrammer.g"
+#line 2174 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~int"),(nc_type)NC_INT,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~int"),static_cast<nco_int>(std::strtol(val_int->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1598 "ncoTree.cpp"
}
@@ -1604,7 +1604,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,SHORT);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2175 "ncoGrammer.g"
+#line 2176 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~short"),(nc_type)NC_SHORT,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~short"),static_cast<nco_short>(std::strtol(val_short->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1610 "ncoTree.cpp"
}
@@ -1616,7 +1616,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,BYTE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2177 "ncoGrammer.g"
+#line 2178 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~byte"),(nc_type)NC_BYTE,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~byte"),static_cast<nco_byte>(std::strtol(val_byte->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1622 "ncoTree.cpp"
}
@@ -1628,7 +1628,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,UBYTE);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2182 "ncoGrammer.g"
+#line 2183 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~ubyte"),(nc_type)NC_UBYTE,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~ubyte"),static_cast<nco_ubyte>(std::strtoul(val_ubyte->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1634 "ncoTree.cpp"
}
@@ -1640,7 +1640,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,USHORT);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2186 "ncoGrammer.g"
+#line 2187 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~ushort"),(nc_type)NC_USHORT,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~ushort"),static_cast<nco_ushort>(std::strtoul(val_ushort->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1646 "ncoTree.cpp"
}
@@ -1652,7 +1652,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,UINT);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2188 "ncoGrammer.g"
+#line 2189 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~uint"),(nc_type)NC_UINT,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~uint"),static_cast<nco_uint>(std::strtoul(val_uint->getText().c_str(),(char **)NULL,NCO_SNG_CNV_BASE10)));
#line 1658 "ncoTree.cpp"
}
@@ -1664,7 +1664,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,INT64);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2190 "ncoGrammer.g"
+#line 2191 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~int64"),(nc_type)NC_INT64,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~int64"),sng2nbr(val_int64->getText(),nco_int64_CEWI));
#line 1670 "ncoTree.cpp"
}
@@ -1676,7 +1676,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,UINT64);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2194 "ncoGrammer.g"
+#line 2195 "ncoGrammer.g"
if(prs_arg->ntl_scn) var=ncap_sclr_var_mk(static_cast<std::string>("~uint64"),(nc_type)NC_UINT64,false); else var=ncap_sclr_var_mk(static_cast<std::string>("~uint64"),sng2nbr(val_uint64->getText(),nco_uint64_CEWI));
#line 1682 "ncoTree.cpp"
}
@@ -1722,7 +1722,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t276;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1845 "ncoGrammer.g"
+#line 1846 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, PLUS );
#line 1728 "ncoTree.cpp"
}
@@ -1767,7 +1767,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t280;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1847 "ncoGrammer.g"
+#line 1848 "ncoGrammer.g"
var=ncap_var_var_op(var1,var2, MINUS );
#line 1773 "ncoTree.cpp"
}
@@ -1820,7 +1820,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t285;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1848 "ncoGrammer.g"
+#line 1849 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,POST_INC,true,prs_arg);
@@ -1875,7 +1875,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t291;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1851 "ncoGrammer.g"
+#line 1852 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,POST_DEC,true,prs_arg);
@@ -1930,7 +1930,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t297;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1854 "ncoGrammer.g"
+#line 1855 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,INC,true,prs_arg);
@@ -1985,7 +1985,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t303;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1857 "ncoGrammer.g"
+#line 1858 "ncoGrammer.g"
var=ncap_var_var_inc(var1,NULL_CEWI,DEC,true,prs_arg);
@@ -2002,7 +2002,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t310;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1874 "ncoGrammer.g"
+#line 1875 "ncoGrammer.g"
var=ncap_var_var_op(var1,NULL_CEWI, MINUS );
#line 2008 "ncoTree.cpp"
}
@@ -2055,7 +2055,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t338;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2049 "ncoGrammer.g"
+#line 2050 "ncoGrammer.g"
// see if hyperslab limit is a single value
if(lmt->getNumberOfChildren()==1 &&
@@ -2075,7 +2075,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,VAR_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2063 "ncoGrammer.g"
+#line 2064 "ncoGrammer.g"
var=prs_arg->ncap_var_init(v->getText(),true);
@@ -2115,7 +2115,7 @@ var_sct * ncoTree::out(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
bool bram
) {
-#line 1303 "ncoGrammer.g"
+#line 1304 "ncoGrammer.g"
var_sct *var;
#line 2121 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST assign_ntl_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
@@ -2127,7 +2127,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
ANTLR_USE_NAMESPACE(antlr)RefAST att = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST att1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST att2 = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 1303 "ncoGrammer.g"
+#line 1304 "ncoGrammer.g"
const std::string fnc_nm("assign_ntl");
var=NULL_CEWI;
@@ -2172,7 +2172,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t242;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1308 "ncoGrammer.g"
+#line 1309 "ncoGrammer.g"
std::string var_nm;
@@ -2242,7 +2242,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t246;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1337 "ncoGrammer.g"
+#line 1338 "ncoGrammer.g"
int idx;
@@ -2319,7 +2319,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
match(_t,VAR_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1406 "ncoGrammer.g"
+#line 1407 "ncoGrammer.g"
std::string var_nm;
@@ -2389,7 +2389,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t250;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1435 "ncoGrammer.g"
+#line 1436 "ncoGrammer.g"
;
@@ -2434,7 +2434,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t254;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1438 "ncoGrammer.g"
+#line 1439 "ncoGrammer.g"
;
@@ -2446,7 +2446,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
match(_t,ATT_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1441 "ncoGrammer.g"
+#line 1442 "ncoGrammer.g"
//In Initial scan all newly defined atts are flagged as Undefined
@@ -2488,7 +2488,7 @@ var_sct * ncoTree::assign_ntl(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
bool bram
) {
-#line 1461 "ncoGrammer.g"
+#line 1462 "ncoGrammer.g"
var_sct *var;
#line 2494 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST assign_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
@@ -2500,7 +2500,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
ANTLR_USE_NAMESPACE(antlr)RefAST att = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST att1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST att2 = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 1461 "ncoGrammer.g"
+#line 1462 "ncoGrammer.g"
const std::string fnc_nm("assign");
var=NULL_CEWI;
@@ -2545,7 +2545,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t259;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1467 "ncoGrammer.g"
+#line 1468 "ncoGrammer.g"
int idx;
@@ -2779,7 +2779,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t263;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1661 "ncoGrammer.g"
+#line 1662 "ncoGrammer.g"
var_sct *var1;
@@ -2866,7 +2866,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
match(_t,VAR_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1740 "ncoGrammer.g"
+#line 1741 "ncoGrammer.g"
// Set class wide variables
var_sct *var1;
@@ -2961,7 +2961,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t267;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1794 "ncoGrammer.g"
+#line 1795 "ncoGrammer.g"
;
@@ -3006,7 +3006,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t271;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1797 "ncoGrammer.g"
+#line 1798 "ncoGrammer.g"
;
@@ -3018,7 +3018,7 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
match(_t,ATT_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 1800 "ncoGrammer.g"
+#line 1801 "ncoGrammer.g"
var_sct *var1;
@@ -3074,14 +3074,14 @@ var_sct * ncoTree::assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
}
var_sct * ncoTree::out_asn(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 2204 "ncoGrammer.g"
+#line 2205 "ncoGrammer.g"
var_sct *var;
#line 3080 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST out_asn_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vid1 = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST vid = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST att = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2204 "ncoGrammer.g"
+#line 2205 "ncoGrammer.g"
const std::string fnc_nm("assign_asn");
var=NULL_CEWI;
@@ -3104,7 +3104,7 @@ var_sct * ncoTree::out_asn(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t340;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2211 "ncoGrammer.g"
+#line 2212 "ncoGrammer.g"
if(vid1->getFirstChild())
err_prn(fnc_nm,"Invalid Lvalue " +vid1->getText() );
@@ -3125,7 +3125,7 @@ var_sct * ncoTree::out_asn(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,VAR_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2222 "ncoGrammer.g"
+#line 2223 "ncoGrammer.g"
if(vid->getFirstChild())
err_prn(fnc_nm,"Invalid Lvalue " +vid->getText() );
@@ -3146,7 +3146,7 @@ var_sct * ncoTree::out_asn(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
match(_t,ATT_ID);
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2233 "ncoGrammer.g"
+#line 2234 "ncoGrammer.g"
// check "output"
NcapVar *Nvar=NULL;
@@ -3203,12 +3203,12 @@ var_sct * ncoTree::out_asn(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
}
var_sct * ncoTree::value_list(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 2267 "ncoGrammer.g"
+#line 2268 "ncoGrammer.g"
var_sct *var;
#line 3209 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST value_list_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vlst = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2267 "ncoGrammer.g"
+#line 2268 "ncoGrammer.g"
const std::string fnc_nm("value_list");
var=NULL_CEWI;
@@ -3222,7 +3222,7 @@ var_sct * ncoTree::value_list(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = _t->getNextSibling();
}
if ( inputState->guessing==0 ) {
-#line 2272 "ncoGrammer.g"
+#line 2273 "ncoGrammer.g"
char *cp;
@@ -3329,11 +3329,11 @@ var_sct * ncoTree::value_list(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
var_sct * ncoTree::value_list_string(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
std::vector<var_sct*> &exp_vtr
) {
-#line 2363 "ncoGrammer.g"
+#line 2364 "ncoGrammer.g"
var_sct *var;
#line 3335 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST value_list_string_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
-#line 2363 "ncoGrammer.g"
+#line 2364 "ncoGrammer.g"
const std::string fnc_nm("value_list_string");
var=NULL_CEWI;
@@ -3342,7 +3342,7 @@ var_sct * ncoTree::value_list_string(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
try { // for error handling
if ( inputState->guessing==0 ) {
-#line 2369 "ncoGrammer.g"
+#line 2370 "ncoGrammer.g"
int idx;
int nbr_lst;
@@ -3410,12 +3410,12 @@ var_sct * ncoTree::value_list_string(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
bool ncoTree::where_assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
var_sct *var_msk
) {
-#line 2420 "ncoGrammer.g"
+#line 2421 "ncoGrammer.g"
bool bret;
#line 3416 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST where_assign_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vid = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2420 "ncoGrammer.g"
+#line 2421 "ncoGrammer.g"
const std::string fnc_nm("where_assign");
var_sct *var_rhs;
@@ -3442,7 +3442,7 @@ bool ncoTree::where_assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t345;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2426 "ncoGrammer.g"
+#line 2427 "ncoGrammer.g"
bool bfr=false;
@@ -3591,12 +3591,12 @@ bool ncoTree::where_assign(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
}
var_sct * ncoTree::var_lmt_one(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 2561 "ncoGrammer.g"
+#line 2562 "ncoGrammer.g"
var_sct *var;
#line 3597 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST var_lmt_one_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vid = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2561 "ncoGrammer.g"
+#line 2562 "ncoGrammer.g"
const std::string fnc_nm("var_lmt_one");
var=NULL_CEWI;
@@ -3626,7 +3626,7 @@ var_sct * ncoTree::var_lmt_one(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t348;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2567 "ncoGrammer.g"
+#line 2568 "ncoGrammer.g"
int idx;
@@ -3746,12 +3746,12 @@ var_sct * ncoTree::var_lmt_one(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
var_sct * ncoTree::var_lmt_one_lhs(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
bool bram
) {
-#line 2671 "ncoGrammer.g"
+#line 2672 "ncoGrammer.g"
var_sct *var;
#line 3752 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST var_lmt_one_lhs_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vid = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2671 "ncoGrammer.g"
+#line 2672 "ncoGrammer.g"
const std::string fnc_nm("var_lmt_one_lhs");
var=NULL_CEWI;
@@ -3781,7 +3781,7 @@ var_sct * ncoTree::var_lmt_one_lhs(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
_t = __t352;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2677 "ncoGrammer.g"
+#line 2678 "ncoGrammer.g"
int idx;
int var_id;
@@ -3943,13 +3943,13 @@ var_sct * ncoTree::var_lmt_one_lhs(ANTLR_USE_NAMESPACE(antlr)RefAST _t,
}
var_sct * ncoTree::var_lmt(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
-#line 2824 "ncoGrammer.g"
+#line 2825 "ncoGrammer.g"
var_sct *var;
#line 3949 "ncoTree.cpp"
ANTLR_USE_NAMESPACE(antlr)RefAST var_lmt_AST_in = (_t == ANTLR_USE_NAMESPACE(antlr)RefAST(ASTNULL)) ? ANTLR_USE_NAMESPACE(antlr)nullAST : _t;
ANTLR_USE_NAMESPACE(antlr)RefAST vid = ANTLR_USE_NAMESPACE(antlr)nullAST;
ANTLR_USE_NAMESPACE(antlr)RefAST lmt = ANTLR_USE_NAMESPACE(antlr)nullAST;
-#line 2824 "ncoGrammer.g"
+#line 2825 "ncoGrammer.g"
const std::string fnc_nm("var_lmt");
var=NULL_CEWI;
@@ -3967,7 +3967,7 @@ var_sct * ncoTree::var_lmt(ANTLR_USE_NAMESPACE(antlr)RefAST _t) {
_t = __t356;
_t = _t->getNextSibling();
if ( inputState->guessing==0 ) {
-#line 2829 "ncoGrammer.g"
+#line 2830 "ncoGrammer.g"
bool bram; // Check for a RAM variable
bool bnrm;
diff --git a/src/nco++/ncoTree.hpp b/src/nco++/ncoTree.hpp
index 923c715..8257546 100644
--- a/src/nco++/ncoTree.hpp
+++ b/src/nco++/ncoTree.hpp
@@ -8,13 +8,14 @@
#line 1 "ncoGrammer.g"
-/* $Header: /cvsroot/nco/nco/src/nco++/ncoTree.hpp,v 1.150 2014/05/02 03:08:27 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/ncoTree.hpp,v 1.155 2014/06/16 23:04:52 zender Exp $ */
/* Purpose: ANTLR Grammar and support files for ncap2 */
-/* Copyright (C) 2005--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// C Standard Headers
#include <assert.h>
@@ -47,10 +48,10 @@
ANTLR_USING_NAMESPACE(std);
ANTLR_USING_NAMESPACE(antlr);
-#line 51 "ncoTree.hpp"
+#line 52 "ncoTree.hpp"
class CUSTOM_API ncoTree : public ANTLR_USE_NAMESPACE(antlr)TreeParser, public ncoParserTokenTypes
{
-#line 619 "ncoGrammer.g"
+#line 620 "ncoGrammer.g"
private:
@@ -385,7 +386,7 @@ RefAST nco_dupList(RefAST tr){
*/
return otr;
}
-#line 55 "ncoTree.hpp"
+#line 56 "ncoTree.hpp"
public:
ncoTree();
static void initializeASTFactory( ANTLR_USE_NAMESPACE(antlr)ASTFactory& factory );
diff --git a/src/nco++/prs_cls.cc b/src/nco++/prs_cls.cc
index 8f620b2..078679b 100644
--- a/src/nco++/prs_cls.cc
+++ b/src/nco++/prs_cls.cc
@@ -1,11 +1,12 @@
-/* $Header: /cvsroot/nco/nco/src/nco++/prs_cls.cc,v 1.33 2014/02/12 17:39:51 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco++/prs_cls.cc,v 1.34 2014/06/15 21:06:25 zender Exp $ */
/* Purpose: netCDF arithmetic processor */
/* prs_cls -- symbol table - class methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Standard C++ headers
#include <algorithm>
diff --git a/src/nco++/prs_cls.hh b/src/nco++/prs_cls.hh
index 150a299..bdd447e 100644
--- a/src/nco++/prs_cls.hh
+++ b/src/nco++/prs_cls.hh
@@ -2,8 +2,9 @@
/* prs_cls -- symbol table - data members & class methods */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#ifndef PRS_CLS_HH
#define PRS_CLS_HH
diff --git a/src/nco++/sdo_utl.cc b/src/nco++/sdo_utl.cc
index 911a3e3..6dc3cb2 100644
--- a/src/nco++/sdo_utl.cc
+++ b/src/nco++/sdo_utl.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco++/sdo_utl.cc,v 1.6 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco++/sdo_utl.cc,v 1.7 2014/06/15 21:06:25 zender Exp $
// Purpose: Implementation (declaration) of SDO stand-alone utilities
-/* Copyright (C) 1997--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "sdo_utl.hh" // SDO stand-alone utilities: dbg/err/wrn_prn()
diff --git a/src/nco++/sdo_utl.hh b/src/nco++/sdo_utl.hh
index b17057d..43b87d6 100644
--- a/src/nco++/sdo_utl.hh
+++ b/src/nco++/sdo_utl.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco++/sdo_utl.hh,v 1.6 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco++/sdo_utl.hh,v 1.7 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of SDO stand-alone utilities
-/* Copyright (C) 1997--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Source: Routines are subset of CSZ's ~/c++/utl.[cc/hh]
diff --git a/src/nco/libnco.h b/src/nco/libnco.h
index 3e6bb7a..f16514f 100644
--- a/src/nco/libnco.h
+++ b/src/nco/libnco.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/libnco.h,v 1.59 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/libnco.h,v 1.60 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: netCDF Operator (NCO) library */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Most libnco.h headers depend on netcdf.h and nco_netcdf.h headers */
diff --git a/src/nco/mpncbo.c b/src/nco/mpncbo.c
index 8abd5eb..60bb72c 100644
--- a/src/nco/mpncbo.c
+++ b/src/nco/mpncbo.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncbo.c,v 1.142 2014/01/06 06:46:04 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncbo.c,v 1.146 2014/07/15 18:48:54 zender Exp $ */
/* mpncbo -- netCDF binary operator */
@@ -6,17 +6,15 @@
from two input netCDF files and output them to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -127,8 +125,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
- const char * const CVS_Id="$Id: mpncbo.c,v 1.142 2014/01/06 06:46:04 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.142 $";
+ const char * const CVS_Id="$Id: mpncbo.c,v 1.146 2014/07/15 18:48:54 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.146 $";
const char * const opt_sht_lst="3467ACcD:d:FhL:l:Oo:p:rRSt:v:X:xy:-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -220,7 +218,6 @@ main(int argc,char **argv)
var_sct **var_prc_out;
#ifdef ENABLE_MPI
- /* #if defined(ENABLE_MPI) && !defined(ENABLE_NETCDF4) */
/* Declare all MPI-specific variables here */
MPI_Status mpi_stt; /* [enm] Status check to decode msg_tag_typ */
@@ -418,6 +415,7 @@ main(int argc,char **argv)
case 'D': /* The debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -689,7 +687,7 @@ main(int argc,char **argv)
rcd=nco_var_lst_mrg(&var_prc_1,&var_prc_2,&nbr_var_prc_1,&nbr_var_prc_2);
/* Make output and input files consanguinous */
- if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt_1;
+ if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt_1;
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
@@ -751,7 +749,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,rnk_mgr,MPI_COMM_WORLD);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,rnk_mgr,MPI_COMM_WORLD);
if(prc_rnk == rnk_mgr){ /* MPI manager code */
diff --git a/src/nco/mpncecat.c b/src/nco/mpncecat.c
index 321ebd7..af82f91 100644
--- a/src/nco/mpncecat.c
+++ b/src/nco/mpncecat.c
@@ -1,21 +1,19 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncecat.c,v 1.119 2014/01/06 06:46:04 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncecat.c,v 1.124 2014/07/15 18:48:54 zender Exp $ */
/* ncecat -- netCDF ensemble concatenator */
/* Purpose: Join variables across files into a new record variable */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -52,8 +50,8 @@
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
#ifdef ENABLE_MPI
-#include <mpi.h> /* MPI definitions */
-#include "nco_mpi.h" /* MPI utilities */
+# include <mpi.h> /* MPI definitions */
+# include "nco_mpi.h" /* MPI utilities */
#endif /* !ENABLE_MPI */
/* Personal headers */
@@ -102,8 +100,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
- const char * const CVS_Id="$Id: mpncecat.c,v 1.119 2014/01/06 06:46:04 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.119 $";
+ const char * const CVS_Id="$Id: mpncecat.c,v 1.124 2014/07/15 18:48:54 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.124 $";
const char * const opt_sht_lst="3467ACcD:d:FHhL:l:n:Oo:p:rRSt:u:v:X:x-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -176,9 +174,7 @@ main(int argc,char **argv)
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
-# if defined(ENABLE_NETCDF4) || defined(ENABLE_PNETCDF)
MPI_Info mpi_nfo=MPI_INFO_NULL; /* [sct] File geometry hints */
-# endif /* !ENABLE_NETCDF4 || !ENABLE_PNETCDF */
MPI_Status mpi_stt; /* [enm] Status check to decode msg_tag_typ */
nco_bool TKN_WRT_FREE=True; /* [flg] Write-access to output file is available */
@@ -374,6 +370,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -715,7 +712,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,mpi_cmm);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,mpi_cmm);
if(prc_rnk == rnk_mgr){ /* MPI manager code */
@@ -753,9 +750,6 @@ main(int argc,char **argv)
#ifdef ENABLE_NETCDF4
rcd=nco_open_par(fl_in,NC_MPIIO|NC_NETCDF4,mpi_cmm,mpi_nfo,&in_id);
#endif /* !ENABLE_NETCDF4 */
-#ifdef ENABLE_PNETCDF
- rcd=ncompi_open(mpi_cmm,fl_in,NC_NOWRITE,mpi_nfo,&in_id);
-#endif /* !ENABLE_PNETCDF */
#endif /* !0 */
/* Perform various error-checks on input file */
if(False) (void)nco_fl_cmp_err_chk();
diff --git a/src/nco/mpncflint.c b/src/nco/mpncflint.c
index def752f..5eca1ae 100644
--- a/src/nco/mpncflint.c
+++ b/src/nco/mpncflint.c
@@ -1,21 +1,19 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncflint.c,v 1.120 2014/01/06 06:46:04 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncflint.c,v 1.123 2014/07/15 18:48:54 zender Exp $ */
/* mpncflint -- netCDF file interpolator */
/* Purpose: Linearly interpolate a third netCDF file from two input files */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -113,8 +111,8 @@ main(int argc,char **argv)
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
- const char * const CVS_Id="$Id: mpncflint.c,v 1.120 2014/01/06 06:46:04 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.120 $";
+ const char * const CVS_Id="$Id: mpncflint.c,v 1.123 2014/07/15 18:48:54 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.123 $";
const char * const opt_sht_lst="3467ACcD:d:Fhi:L:l:Oo:p:rRSt:v:xw:-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -388,6 +386,7 @@ main(int argc,char **argv)
case 'D': /* The debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -676,7 +675,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,MPI_COMM_WORLD);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,MPI_COMM_WORLD);
if(prc_rnk == rnk_mgr){ /* MPI manager code */
diff --git a/src/nco/mpncpdq.c b/src/nco/mpncpdq.c
index b73dda7..395dca9 100644
--- a/src/nco/mpncpdq.c
+++ b/src/nco/mpncpdq.c
@@ -1,21 +1,19 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncpdq.c,v 1.114 2014/01/06 06:46:04 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncpdq.c,v 1.117 2014/07/15 18:48:54 zender Exp $ */
/* mpncpdq -- netCDF pack, re-dimension, query */
/* Purpose: Pack, re-dimension, query single netCDF file and output to a single file */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -119,8 +117,8 @@ main(int argc,char **argv)
char add_fst_sng[]="add_offset"; /* [sng] Unidata standard string for add offset */
char scl_fct_sng[]="scale_factor"; /* [sng] Unidata standard string for scale factor */
- const char * const CVS_Id="$Id: mpncpdq.c,v 1.114 2014/01/06 06:46:04 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.114 $";
+ const char * const CVS_Id="$Id: mpncpdq.c,v 1.117 2014/07/15 18:48:54 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.117 $";
const char * const opt_sht_lst="3467Aa:CcD:d:FhL:l:M:Oo:P:p:RrSt:v:Ux-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -399,6 +397,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -898,7 +897,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,MPI_COMM_WORLD);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,MPI_COMM_WORLD);
#endif /* !ENABLE_MPI */
diff --git a/src/nco/mpncra.c b/src/nco/mpncra.c
index df9a929..d6858f5 100644
--- a/src/nco/mpncra.c
+++ b/src/nco/mpncra.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncra.c,v 1.150 2014/01/06 06:46:05 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncra.c,v 1.153 2014/07/15 18:48:54 zender Exp $ */
/* This single source file may be called as three separate executables:
ncra -- netCDF record averager
@@ -10,17 +10,15 @@
to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -152,8 +150,8 @@ main(int argc,char **argv)
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
- const char * const CVS_Id="$Id: mpncra.c,v 1.150 2014/01/06 06:46:05 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.150 $";
+ const char * const CVS_Id="$Id: mpncra.c,v 1.153 2014/07/15 18:48:54 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.153 $";
const char * const opt_sht_lst="3467ACcD:d:FHhL:l:n:Oo:p:P:rRSt:v:xY:y:-:";
dmn_sct **dim;
@@ -431,6 +429,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -733,7 +732,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,MPI_COMM_WORLD);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,MPI_COMM_WORLD);
#endif /* !ENABLE_MPI */
diff --git a/src/nco/mpncwa.c b/src/nco/mpncwa.c
index 40d7745..f36343b 100644
--- a/src/nco/mpncwa.c
+++ b/src/nco/mpncwa.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/mpncwa.c,v 1.142 2014/01/06 06:46:05 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/mpncwa.c,v 1.146 2014/07/15 18:48:55 zender Exp $ */
/* mpncwa -- netCDF weighted averager */
@@ -6,17 +6,15 @@
in a single input netCDF file and output them to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -128,8 +126,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char *wgt_nm=NULL;
- const char * const CVS_Id="$Id: mpncwa.c,v 1.142 2014/01/06 06:46:05 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.142 $";
+ const char * const CVS_Id="$Id: mpncwa.c,v 1.146 2014/07/15 18:48:55 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.146 $";
const char * const opt_sht_lst="3467Aa:B:bCcD:d:FhIL:l:M:m:nNOo:p:rRST:t:v:Ww:xy:-:";
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -455,6 +453,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -830,7 +829,7 @@ main(int argc,char **argv)
/* Manager obtains output filename and broadcasts to workers */
if(prc_rnk == rnk_mgr) fl_nm_lng=(int)strlen(fl_out_tmp);
MPI_Bcast(&fl_nm_lng,1,MPI_INT,0,MPI_COMM_WORLD);
- if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)malloc((fl_nm_lng+1)*sizeof(char));
+ if(prc_rnk != rnk_mgr) fl_out_tmp=(char *)nco_malloc((fl_nm_lng+1)*sizeof(char));
MPI_Bcast(fl_out_tmp,fl_nm_lng+1,MPI_CHAR,0,MPI_COMM_WORLD);
if(prc_rnk == rnk_mgr){ /* MPI manager code */
@@ -1334,6 +1333,7 @@ main(int argc,char **argv)
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
+ if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
diff --git a/src/nco/ncap.c b/src/nco/ncap.c
index 4bb84ac..755836b 100644
--- a/src/nco/ncap.c
+++ b/src/nco/ncap.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncap.c,v 1.284 2014/01/06 19:00:49 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncap.c,v 1.287 2014/07/09 20:47:53 zender Exp $ */
/* ncap -- netCDF arithmetic processor */
/* Purpose: Compute user-defined derived fields using forward algebraic notation applied to netCDF files */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -128,8 +126,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
- const char * const CVS_Id="$Id: ncap.c,v 1.284 2014/01/06 19:00:49 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.284 $";
+ const char * const CVS_Id="$Id: ncap.c,v 1.287 2014/07/09 20:47:53 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.287 $";
const char * const opt_sht_lst="3467ACcD:FfhL:l:n:Oo:p:Rrs:S:vx-:"; /* [sng] Single letter command line options */
cnk_dmn_sct **cnk_dmn=NULL_CEWI;
@@ -424,6 +422,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -964,8 +963,8 @@ main(int argc,char **argv)
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncap.h b/src/nco/ncap.h
index 05d6509..feabede 100644
--- a/src/nco/ncap.h
+++ b/src/nco/ncap.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncap.h,v 1.99 2014/03/05 22:02:43 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncap.h,v 1.100 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: netCDF arithmetic processor definitions and function prototypes for ncap.c, ncap_utl.c, ncap_lex.l, and ncap_yacc.y */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "ncap.h" *//* netCDF arithmetic processor-specific definitions (symbol table, ...) */
diff --git a/src/nco/ncap_utl.c b/src/nco/ncap_utl.c
index 807ee19..8b9683b 100644
--- a/src/nco/ncap_utl.c
+++ b/src/nco/ncap_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncap_utl.c,v 1.158 2014/02/04 22:40:20 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncap_utl.c,v 1.159 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: netCDF arithmetic processor */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <assert.h>
#include "ncap.h" /* netCDF arithmetic processor */
diff --git a/src/nco/ncap_yacc.y b/src/nco/ncap_yacc.y
index 66a316a..6bfc4ad 100644
--- a/src/nco/ncap_yacc.y
+++ b/src/nco/ncap_yacc.y
@@ -1,15 +1,13 @@
-%{ /* $Header: /cvsroot/nco/nco/src/nco/ncap_yacc.y,v 1.67 2014/02/04 22:40:20 zender Exp $ -*-C-*- */
+%{ /* $Header: /cvsroot/nco/nco/src/nco/ncap_yacc.y,v 1.68 2014/06/17 00:10:32 zender Exp $ -*-C-*- */
/* Begin C declarations section */
/* Purpose: Grammar parser for ncap */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
diff --git a/src/nco/ncatted.c b/src/nco/ncatted.c
index 1b30894..bc10b1d 100644
--- a/src/nco/ncatted.c
+++ b/src/nco/ncatted.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncatted.c,v 1.187 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncatted.c,v 1.193 2014/07/11 20:55:45 zender Exp $ */
/* ncatted -- netCDF attribute editor */
/* Purpose: Add, create, delete, or overwrite attributes in a netCDF file */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -123,8 +121,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
#define MAIN_PROGRAM_FILE
@@ -158,8 +174,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncatted.c,v 1.187 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.187 $";
+ const char * const CVS_Id="$Id: ncatted.c,v 1.193 2014/07/11 20:55:45 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.193 $";
const char * const opt_sht_lst="Aa:D:hl:Oo:p:Rr-:";
#if defined(__cplusplus) || defined(PGI_CC)
@@ -188,6 +204,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -240,6 +263,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -281,6 +312,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
@@ -367,7 +399,7 @@ main(int argc,char **argv)
/* Get number of variables in file */
(void)nco_inq(nc_id,(int *)NULL,&nbr_var_fl,(int *)NULL,(int *)NULL);
- /* Initialize traversal table */
+ /* Initialize traversal table */
trv_tbl_init(&trv_tbl);
/* Construct GTT (Group Traversal Table) */
@@ -409,7 +441,7 @@ main(int argc,char **argv)
} /* Loop input names */
- /* Catenate the timestamped command line to the "history" global attribute */
+ /* Catenate the time-stamped command line to the "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(nc_id,cmd_ln);
/* Take output file out of define mode */
@@ -452,11 +484,15 @@ main(int argc,char **argv)
trv_tbl_free(trv_tbl);
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncbo.c b/src/nco/ncbo.c
index 4787f8a..8108623 100644
--- a/src/nco/ncbo.c
+++ b/src/nco/ncbo.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncbo.c,v 1.301 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncbo.c,v 1.307 2014/07/11 20:55:45 zender Exp $ */
/* ncbo -- netCDF binary operator */
@@ -6,17 +6,15 @@
from two input netCDF files and output them to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -74,10 +72,24 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
#ifdef ENABLE_MPI
# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
# include "nco_mpi.h" /* MPI utilities */
#endif /* !ENABLE_MPI */
@@ -132,8 +144,8 @@ main(int argc,char **argv)
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncbo.c,v 1.301 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.301 $";
+ const char * const CVS_Id="$Id: ncbo.c,v 1.307 2014/07/11 20:55:45 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.307 $";
const char * const opt_sht_lst="3467ACcD:d:FG:g:hL:l:Oo:p:rRt:v:X:xzy:-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -216,6 +228,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne2=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -306,7 +325,6 @@ main(int argc,char **argv)
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
-
int opt_idx=0; /* Index of current long option into opt_lng array */
nbr_gpe_nm=0;
@@ -320,6 +338,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -407,6 +433,7 @@ main(int argc,char **argv)
case 'D': /* The debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -546,7 +573,7 @@ main(int argc,char **argv)
for(int lmt_idx=0;lmt_idx<lmt_nbr;lmt_idx++) flg_dne[lmt_idx]=flg_dne1[lmt_idx];
for(int lmt_idx=0;lmt_idx<lmt_nbr;lmt_idx++) flg_dne[lmt_nbr+lmt_idx]=flg_dne2[lmt_idx];
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
@@ -583,7 +610,7 @@ main(int argc,char **argv)
/* Copy global attributes from file 1 */
(void)nco_att_cpy(in_id_1,out_id,NC_GLOBAL,NC_GLOBAL,(nco_bool)True);
- /* Catenate timestamped command line to "history" global attribute */
+ /* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
@@ -655,12 +682,15 @@ main(int argc,char **argv)
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
-
} /* end main() */
diff --git a/src/nco/ncecat.c b/src/nco/ncecat.c
index 9a8488a..a7cfb18 100644
--- a/src/nco/ncecat.c
+++ b/src/nco/ncecat.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncecat.c,v 1.366 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncecat.c,v 1.372 2014/08/21 18:22:44 zender Exp $ */
/* ncecat -- netCDF ensemble concatenator */
/* Purpose: Join variables across files with new record variable or aggregate files as groups */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -62,8 +60,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
-/* 3rd party vendors */
-#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
+/* 3rd party vendors */
+#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* Personal headers */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
@@ -124,8 +140,8 @@ main(int argc,char **argv)
char grp_out_sfx[NCO_GRP_OUT_SFX_LNG+1L];
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncecat.c,v 1.366 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.366 $";
+ const char * const CVS_Id="$Id: ncecat.c,v 1.372 2014/08/21 18:22:44 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.372 $";
const char * const opt_sht_lst="3467ACcD:d:Fg:G:HhL:l:Mn:Oo:p:rRt:u:v:X:x-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -200,6 +216,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -234,6 +257,7 @@ main(int argc,char **argv)
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
+ {"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
@@ -308,6 +332,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -400,6 +432,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -539,7 +572,7 @@ main(int argc,char **argv)
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
@@ -824,7 +857,7 @@ main(int argc,char **argv)
/* Write variable into current record in output file */
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,var_trv->grp_nm_fll,&grp_out_id);
/* Get variable ID */
@@ -912,11 +945,15 @@ main(int argc,char **argv)
} /* RECORD_AGGREGATE */
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncflint.c b/src/nco/ncflint.c
index 0af0b11..9bbd067 100644
--- a/src/nco/ncflint.c
+++ b/src/nco/ncflint.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncflint.c,v 1.290 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncflint.c,v 1.295 2014/07/15 18:48:55 zender Exp $ */
/* ncflint -- netCDF file interpolator */
/* Purpose: Linearly interpolate a third netCDF file from two input files */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -60,8 +58,27 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
-/* 3rd party vendors */
-#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
+/* 3rd party vendors */
+#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
+
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
#define MAIN_PROGRAM_FILE
#include "libnco.h" /* netCDF Operator (NCO) library */
@@ -116,8 +133,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncflint.c,v 1.290 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.290 $";
+ const char * const CVS_Id="$Id: ncflint.c,v 1.295 2014/07/15 18:48:55 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.295 $";
const char * const opt_sht_lst="3467ACcD:d:Fg:G:hi:L:l:Oo:p:rRt:v:X:xw:-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -203,6 +220,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -307,6 +331,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -394,6 +426,7 @@ main(int argc,char **argv)
case 'D': /* The debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -561,7 +594,7 @@ main(int argc,char **argv)
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id_1,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
@@ -754,7 +787,7 @@ main(int argc,char **argv)
nco_exit(EXIT_FAILURE);
} /* endif */
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id_1,var_trv_1->grp_nm_fll,&grp_id_1);
(void)nco_inq_grp_full_ncid(in_id_2,var_trv_2->grp_nm_fll,&grp_id_2);
@@ -799,7 +832,7 @@ main(int argc,char **argv)
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv_1->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv_1->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
@@ -887,11 +920,15 @@ main(int argc,char **argv)
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncks.c b/src/nco/ncks.c
index d9680b4..34debed 100644
--- a/src/nco/ncks.c
+++ b/src/nco/ncks.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncks.c,v 1.718 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncks.c,v 1.737 2014/07/15 18:48:55 zender Exp $ */
/* ncks -- netCDF Kitchen Sink */
@@ -6,11 +6,9 @@
Print them to screen, or copy them to a new file, or both */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -81,8 +79,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* Personal headers */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
@@ -118,7 +134,7 @@ main(int argc,char **argv)
nco_bool PRN_XML=False; /* [flg] Print XML (NcML) */
nco_bool PRN_XML_LOCATION=True; /* [flg] Print XML location tag */
nco_bool PRN_DMN_IDX_CRD_VAL=True; /* [flg] Print leading dimension/coordinate indices/values Option Q */
- nco_bool PRN_DMN_UNITS=False; /* [flg] Print dimensional units Option u */
+ nco_bool PRN_DMN_UNITS=True; /* [flg] Print dimensional units Option u */
nco_bool PRN_DMN_VAR_NM=True; /* [flg] Print dimension/variable names */
nco_bool PRN_DMN_UNITS_TGL=False; /* [flg] Toggle print dimensional units Option u */
nco_bool PRN_GLB_METADATA=False; /* [flg] Print global metadata */
@@ -167,8 +183,8 @@ main(int argc,char **argv)
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncks.c,v 1.718 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.718 $";
+ const char * const CVS_Id="$Id: ncks.c,v 1.737 2014/07/15 18:48:55 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.737 $";
const char * const opt_sht_lst="34567aABb:CcD:d:FG:g:HhL:l:MmOo:Pp:qQrRs:uv:X:xz-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -227,6 +243,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -237,18 +260,21 @@ main(int argc,char **argv)
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
- {"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
- {"md5_dgs",no_argument,0,0}, /* [flg] Perform MD5 digests */
- {"md5_digest",no_argument,0,0}, /* [flg] Perform MD5 digests */
- {"md5_wrt_att",no_argument,0,0}, /* [flg] Write MD5 digests as attributes */
- {"md5_write_attribute",no_argument,0,0}, /* [flg] Write MD5 digests as attributes */
{"cmp",no_argument,0,0},
{"compiler",no_argument,0,0},
- {"id",no_argument,0,0}, /* [flg] Print normally hidden information, like file, group, and variable IDs */
+ {"copyright",no_argument,0,0},
+ {"cpy",no_argument,0,0},
+ {"license",no_argument,0,0},
+ {"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"hdn",no_argument,0,0}, /* [flg] Print hidden attributes */
{"hidden",no_argument,0,0}, /* [flg] Print hidden attributes */
+ {"id",no_argument,0,0}, /* [flg] Print normally hidden information, like file, group, and variable IDs */
{"lbr",no_argument,0,0},
{"library",no_argument,0,0},
+ {"md5_dgs",no_argument,0,0}, /* [flg] Perform MD5 digests */
+ {"md5_digest",no_argument,0,0}, /* [flg] Perform MD5 digests */
+ {"md5_wrt_att",no_argument,0,0}, /* [flg] Write MD5 digests as attributes */
+ {"md5_write_attribute",no_argument,0,0}, /* [flg] Write MD5 digests as attributes */
{"mpi_implementation",no_argument,0,0},
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
@@ -320,6 +346,8 @@ main(int argc,char **argv)
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
+ {"pnetcdf",no_argument,0,'5'},
+ {"5",no_argument,0,'5'},
{"7",no_argument,0,'7'},
{"abc",no_argument,0,'a'},
{"alphabetize",no_argument,0,'a'},
@@ -335,6 +363,7 @@ main(int argc,char **argv)
{"no-crd",no_argument,0,'C'},
{"data",required_argument,0,'H'},
{"debug",required_argument,0,'D'},
+ {"dbg_lvl",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
@@ -365,6 +394,7 @@ main(int argc,char **argv)
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
+ {"spinlock",no_argument,0,'S'}, /* [flg] Suspend with signal handler to facilitate debugging */
{"sng_fmt",required_argument,0,'s'},
{"string",required_argument,0,'s'},
{"units",no_argument,0,'u'},
@@ -381,6 +411,13 @@ main(int argc,char **argv)
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
+#ifdef _LIBINTL_H
+ setlocale(LC_ALL,""); /* LC_ALL sets all localization tokens to same value */
+ bindtextdomain("nco","/home/zender/share/locale"); /* ${LOCALEDIR} is e.g., /usr/share/locale */
+ /* MO files should be in ${LOCALEDIR}/es/LC_MESSAGES */
+ textdomain("nco"); /* PACKAGE is name of program or library */
+#endif /* not _LIBINTL_H */
+
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
@@ -390,6 +427,22 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+/* MPI I/O: Either Parallel netCDF (PnetCDF) or HDF5-based
+ export NETCDF_ROOT=/usr/local/parallel;export NETCDF_INC=/usr/local/parallel/include;export NETCDF_LIB=/usr/local/parallel/lib;export NETCDF4_ROOT=/usr/local/parallel;
+ cd ~/nco/bld;make MPI=Y;cd -
+ LD_LIBRARY_PATH=/usr/local/parallel/lib\:${LD_LIBRARY_PATH}
+ ldd `which ncks`
+ ncks -O -5 ~/nco/data/in.nc ~/foo.nc # PnetCDF
+ mpiexec -n 1 ncks -O -4 ~/nco/data/in.nc ~/foo.nc # HDF5
+ od -An -c -N4 ~/foo.nc */
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -431,6 +484,10 @@ main(int argc,char **argv)
(void)fprintf(stdout,"%s\n",nco_cmp_get());
nco_exit(EXIT_SUCCESS);
} /* endif "cmp" */
+ if(!strcmp(opt_crr,"cpy") || !strcmp(opt_crr,"copyright") || !strcmp(opt_crr,"license")){
+ (void)nco_cpy_prn();
+ nco_exit(EXIT_SUCCESS);
+ } /* endif "copyright" */
if(!strcmp(opt_crr,"cdl")) PRN_CDL=True; /* [flg] Print CDL */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
@@ -478,7 +535,7 @@ main(int argc,char **argv)
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"secret") || !strcmp(opt_crr,"scr") || !strcmp(opt_crr,"shh")){
- (void)fprintf(stdout,"Hidden/unsupported NCO options:\nCompiler used\t\t--cmp, --compiler\nHidden functions\t--scr, --ssh, --secret\nLibrary used\t\t--lbr, --library\nMemory clean\t\t--mmr_cln, --cln, --clean\nMemory dirty\t\t--mmr_drt, --drt, --dirty\nMPI implementation\t--mpi_implementation\nNameless printing\t--no_nm_prn, --no_dmn_var_nm\nNo-clobber files\t--no_clb, --no-clobber\nPseudonym\t\t--pseudonym, -Y (ncra only)\nStreams\t\t\t--srm\nSysconf\t\t\t--sysconf\nTest UDUnits [...]
+ (void)fprintf(stdout,"Hidden/unsupported NCO options:\nCompiler used\t\t--cmp, --compiler\nCopyright\t\t--cpy, --copyright, --license\nHidden functions\t--scr, --ssh, --secret\nLibrary used\t\t--lbr, --library\nMemory clean\t\t--mmr_cln, --cln, --clean\nMemory dirty\t\t--mmr_drt, --drt, --dirty\nMPI implementation\t--mpi_implementation\nNameless printing\t--no_nm_prn, --no_dmn_var_nm\nNo-clobber files\t--no_clb, --no-clobber\nPseudonym\t\t--pseudonym, -Y (ncra only)\nSpinlock\t\t [...]
nco_exit(EXIT_SUCCESS);
} /* endif "shh" */
if(!strcmp(opt_crr,"srm")) PRN_SRM=True; /* [flg] Print ncStream */
@@ -538,6 +595,7 @@ main(int argc,char **argv)
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '5': /* Print using new print format */
+ fl_out_fmt=NC_FORMAT_CDF5;
PRN_NEW_FMT=!PRN_NEW_FMT;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
@@ -564,6 +622,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -632,6 +691,12 @@ main(int argc,char **argv)
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
+#ifdef ENABLE_MPI
+ case 'S': /* Suspend with signal handler to facilitate debugging */
+ if(signal(SIGUSR1,nco_cnt_run) == SIG_ERR) (void)fprintf(stdout,"%s: ERROR Could not install suspend handler.\n",nco_prg_nm);
+ while(!nco_spn_lck_brk) usleep(nco_spn_lck_us); /* Spinlock. fxm: should probably insert a sched_yield */
+ break;
+#endif /* !ENABLE_MPI */
case 's': /* User specified delimiter string for printed output */
dlm_sng=(char *)strdup(optarg);
break;
@@ -675,6 +740,27 @@ main(int argc,char **argv)
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
+#ifdef _LANGINFO_H
+/* Internationalization i18n
+ Linux Journal 200211 p. 57--59 http://www.linuxjournal.com/article/6176
+ Fedora: http://fedoraproject.org/wiki/How_to_do_I18N_through_gettext
+ cd ~/nco/bld;make I18N=Y
+ cd ~/nco/bld;xgettext --default-domain=nco --join-existing -o ../po/nco.pot ../src/nco/ncks.c ../src/nco/ncra.c
+ for LL in fr es; do
+ mkdir -p ~/share/locale/${LL}/LC_MESSAGES
+ msgfmt ~/nco/po/${LL}/nco.po -o ~/nco/po/${LL}/nco.mo
+ /bin/cp ~/nco/po/${LL}/nco.mo ~/share/locale/${LL}/LC_MESSAGES
+# sudo /bin/cp ~/nco/po/${LL}/nco.mo /usr/share/locale/${LL}/LC_MESSAGES
+ done
+ export LOCALEDIR=${HOME}/share/locale
+ LC_ALL=en ncks -D 1 -O ~/nco/data/in.nc ~/foo.nc
+ LANG=en_GB.utf8 LANGUAGE=en_GB:en:fr_FR:fr LC_ALL=en_GB.utf8 ncks -D 1 -O ~/nco/data/in.nc ~/foo.nc
+ LANG=es ncks -D 1 -O ~/nco/data/in.nc ~/foo.nc
+ LANG=fr_FR.utf8 LANGUAGE=fr_FR:fr:en_GB:en LC_ALL=fr_FR.utf8 ncks -D 1 -O ~/nco/data/in.nc ~/foo.nc */
+ if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stdout,gettext("%s: I18N Current charset = %s\n"),nco_prg_nm,nl_langinfo(CODESET));
+ if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stdout,gettext("%s: I18N This text may appear in a foreign language\n"),nco_prg_nm);
+#endif /* !_LANGINFO_H */
+
/* Initialize traversal table */
(void)trv_tbl_init(&trv_tbl);
@@ -695,7 +781,7 @@ main(int argc,char **argv)
/* Construct GTT (Group Traversal Table), check -v and -g input names and create extraction list*/
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,GRP_XTR_VAR_XCL,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file */
@@ -705,6 +791,12 @@ main(int argc,char **argv)
(void)nco_inq_format(in_id,&fl_in_fmt);
if(fl_out && fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
+#ifdef ENABLE_MPI
+ if(prc_rnk == rnk_mgr) (void)fprintf(stdout,"%s: MPI process rank %d reports %d process%s\n",nco_prg_nm,prc_rnk,prc_nbr,(prc_nbr == 1) ? "" : "es");
+ /* Roll call */
+ (void)fprintf(stdout,"%s: MPI process rank %d reports %d process%s\n",nco_prg_nm,prc_rnk,prc_nbr,(prc_nbr == 1) ? "" : "es");
+#endif /* !ENABLE_MPI */
+
/* Process -z option if requested */
if(GET_LIST){
if(ALPHABETIZE_OUTPUT) trv_tbl_srt(trv_tbl);
@@ -787,14 +879,16 @@ main(int argc,char **argv)
/* Create structure with all chunking information */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_sz_byt,cnk_sz_scl,&cnk);
- if(nco_dbg_lvl == nco_dbg_old) (void)nco_prn_var(in_id,trv_tbl);
-
/* Define extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,PRN_GLB_METADATA,PRN_VAR_METADATA,RETAIN_ALL_DIMS,nco_pck_plc_nil,rec_dmn_nm,trv_tbl);
- /* Catenate timestamped command line to "history" global attribute */
+ /* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
+#ifdef ENABLE_MPI
+ if(prc_rnk == rnk_mgr)
+ if(prc_nbr > 0 && HISTORY_APPEND) (void)nco_mpi_att_cat(out_id,prc_nbr);
+#endif /* !ENABLE_MPI */
/* Turn off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
@@ -823,7 +917,7 @@ main(int argc,char **argv)
if(nco_dbg_lvl_get() == 14){
(void)nco_wrt_trv_tbl(in_id,trv_tbl,True);
(void)nco_wrt_trv_tbl(out_id,trv_tbl,True);
- }
+ } /* endif */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
@@ -832,8 +926,6 @@ main(int argc,char **argv)
nco_bool ALPHA_BY_FULL_GROUP=False; /* [flg] Print alphabetically by full group */
nco_bool ALPHA_BY_STUB_GROUP=True; /* [flg] Print alphabetically by stub group */
- // nco_bool ALPHA_BY_FULL_OBJECT=False; /* [flg] Print alphabetically by full object */
- // nco_bool ALPHA_BY_STUB_OBJECT=False; /* [flg] Print alphabetically by stub object */
char *fl_nm_stub;
char *fl_in_dpl=NULL;
char *sfx_ptr;
@@ -878,9 +970,7 @@ main(int argc,char **argv)
if(prn_flg.xml) prn_flg.nwl_pst_val=False; else prn_flg.nwl_pst_val=True;
prn_flg.dlm_sng=dlm_sng;
prn_flg.ALPHA_BY_FULL_GROUP=ALPHA_BY_FULL_GROUP;
- // prn_flg.ALPHA_BY_FULL_OBJECT=ALPHA_BY_FULL_OBJECT;
prn_flg.ALPHA_BY_STUB_GROUP=ALPHA_BY_STUB_GROUP;
- // prn_flg.ALPHA_BY_STUB_OBJECT=ALPHA_BY_STUB_OBJECT;
prn_flg.FORTRAN_IDX_CNV=FORTRAN_IDX_CNV;
prn_flg.PRN_DMN_IDX_CRD_VAL=PRN_DMN_IDX_CRD_VAL;
prn_flg.PRN_DMN_UNITS=PRN_DMN_UNITS;
@@ -940,33 +1030,21 @@ main(int argc,char **argv)
}else{
- /* New file dump format developed 201307 for CDL, TRD, XML, SRM */
+ /* New file dump format(s) developed 201307 for CDL, JSN, SRM, TRD, XML */
if(PRN_SRM){
+ /* Stream printing is pre-alpha. Great project for volunteers! */
nco_srm_hdr();
goto close_and_free;
} /* !PRN_SRM */
if(ALPHA_BY_FULL_GROUP || ALPHA_BY_STUB_GROUP){
+ /* Ineptly named nco_grp_prn() emits full CDL and XML formats, and partial JSN */
rcd+=nco_grp_prn(in_id,trv_pth,&prn_flg,trv_tbl);
}else{
- trv_sct trv_obj; /* [sct] Traversal table object */
- for(unsigned int obj_idx=0;obj_idx<trv_tbl->nbr;obj_idx++){
- /* Shallow copy to avoid indirection */
- trv_obj=trv_tbl->lst[obj_idx];
- /* Print this group */
- if(trv_obj.nco_typ == nco_obj_typ_grp){
- /* Print dimensions defined in this group */
- // (void)nco_prn_dmn_xtr(in_id,trv_tbl);
- /* Print group attributes */
- //if(PRN_GLB_METADATA) (void)nco_prn_grp_att(in_id,trv_tbl);
- ;
- } /* endif group */
- if(trv_obj.nco_typ == nco_obj_typ_var){
- if(PRN_VAR_METADATA) (void)nco_prn_xtr_mtd(in_id,&prn_flg,trv_tbl);
- if(PRN_VAR_DATA) (void)nco_prn_xtr_val(in_id,&prn_flg,trv_tbl);
- } /* endif variable */
- } /* end loop over obj_idx */
+ /* Place-holder for other options for organization/alphabetization */
+ if(PRN_VAR_METADATA) (void)nco_prn_xtr_mtd(in_id,&prn_flg,trv_tbl);
+ if(PRN_VAR_DATA) (void)nco_prn_xtr_val(in_id,&prn_flg,trv_tbl);
} /* end if */
} /* endif new format */
@@ -1021,12 +1099,15 @@ close_and_free:
rec_dmn_nm_fix=(char *)nco_free(rec_dmn_nm_fix);
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
-
} /* end main() */
diff --git a/src/nco/nco.h b/src/nco/nco.h
index 6001ff9..55ff133 100644
--- a/src/nco/nco.h
+++ b/src/nco/nco.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco.h,v 1.510 2014/05/27 03:26:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco.h,v 1.514 2014/07/07 06:04:22 zender Exp $ */
/* Purpose: netCDF Operator (NCO) definitions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco.h" *//* netCDF Operator (NCO) definitions */
@@ -240,9 +241,25 @@ extern "C" {
/* Compatibility tokens for when NCO compiled with older netcdf.h
It is hard to track where/when many tokens defined
Easiest to individually check for pre-definition of each */
-/* Three compatibility tokens new to netCDF4 netcdf.h: */
+/* Compatibility tokens new to netCDF4 netcdf.h: */
#ifndef NC_NETCDF4
-# define NC_NETCDF4 (0x1000) /* Use netCDF-4/HDF5 format */
+# define NC_NETCDF4 0x1000 /* Use netCDF-4/HDF5 format. Mode flag for nc_create(). */
+#endif
+#ifndef NC_MPIIO
+# define NC_MPIIO 0x2000 /* Turn on MPI I/O. Mode flag for both nc_create() and nc_open(). */
+#endif
+#ifndef NC_MPIPOSIX
+# define NC_MPIPOSIX 0x4000 /* Turn on MPI POSIX I/O. Mode flag for both nc_create() and nc_open(). */
+#endif
+#ifndef NC_PNETCDF
+# define NC_PNETCDF 0x8000 /* Use parallel-netcdf library. Mode flag for nc_open(). */
+#endif
+/* Use these with nc_var_par_access(). */
+#ifndef NC_INDEPENDENT
+# define NC_INDEPENDENT 0
+#endif
+#ifndef NC_COLLECTIVE
+# define NC_COLLECTIVE 1
#endif
#ifndef NC_ENDIAN_NATIVE
# define NC_ENDIAN_NATIVE 0
@@ -315,6 +332,18 @@ extern "C" {
# define NC_FORMAT_DAP4 (6)
#endif
+ /* Three compatibility tokens from pnetcdf.h introduced to NCO 20140604
+ None are used yet */
+#ifndef NC_64BIT_DATA
+# define NC_64BIT_DATA 0x0010 /* CDF-5 format, (64-bit) supported */
+#endif
+#ifndef NC_FORMAT_CDF5
+# define NC_FORMAT_CDF5 5 /* CDF-5 format, with NC_64BIT_DATA. */
+#endif
+#ifndef NC_FORMAT_64BIT_DATA
+# define NC_FORMAT_64BIT_DATA NC_FORMAT_CDF5
+#endif
+
/* Backwards-compatibility error codes for netCDF4
Currently used only in nco_grp_utl.c and nco_netcdf.c */
#ifndef NC_EBADGRPID
diff --git a/src/nco/nco_att_utl.c b/src/nco/nco_att_utl.c
index 00038e5..8e0e661 100644
--- a/src/nco/nco_att_utl.c
+++ b/src/nco/nco_att_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_att_utl.c,v 1.173 2014/05/27 02:04:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_att_utl.c,v 1.174 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Attribute utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_att_utl.h" /* Attribute utilities */
diff --git a/src/nco/nco_att_utl.h b/src/nco/nco_att_utl.h
index 4f0ab25..371a277 100644
--- a/src/nco/nco_att_utl.h
+++ b/src/nco/nco_att_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_att_utl.h,v 1.48 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_att_utl.h,v 1.49 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Attribute utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_att_utl.h" *//* Attribute utilities */
diff --git a/src/nco/nco_aux.c b/src/nco/nco_aux.c
index 705449a..9633f1b 100644
--- a/src/nco/nco_aux.c
+++ b/src/nco/nco_aux.c
@@ -1,8 +1,9 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_aux.c,v 1.81 2014/05/27 02:04:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_aux.c,v 1.83 2014/07/15 18:48:55 zender Exp $ */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Purpose: Support hyperslabbing cell-based grids over coordinate ranges
This works on datasets that contain CF-convention auxiliary coordinate variables.
@@ -424,7 +425,7 @@ nco_aux_evl_trv
*aux_lmt_nbr=0;
- /* Obtain group ID of 'latitude' and 'longitude' from netCDF API using full group name */
+ /* Obtain group ID of 'latitude' and 'longitude' */
(void)nco_inq_grp_full_ncid(nc_id,lat_trv->grp_nm_fll,&grp_id_lat);
(void)nco_inq_grp_full_ncid(nc_id,lon_trv->grp_nm_fll,&grp_id_lon);
@@ -580,7 +581,7 @@ nco_find_lat_lon_trv
assert(var_trv->nco_typ == nco_obj_typ_var);
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
/* Obtain variable ID */
diff --git a/src/nco/nco_aux.h b/src/nco/nco_aux.h
index b808840..5408eab 100644
--- a/src/nco/nco_aux.h
+++ b/src/nco/nco_aux.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_aux.h,v 1.34 2014/05/27 02:04:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_aux.h,v 1.35 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Sub-set cell-based grids using auxiliary coordinate variable */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_aux.h" *//* Auxiliary coordinates */
diff --git a/src/nco/nco_bnr.c b/src/nco/nco_bnr.c
index 5dc44eb..5bef80d 100644
--- a/src/nco/nco_bnr.c
+++ b/src/nco/nco_bnr.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_bnr.c,v 1.26 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_bnr.c,v 1.27 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Binary write utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_bnr.h" /* Binary write utilities */
diff --git a/src/nco/nco_bnr.h b/src/nco/nco_bnr.h
index 34d1512..fa8b97b 100644
--- a/src/nco/nco_bnr.h
+++ b/src/nco/nco_bnr.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_bnr.h,v 1.21 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_bnr.h,v 1.22 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Binary write utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_bnr.h" *//* Binary write utilities */
diff --git a/src/nco/nco_cln_utl.c b/src/nco/nco_cln_utl.c
index ca4f953..feb23d4 100644
--- a/src/nco/nco_cln_utl.c
+++ b/src/nco/nco_cln_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cln_utl.c,v 1.47 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cln_utl.c,v 1.48 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Calendar utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_cln_utl.h" /* Calendar utilities */
diff --git a/src/nco/nco_cln_utl.h b/src/nco/nco_cln_utl.h
index f09bbac..4858273 100644
--- a/src/nco/nco_cln_utl.h
+++ b/src/nco/nco_cln_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cln_utl.h,v 1.35 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cln_utl.h,v 1.36 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Calendar utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cln_utl.h" *//* Calendar utilities */
diff --git a/src/nco/nco_cnf_dmn.c b/src/nco/nco_cnf_dmn.c
index 1ecf4d7..dd71a0d 100644
--- a/src/nco/nco_cnf_dmn.c
+++ b/src/nco/nco_cnf_dmn.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_dmn.c,v 1.94 2014/02/18 17:44:07 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_dmn.c,v 1.95 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Conform dimensions between variables */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_cnf_dmn.h" /* Conform dimensions */
diff --git a/src/nco/nco_cnf_dmn.h b/src/nco/nco_cnf_dmn.h
index 37c20a8..48cc850 100644
--- a/src/nco/nco_cnf_dmn.h
+++ b/src/nco/nco_cnf_dmn.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_dmn.h,v 1.39 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_dmn.h,v 1.40 2014/06/15 21:06:21 zender Exp $ */
/* Purpose: Conform dimensions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cnf_dmn.h" *//* Conform dimensions */
diff --git a/src/nco/nco_cnf_typ.c b/src/nco/nco_cnf_typ.c
index a6d2c26..259435b 100644
--- a/src/nco/nco_cnf_typ.c
+++ b/src/nco/nco_cnf_typ.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_typ.c,v 1.76 2014/02/19 21:36:44 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_typ.c,v 1.77 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Conform variable types */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_cnf_typ.h" /* Conform variable types */
diff --git a/src/nco/nco_cnf_typ.h b/src/nco/nco_cnf_typ.h
index d4666c6..68e1c55 100644
--- a/src/nco/nco_cnf_typ.h
+++ b/src/nco/nco_cnf_typ.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_typ.h,v 1.42 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnf_typ.h,v 1.43 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Conform variable types */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cnf_typ.h" *//* Conform variable types */
diff --git a/src/nco/nco_cnk.c b/src/nco/nco_cnk.c
index a233dd7..c4edaad 100644
--- a/src/nco/nco_cnk.c
+++ b/src/nco/nco_cnk.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnk.c,v 1.122 2014/05/20 05:53:20 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnk.c,v 1.128 2014/08/22 01:01:21 zender Exp $ */
/* Purpose: NCO utilities for chunking */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
ncks -O -4 -D 4 --cnk_scl=8 ~/nco/data/in.nc ~/foo.nc
@@ -85,6 +86,8 @@ nco_cnk_plc_sng_get /* [fnc] Convert chunking policy enum to string */
return "g2d";
case nco_cnk_plc_g3d:
return "g3d";
+ case nco_cnk_plc_r1d:
+ return "r1d";
case nco_cnk_plc_xpl:
return "xpl";
case nco_cnk_plc_xst:
@@ -181,9 +184,18 @@ nco_cnk_ini /* [fnc] Create structure with all chunking information */
/* Make uniform list of user-specified per-dimension chunksizes */
if(cnk->cnk_nbr > 0) cnk->cnk_dmn=nco_cnk_prs(cnk_nbr,cnk_arg);
- /* Set actual chunk policy and map to defaults as necessary */
- if(cnk_map == nco_cnk_map_nil) cnk->cnk_map=nco_cnk_map_get((char *)NULL);
- if(cnk_plc == nco_cnk_plc_nil) cnk->cnk_plc=nco_cnk_plc_get((char *)NULL);
+ /* Set actual chunk policy and map to defaults as necessary
+ 20140821: Until today, defaults for map and policy were set independently
+ Now we consider four distinct cases:
+ 1. Neither map nor policy was explicitly set, and something else, e.g., size, was
+ 2. User set map not policy
+ 3. User set policy not map */
+ if(cnk->flg_usr_rqs && (cnk_map == nco_cnk_map_nil) && (cnk_plc == nco_cnk_plc_nil)){
+ cnk->cnk_map=nco_cnk_map_rd1;
+ cnk->cnk_plc=nco_cnk_plc_g2d;
+ } /* endif */
+ if(cnk_map == nco_cnk_map_nil && cnk_plc != nco_cnk_plc_nil) cnk->cnk_map=nco_cnk_map_rd1;
+ if(cnk_plc == nco_cnk_plc_nil && cnk_map != nco_cnk_map_nil) cnk->cnk_plc=nco_cnk_plc_g2d;
return rcd;
} /* end nco_cnk_ini() */
@@ -294,14 +306,15 @@ nco_cnk_map_get /* [fnc] Convert user-specified chunking map to key */
(const char *nco_cnk_map_sng) /* [sng] User-specified chunking map */
{
/* Purpose: Convert user-specified string to chunking map
- Return nco_cnk_map_rd1 by default */
+ Return nco_cnk_map_xst by default */
const char fnc_nm[]="nco_cnk_map_get()"; /* [sng] Function name */
char *nco_prg_nm; /* [sng] Program name */
nco_prg_nm=nco_prg_nm_get(); /* [sng] Program name */
if(nco_cnk_map_sng == NULL){
- if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stdout,"%s: INFO %s reports %s invoked without explicit chunking map. Defaulting to chunking map \"rd1\".\n",nco_prg_nm,fnc_nm,nco_prg_nm);
- return nco_cnk_map_rd1;
+ /* 20140815: Change default from rd1 to xst */
+ if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stdout,"%s: INFO %s reports %s invoked without explicit chunking map. Defaulting to chunking map \"xst\".\n",nco_prg_nm,fnc_nm,nco_prg_nm);
+ return nco_cnk_map_xst;
} /* endif */
if(!strcmp(nco_cnk_map_sng,"nil")) return nco_cnk_map_nil;
@@ -331,14 +344,15 @@ nco_cnk_plc_get /* [fnc] Convert user-specified chunking policy to key */
(const char *nco_cnk_plc_sng) /* [sng] User-specified chunking policy */
{
/* Purpose: Convert user-specified string to chunking operation type
- Return nco_cnk_plc_g2d by default */
+ Return nco_cnk_plc_xst by default */
const char fnc_nm[]="nco_cnk_plc_get()"; /* [sng] Function name */
char *nco_prg_nm; /* [sng] Program name */
nco_prg_nm=nco_prg_nm_get(); /* [sng] Program name */
if(nco_cnk_plc_sng == NULL){
- if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stdout,"%s: INFO %s reports %s invoked without explicit chunking policy. Defaulting to chunking policy \"g2d\".\n",nco_prg_nm,fnc_nm,nco_prg_nm);
- return nco_cnk_plc_g2d;
+ /* 20140815: Change default from g2d to xst */
+ if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stdout,"%s: INFO %s reports %s invoked without explicit chunking policy. Defaulting to chunking policy \"xst\".\n",nco_prg_nm,fnc_nm,nco_prg_nm);
+ return nco_cnk_plc_xst;
} /* endif */
if(!strcmp(nco_cnk_plc_sng,"nil")) return nco_cnk_plc_nil;
@@ -354,6 +368,9 @@ nco_cnk_plc_get /* [fnc] Convert user-specified chunking policy to key */
if(!strcmp(nco_cnk_plc_sng,"cnk_g3d")) return nco_cnk_plc_g3d;
if(!strcmp(nco_cnk_plc_sng,"plc_g3d")) return nco_cnk_plc_g3d;
if(!strcmp(nco_cnk_plc_sng,"xpl")) return nco_cnk_plc_xpl;
+ if(!strcmp(nco_cnk_plc_sng,"r1d")) return nco_cnk_plc_r1d;
+ if(!strcmp(nco_cnk_plc_sng,"cnk_r1d")) return nco_cnk_plc_r1d;
+ if(!strcmp(nco_cnk_plc_sng,"plc_r1d")) return nco_cnk_plc_r1d;
if(!strcmp(nco_cnk_plc_sng,"cnk_xpl")) return nco_cnk_plc_xpl;
if(!strcmp(nco_cnk_plc_sng,"plc_xpl")) return nco_cnk_plc_xpl;
if(!strcmp(nco_cnk_plc_sng,"xst")) return nco_cnk_plc_xst;
@@ -791,6 +808,7 @@ nco_cnk_sz_set_trv /* [fnc] Set chunksize parameters (GTT version of nco_cnk_sz_
nc_type var_typ_dsk; /* [nbr] Variable type */
nco_bool *flg_mch; /* [flg] Name match (absolute or relative) between chunking structure 'cnk_sct' and dimension 'dmn_cmn' */
+ nco_bool flg_ovr; /* [flg] Override default chunking with user-specified chunking for this dimension */
nco_bool flg_usr_rqs; /* [flg] User requested checking */
nco_bool is_rec_var; /* [flg] Record variable */
nco_bool is_chk_var; /* [flg] Check-summed variable */
@@ -861,7 +879,7 @@ nco_cnk_sz_set_trv /* [fnc] Set chunksize parameters (GTT version of nco_cnk_sz_
is_chunked=False; /* [flg] Chunked variable */
is_xpl_cnk=False; /* [flg] Explicitly chunked variable */
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id_out,var_nm,&var_id_out);
(void)nco_inq_varid(grp_id_in,var_nm,&var_id_in);
@@ -909,7 +927,7 @@ nco_cnk_sz_set_trv /* [fnc] Set chunksize parameters (GTT version of nco_cnk_sz_
/* Some variables simply must be chunked */
if(nco_dbg_lvl_get() >= nco_dbg_var && nco_dbg_lvl_get() != nco_dbg_dev) (void)fprintf(stdout,"%s: INFO %s %s must be chunked (record, compressed, or check-summed variable)\n",nco_prg_nm_get(),fnc_nm,var_nm);
}else{
- /* Explicitly turn-off chunking for arrays that are... */
+ /* Explicitly exit this chunking function now (and thus implement netCDF4-default chunking behavior) for variables that are... */
if((cnk_plc == nco_cnk_plc_xpl && !is_xpl_cnk) || /* ...not explicitly chunked... */
(cnk_plc == nco_cnk_plc_xst && !is_chunked) || /* ...not already chunked... */
(cnk_plc == nco_cnk_plc_g2d && dmn_nbr < 2) || /* ...much too small... */
@@ -1095,11 +1113,13 @@ cnk_xpl_override: /* end goto */
/* Override "reasonable" defaults with explicitly set per-dimension sizes, if any */
flg_mch=(nco_bool *)nco_malloc(dmn_nbr*sizeof(nco_bool));
+ /* Loop over all dimensions in this variable */
for(dmn_idx=0;dmn_idx<dmn_nbr;dmn_idx++){
/* Initialize to false then override */
flg_mch[dmn_idx]=False;
+ /* Loop over all user-specified chunk-sizes */
for(cnk_idx=0;cnk_idx<cnk_nbr;cnk_idx++){
if(cnk_dmn[cnk_idx]->nm_fll){
@@ -1108,32 +1128,49 @@ cnk_xpl_override: /* end goto */
if(!strcmp(cnk_dmn[cnk_idx]->nm,dmn_cmn[dmn_idx].nm)) flg_mch[dmn_idx]=True;
} /* end else */
- /* Name match found */
+ /* User-specified name matches current dimension name */
if(flg_mch[dmn_idx]){
- cnk_sz[dmn_idx]=cnk_dmn[cnk_idx]->sz;
- /* Is this a record dimension? */
- if(dmn_cmn[dmn_idx].is_rec_dmn){
- /* dmn_sz of record dimension can/will be zero in output file
- Allow (though warn) when cnk_sz > dmn_sz in such cases */
- if(dmn_cmn[dmn_idx].NON_HYP_DMN){
- if(dmn_cmn[dmn_idx].sz > 0 && /* Warn only after records have been written */
- cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].sz){
- (void)fprintf(stderr,"%s: WARNING %s allowing user-specified record dimension %s chunksize %lu which exceeds current output file record dimension size = %lu. May fail if output file is not concatenated from multiple inputs.\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].sz);
- } /* endif too big */
- }else{ /* !NON_HYP_DMN */
- if(cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].dmn_cnt){
- (void)fprintf(stderr,"%s: WARNING %s allowing user-specified record dimension %s chunksize = %lu which exceeds user-specified record dimension input hyperslab size = %lu. May fail if output file is not concatenated from multiple inputs.\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].dmn_cnt);
- } /* endif too big */
- } /* !NON_HYP_DMN */
- }else{ /* !rcd_dmn_id */
- if(cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].sz){
- /* Unlike record dimensions, non-record dimensions must have cnk_sz <= dmn_sz */
- (void)fprintf(stderr,"%s: WARNING %s trimming user-specified fixed dimension %s chunksize from %lu to %lu\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].sz);
- /* Trim else out-of-bounds sizes will fail in HDF library in nc_enddef() */
- cnk_sz[dmn_idx]=(size_t)dmn_cmn[dmn_idx].sz;
- } /* endif */
- } /* !rcd_dmn_id */
- break;
+ flg_ovr=False;
+
+ /* Override default chunking with user-specified chunking for this dimension if... */
+ if(
+ /* ... Policy is anything but r1d or ...*/
+ (cnk_plc != nco_cnk_plc_r1d) ||
+ /* ... Policy is r1d and this is the matching r1d coordinate or ... */
+ (cnk_plc == nco_cnk_plc_r1d && (dmn_nbr == 1 && is_rec_var)) ||
+ False){
+ /* Perform override */
+ cnk_sz[dmn_idx]=cnk_dmn[cnk_idx]->sz;
+ flg_ovr=True;
+ } /* endif */
+
+ /* Sanity checks for dimensions that were over-ridden by user-specified chunksizes */
+ if(flg_ovr){
+ /* Is this a record dimension? */
+ if(dmn_cmn[dmn_idx].is_rec_dmn){
+ /* dmn_sz of record dimension can/will be zero in output file
+ Allow (though warn) when cnk_sz > dmn_sz in such cases */
+ if(dmn_cmn[dmn_idx].NON_HYP_DMN){
+ if(dmn_cmn[dmn_idx].sz > 0 && /* Warn only after records have been written */
+ cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].sz){
+ (void)fprintf(stderr,"%s: WARNING %s allowing user-specified record dimension %s chunksize %lu which exceeds current output file record dimension size = %lu. May fail if output file is not concatenated from multiple inputs.\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].sz);
+ } /* endif too big */
+ }else{ /* !NON_HYP_DMN */
+ if(cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].dmn_cnt){
+ (void)fprintf(stderr,"%s: WARNING %s allowing user-specified record dimension %s chunksize = %lu which exceeds user-specified record dimension input hyperslab size = %lu. May fail if output file is not concatenated from multiple inputs.\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].dmn_cnt);
+ } /* endif too big */
+ } /* !NON_HYP_DMN */
+ }else{ /* !rcd_dmn_id */
+ if(cnk_sz[dmn_idx] > (size_t)dmn_cmn[dmn_idx].sz){
+ /* Unlike record dimensions, non-record dimensions must have cnk_sz <= dmn_sz */
+ (void)fprintf(stderr,"%s: WARNING %s trimming user-specified fixed dimension %s chunksize from %lu to %lu\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[dmn_idx].nm,(unsigned long)cnk_dmn[cnk_idx]->sz,(unsigned long)dmn_cmn[dmn_idx].sz);
+ /* Trim else out-of-bounds sizes will fail in HDF library in nc_enddef() */
+ cnk_sz[dmn_idx]=(size_t)dmn_cmn[dmn_idx].sz;
+ } /* endif */
+ } /* !rcd_dmn_id */
+ } /* !flg_ovr */
+ /* Dimension matched this chunk name, no need to search other chunk names */
+ break;
} /* cnk_nm != dmn_nm */
} /* end loop over dimensions */
} /* end loop over cnk */
diff --git a/src/nco/nco_cnk.h b/src/nco/nco_cnk.h
index afe10b0..609191f 100644
--- a/src/nco/nco_cnk.h
+++ b/src/nco/nco_cnk.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnk.h,v 1.37 2014/02/01 02:52:30 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnk.h,v 1.39 2014/08/14 22:44:39 zender Exp $ */
/* Purpose: Description (definition) of chunking functions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cnk.h" *//* Chunking */
@@ -36,7 +37,8 @@ enum nco_cnk_plc{ /* [enm] Chunking policy */
nco_cnk_plc_g3d, /* 3 [enm] Chunk variables >= three dimensions */
nco_cnk_plc_xpl, /* 4 [enm] Chunk variables with explicitly chunked dimensions */
nco_cnk_plc_xst, /* 5 [enm] Chunk variables that are chunked in input */
- nco_cnk_plc_uck /* 6 [enm] Unchunk all chunked variables */
+ nco_cnk_plc_uck, /* 6 [enm] Unchunk all chunked variables */
+ nco_cnk_plc_r1d /* 7 [enm] Chunk record coordinates == one dimension */
}; /* end nco_cnk_plc enum */
/* Chunking type maps: */
diff --git a/src/nco/nco_cnv_arm.c b/src/nco/nco_cnv_arm.c
index c4c6ee3..81f8288 100644
--- a/src/nco/nco_cnv_arm.c
+++ b/src/nco/nco_cnv_arm.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_arm.c,v 1.35 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_arm.c,v 1.36 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: ARM conventions, e.g., http://www.arm.gov/data/time.stm */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_cnv_arm.h" /* ARM conventions */
diff --git a/src/nco/nco_cnv_arm.h b/src/nco/nco_cnv_arm.h
index 8b129a1..12dd3c3 100644
--- a/src/nco/nco_cnv_arm.h
+++ b/src/nco/nco_cnv_arm.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_arm.h,v 1.29 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_arm.h,v 1.30 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: ARM conventions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cnv_arm.h" *//* ARM conventions */
diff --git a/src/nco/nco_cnv_csm.c b/src/nco/nco_cnv_csm.c
index c4234e7..ea2bab8 100644
--- a/src/nco/nco_cnv_csm.c
+++ b/src/nco/nco_cnv_csm.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_csm.c,v 1.113 2014/03/26 18:55:58 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_csm.c,v 1.115 2014/07/15 18:48:55 zender Exp $ */
/* Purpose: CCM/CCSM/CF conventions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_cnv_csm.h" /* CCM/CCSM/CF conventions */
@@ -302,7 +303,7 @@ nco_cnv_cf_cll_mth_add /* [fnc] Add cell_methods attributes */
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
diff --git a/src/nco/nco_cnv_csm.h b/src/nco/nco_cnv_csm.h
index 9436bdb..5ce80e1 100644
--- a/src/nco/nco_cnv_csm.h
+++ b/src/nco/nco_cnv_csm.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_csm.h,v 1.42 2014/02/17 23:12:38 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_cnv_csm.h,v 1.43 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: CCM/CCSM/CF conventions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_cnv_csm.h" *//* CCM/CCSM/CF conventions */
diff --git a/src/nco/nco_ctl.c b/src/nco/nco_ctl.c
index 96a74a5..09ee35f 100644
--- a/src/nco/nco_ctl.c
+++ b/src/nco/nco_ctl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_ctl.c,v 1.471 2014/05/27 22:13:54 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_ctl.c,v 1.491 2014/08/27 04:44:01 zender Exp $ */
/* Purpose: Program flow control functions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_ctl.h" /* Program flow control functions */
@@ -23,11 +24,11 @@ nco_cmp_get(void) /* [fnc] Return compiler and version */
static const char cmp_nm[]="xlC"; /* [sng] Compiler name */
static const char cmp_sng[]="Token __xlC__ defined in nco_cmp_get(), probably compiled with AIX xlC_r or xlC"; /* [sng] Compiler string */
#endif /* !__xlC__ */
-#if defined(__GNUC__) && !defined(__INTEL_COMPILER) && !defined(__PATHCC__) && !defined(PGI_CC)
+#if defined(__GNUC__) && !defined(__clang) && !defined(__INTEL_COMPILER) && !defined(__PATHCC__) && !defined(PGI_CC)
/* Testing for GCC macros early is dangerous because some compilers,
including Intel's, define GCC macros for compatibility */
static const char cmp_nm[]="gcc"; /* [sng] Compiler name */
- static const char cmp_sng[]="Token __GNUC__ defined in nco_cmp_get(), probably compiled with GNU gcc"; /* [sng] Compiler string */
+ static const char cmp_sng[]="Token __GNUC__ defined in nco_cmp_get(). Compiled with GNU gcc (or a compiler that emulates gcc)."; /* [sng] Compiler string */
static const char cmp_vrs[]=TKN2SNG(__VERSION__); // [sng] Compiler version
static const char cmp_vrs_mjr[]=TKN2SNG(__GNUC__); // [sng] Compiler major version
static const char cmp_vrs_mnr[]=TKN2SNG(__GNUC_MINOR__); // [sng] Compiler minor version
@@ -42,6 +43,11 @@ nco_cmp_get(void) /* [fnc] Return compiler and version */
(void)fprintf(stderr,"%s: INFO GCC version is %s\n",nco_prg_nm_get(),cmp_vrs);
} /* endif dbg */
#endif /* !__GNUC__ */
+#ifdef __clang
+ /* Some compilers, including clang, also define __GNUC__ by default */
+ static const char cmp_nm[]="clang";
+ static const char cmp_sng[]="Token __clang defined in nco_cmp_get(), probably compiled with LLVM clang"; /* [sng] Compiler string */
+#endif /* !__clang */
#ifdef __INTEL_COMPILER
/* Some compilers, including icc, also define __GNUC__ by default */
static const char cmp_nm[]="icc";
@@ -57,8 +63,8 @@ nco_cmp_get(void) /* [fnc] Return compiler and version */
static const char cmp_sng[]="Token PGI_CC defined in nco_cmp_get(), probably compiled with PGI pgcc"; /* [sng] Compiler string */
#endif /* !PGI_CC */
- /* In case none of the above tokens matched */
-#if !defined(NCO_XLC_LIKELY) && !defined(__GNUC__) && !defined(__INTEL_COMPILER) && !defined(__PATHCC__) && !defined(PGI_CC)
+ /* No tokens matched */
+#if !defined(NCO_XLC_LIKELY) && !defined(__clang) && !defined(__GNUC__) && !defined(__INTEL_COMPILER) && !defined(__PATHCC__) && !defined(PGI_CC)
/* Unknown compiler */
static const char cmp_nm[]="unknown"; /* [sng] Compiler name */
static const char cmp_sng[]="Unknown compiler tokens in nco_cmp_get(), compiler is unknown"; /* [sng] Compiler string */
@@ -91,9 +97,13 @@ nco_mpi_get(void) /* [fnc] Return MPI implementation */
static const char mpi_nm[]="MPICH2"; /* [sng] MPI name */
static const char mpi_sng[]="Token MPICH2 defined in nco_mpi_get(), MPI environment is probably MPICH2, i.e., MPICH version 2"; /* [sng] MPI string */
#endif /* !MPICH2 */
+#ifdef OMPI_MPI_H
+ static const char mpi_nm[]="OPENMPI"; /* [sng] MPI name */
+ static const char mpi_sng[]="Token OMPI_MPI_H defined in nco_mpi_get(), MPI environment is probably OpenMPI"; /* [sng] MPI string */
+#endif /* !OMPI_MPI_H */
/* In case no token matched */
-#if !defined(_H_MPI) && !defined(LAM_MPI) && (MPICH_NAME != '1') && !defined(MPICH2)
+#if !defined(_H_MPI) && !defined(LAM_MPI) && (MPICH_NAME != '1') && !defined(MPICH2) && !defined(OMPI_MPI_H)
#ifndef MPI_VERSION
/* MPI is not installed */
static const char mpi_nm[]="none"; /* [sng] MPI name */
@@ -680,30 +690,20 @@ nco_cnf_prn(void) /* [fnc] Print NCO configuration and help text */
/* Purpose: Print NCO configuration and help text */
(void)fprintf(stdout,"Homepage: http://nco.sf.net\n");
- (void)fprintf(stdout,"User's Guide: http://nco.sf.net/nco.html\n");
+ (void)fprintf(stdout,"User Guide: http://nco.sf.net/nco.html\n");
/* fxm: TKN2YESNO breaks when TKN is undefined
Full macro language like M4 might be useful here, though probably too much trouble */
#define TKN2YESNO(x) ((x+0) ? ("No"):("Yes"))
/* NB: Keep configuration option tokens consistent among configure.ac, bld/Makefile, and nco_ctl.c
Alphabetize list by first word in English text description of token */
- (void)fprintf(stdout,"Configuration Option:\tActive?\tMeaning or Reference:\nCheck _FillValue\t%s\thttp://nco.sf.net/nco.html#mss_val\nCheck missing_value\t%s\thttp://nco.sf.net/nco.html#mss_val\nCompressed netCDF3\t%s\thttp://nco.sf.net/nco.html#znetcdf (pre-alpha)\nDAP clients (libdap)\t%s\thttp://nco.sf.net/nco.html#dap\nDAP clients (libnetcdf)\t%s\thttp://nco.sf.net/nco.html#dap\nDebugging: Custom\t%s\tPedantic, bounds checking (slowest execution)\nDebugging: Symbols\t%s\tProduce s [...]
+ (void)fprintf(stdout,"Configuration Option:\tActive?\tMeaning or Reference:\nCheck _FillValue\t%s\thttp://nco.sf.net/nco.html#mss_val\nCheck missing_value\t%s\thttp://nco.sf.net/nco.html#mss_val\nDAP clients\t\t%s\thttp://nco.sf.net/nco.html#dap\nDebugging: Custom\t%s\tPedantic, bounds checking (slowest execution)\nDebugging: Symbols\t%s\tProduce symbols for debuggers (e.g., dbx, gdb)\nGNU Scientific Library\t%s\thttp://nco.sf.net/nco.html#gsl\nHDF4 support\t\t%s\thttp://nco.sf.net/nco [...]
(!strcmp("_FillValue",nco_mss_val_sng_get())) ? "Yes" : "No",
(!strcmp("missing_value",nco_mss_val_sng_get())) ? "Yes" : "No",
-#if defined(ENABLE_ZNETCDF) && (ENABLE_ZNETCDF)
+#if defined(ENABLE_DAP) && (ENABLE_DAP)
"Yes",
-#else /* !ENABLE_ZNETCDF */
+#else /* !ENABLE_DAP */
"No",
-#endif /* !ENABLE_ZNETCDF */
-#if defined(ENABLE_DAP_OPENDAP) && (ENABLE_DAP_OPENDAP)
- "Yes",
-#else /* !ENABLE_DAP_OPENDAP */
- "No",
-#endif /* !ENABLE_DAP_OPENDAP */
-#if defined(ENABLE_DAP_NETCDF) && (ENABLE_DAP_NETCDF)
- "Yes",
-#else /* !ENABLE_DAP_NETCDF */
- "No",
-#endif /* !ENABLE_DAP_NETCDF */
+#endif /* !ENABLE_DAP */
#if defined(ENABLE_DEBUG_CUSTOM) && (ENABLE_DEBUG_CUSTOM)
"Yes",
#else /* !ENABLE_DEBUG_CUSTOM */
@@ -799,7 +799,7 @@ nco_nmn_get(void) /* [fnc] Return mnemonic that describes current NCO version */
{
/* Purpose: Return mnemonic describing current NCO version
Always Include terminal \n so mnemonic does not dangle */
- return "Staycation: New records set\n";
+ return "UHS Registration. Go Trojans!\n";
} /* end nco_nmn_get() */
char * /* O [sng] nm_in stripped of any path (i.e., program name stub) */
@@ -922,7 +922,7 @@ nco_usg_prn(void)
opt_sng=(char *)strdup("[-3] [-4] [-6] [-7] [-A] [--bfr sz] [-C] [-c] [--cnk_byt sz] [--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz] [-D nco_dbg_lvl] [-d ...] [-F] [--fix_rec_crd] [--fl_fmt fmt] [-h] [--hdf] [--hdr_pad nbr] [-i var,val] [-L lvl] [-l path] [--msa] [--no_tmp_fl] [-O] [-o out.nc] [-p path] [-R] [-r] [--ram_all] [-t thr_nbr] [-v ...] [-X box] [-x] [-w wgt_1[,wgt_2]] in_1.nc in_2.nc [out.nc]\n");
break;
case ncks:
- opt_sng=(char *)strdup("[-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b fl_bnr] [--bfr sz] [-C] [-c] [--cdl] [--cnk_byt sz] [--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz] [-D nco_dbg_lvl] [-d ...] [-F] [--fix_rec_dmn dim] [--fl_fmt fmt] [-G grp:lvl] [-g ...] [-H] [-h] [--hdn] [--hdr_pad nbr] [-L lvl] [-l path] [-M] [-m] [--md5_dgs] [--md5_wrt] [--mk_rec_dmn dim] [--msa] [--no_blank] [--no_tmp_fl] [-O] [-o out.nc] [-P] [-p path] [-Q] [-q] [-R] [-r] [--rad] [--ram_all] [-s for [...]
+ opt_sng=(char *)strdup("[-3] [-4] [-5] [-6] [-7] [-A] [-a] [-b fl_bnr] [--bfr sz] [-C] [-c] [--cdl] [--cnk_byt sz] [--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz] [-D nco_dbg_lvl] [-d ...] [-F] [--fix_rec_dmn dim] [--fl_fmt fmt] [-G grp:lvl] [-g ...] [--grp_xtr_var_xcl] [-H] [-h] [--hdn] [--hdr_pad nbr] [-L lvl] [-l path] [-M] [-m] [--md5_dgs] [--md5_wrt] [--mk_rec_dmn dim] [--msa] [--no_blank] [--no_tmp_fl] [-O] [-o out.nc] [-P] [-p path] [-Q] [-q] [-R] [-r] [--rad] [...]
break;
case ncpdq:
opt_sng=(char *)strdup("[-3] [-4] [-6] [-7] [-A] [-a ...] [--bfr sz] [-C] [-c] [--cnk_byt sz] [--cnk_dmn nm,sz] [--cnk_map map] [--cnk_plc plc] [--cnk_scl sz] [-D nco_dbg_lvl] [-d ...] [-F] [--fl_fmt fmt] [-G grp:lvl] [-g ...] [-h] [--hdf] [--hdr_pad nbr] [-L lvl] [-l path] [-M pck_map] [--mrd] [--msa] [--no_tmp_fl] [-O] [-o out.nc] [-P pck_plc] [-p path] [-R] [-r] [--ram_all] [-t thr_nbr] [--unn] [-U] [-v ...] [-X box] [-x] in.nc [out.nc]\n");
@@ -1009,6 +1009,7 @@ nco_usg_prn(void)
if(prg_lcl == ncrename) (void)fprintf(stdout,"-g, --grp --group\told_grp,new_grp Group's old and new names\n");
if(prg_lcl != ncrename) (void)fprintf(stdout,"-g, --grp grp1[,grp2[...]] Group(s) to process (regular expressions supported)\n");
} /* end if */
+ if(strstr(opt_sng,"--gxvx, --grp_xtr_var_xcl")) (void)fprintf(stdout," --gxvx, --grp_xtr_var_xcl\tGroup Extraction Variable Exclusion\n");
#endif /* !ENABLE_NETCDF4 */
if(strstr(opt_sng,"[-H]")){
if(prg_lcl == ncks) (void)fprintf(stdout,"-H, --data, --hieronymus\tToggle printing data\n");
@@ -1112,7 +1113,7 @@ nco_usg_prn(void)
(void)fprintf(stdout,"\nEight ways to find more help on %s and/or NCO:\n",nco_prg_nm_get());
(void)fprintf(stdout,"1. Examples: http://nco.sf.net/nco.html#xmp_%s\n",nco_prg_nm_get());
(void)fprintf(stdout,"2. Ref. manual: http://nco.sf.net/nco.html#%s\n",nco_prg_nm_get());
- (void)fprintf(stdout,"3. User's Guide: http://nco.sf.net#RTFM\n");
+ (void)fprintf(stdout,"3. User Guide: http://nco.sf.net#RTFM\n");
(void)fprintf(stdout,"4. Manual pages: \'man %s\', \'man nco\', ...\n",nco_prg_nm_get());
(void)fprintf(stdout,"5. Homepage: http://nco.sf.net\n");
(void)fprintf(stdout,"6. FAQ: http://nco.sf.net#FAQ\n");
@@ -1121,4 +1122,3 @@ nco_usg_prn(void)
(void)fprintf(stdout,"Post questions, suggestions, patches at http://sf.net/projects/nco\n");
} /* end nco_usg_prn() */
-
diff --git a/src/nco/nco_ctl.h b/src/nco/nco_ctl.h
index 23c4550..4809425 100644
--- a/src/nco/nco_ctl.h
+++ b/src/nco/nco_ctl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_ctl.h,v 1.47 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_ctl.h,v 1.48 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Program flow control functions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_ctl.h" *//* Program flow control functions */
diff --git a/src/nco/nco_dbg.c b/src/nco/nco_dbg.c
index 8d9c984..3f6809a 100644
--- a/src/nco/nco_dbg.c
+++ b/src/nco/nco_dbg.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_dbg.c,v 1.21 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_dbg.c,v 1.22 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Debugging */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_dbg.h" /* Debugging */
diff --git a/src/nco/nco_dbg.h b/src/nco/nco_dbg.h
index d4d6711..6b83ac4 100644
--- a/src/nco/nco_dbg.h
+++ b/src/nco/nco_dbg.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_dbg.h,v 1.19 2013/12/31 05:14:01 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_dbg.h,v 1.20 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Debugging */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_dbg.h" *//* Debugging */
diff --git a/src/nco/nco_dmn_utl.c b/src/nco/nco_dmn_utl.c
index 2dbe76a..1e9f5ce 100644
--- a/src/nco/nco_dmn_utl.c
+++ b/src/nco/nco_dmn_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_dmn_utl.c,v 1.69 2014/05/10 05:33:52 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_dmn_utl.c,v 1.70 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Dimension utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_dmn_utl.h" /* Dimension utilities */
diff --git a/src/nco/nco_dmn_utl.h b/src/nco/nco_dmn_utl.h
index 6235817..6e2cffa 100644
--- a/src/nco/nco_dmn_utl.h
+++ b/src/nco/nco_dmn_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_dmn_utl.h,v 1.49 2014/01/02 22:56:39 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_dmn_utl.h,v 1.50 2014/06/15 21:06:22 zender Exp $ */
/* Purpose: Dimension utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_dmn_utl.h" *//* Dimension utilities */
diff --git a/src/nco/nco_fl_utl.c b/src/nco/nco_fl_utl.c
index 7a108f9..0faae3b 100644
--- a/src/nco/nco_fl_utl.c
+++ b/src/nco/nco_fl_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_fl_utl.c,v 1.240 2014/05/22 15:40:34 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_fl_utl.c,v 1.249 2014/08/22 20:27:48 zender Exp $ */
/* Purpose: File manipulation */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_fl_utl.h" /* File manipulation */
@@ -33,6 +34,8 @@ nco_create_mode_mrg /* [fnc] Merge clobber mode with user-specified file format
md_create=md_clobber;
if(fl_out_fmt == NC_FORMAT_64BIT){
md_create|=NC_64BIT_OFFSET;
+ }else if(fl_out_fmt == NC_FORMAT_CDF5){
+ md_create|=NC_64BIT_DATA;
}else if(fl_out_fmt == NC_FORMAT_NETCDF4){
md_create|=NC_NETCDF4;
}else if(fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC){
@@ -44,6 +47,10 @@ nco_create_mode_mrg /* [fnc] Merge clobber mode with user-specified file format
nco_exit(EXIT_FAILURE);
} /* end else fl_out_fmt */
+#ifdef ENABLE_MPI
+ md_create|=NC_NETCDF4|NC_MPIIO;
+#endif /* !ENABLE_MPI */
+
return md_create;
} /* end nco_create_mode_mrg() */
@@ -54,7 +61,9 @@ nco_create_mode_prs /* [fnc] Parse user-specified file format */
{
int rcd=NC_NOERR; /* [rcd] Return code */
- /* Careful! Some valid format strings are subsets of other valid format strings */
+ /* Careful! Some valid format strings are subsets of other valid format strings:
+ "classic" is a sub-string of itself and of "netcdf4_classic"
+ "netcdf4" is a sub-string of itself and of "netcdf4_classic" */
if(strcasestr("classic",fl_fmt_sng) && !strcasestr(fl_fmt_sng,"netcdf4")){
/* If "classic" contains string and string does not contain "netcdf4" */
*fl_fmt_enm=NC_FORMAT_CLASSIC;
@@ -75,13 +84,13 @@ nco_create_mode_prs /* [fnc] Parse user-specified file format */
(void)fprintf(stderr,"%s: ERROR This NCO was not built with netCDF4 and cannot create the requested netCDF4 file format. HINT: Re-try with netCDF3 file format, either by omitting the filetype specification, or by explicitly specifying the \"-3\", \"--fl_fmt=classic\", \"-6\", or \"--fl_fmt=64bit\" options.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
#endif /* !ENABLE_NETCDF4 */
- }else if(strcasestr("znetcdf",fl_fmt_sng)){
-#ifdef ENABLE_ZNETCDF
- /* If "znetcdf" contains string */
- *fl_fmt_enm=NC_COMPRESS;
-#else /* !ENABLE_ZNETCDF */
- (void)fprintf(stderr,"%s: ERROR This NCO was not built with znetCDF (http://snow.cit.cornell.edu/noon/z_netcdf.html) and cannot create the requested znetCDF file format. HINT: Re-try with different (or no) specified file format, such as \"classic\" or \"64bit\".\n",nco_prg_nm_get());
-#endif /* !ENABLE_ZNETCDF */
+ }else if(strcasestr("pnetcdf",fl_fmt_sng)){
+#ifdef ENABLE_MPI
+ /* If "pnetcdf" contains string */
+ *fl_fmt_enm=NC_FORMAT_CDF5;
+#else /* !ENABLE_MPI */
+ (void)fprintf(stderr,"%s: ERROR This NCO was not built with PnetCDF (http://trac.mcs.anl.gov/projects/parallel-netcdf) and cannot create the requested PnetCDF file format. HINT: Re-try with supported file format such as \"classic\" or \"64bit\".\n",nco_prg_nm_get());
+#endif /* !ENABLE_MPI */
}else{
(void)fprintf(stderr,"%s: ERROR Unknown output file format \"%s\" requested. Valid formats are (unambiguous leading characters of) \"classic\", \"64bit\", \"netcdf4\", and \"netcdf4_classic\".\n",nco_prg_nm_get(),fl_fmt_sng);
nco_exit(EXIT_FAILURE);
@@ -233,8 +242,8 @@ nco_fl_cp /* [fnc] Copy first file to second */
/* 20131227 Allow for whitespace characters in fl_dst
Assume CDL translation results in acceptable name for shell commands */
- fl_src_cdl=nm2sng_cdl(fl_src);
- fl_dst_cdl=nm2sng_cdl(fl_dst);
+ fl_src_cdl=nm2sng_fl(fl_src);
+ fl_dst_cdl=nm2sng_fl(fl_dst);
/* Construct and execute copy command */
cmd_cp=(char *)nco_malloc((strlen(cmd_cp_fmt)+strlen(fl_src_cdl)+strlen(fl_dst_cdl)-fmt_chr_nbr+1UL)*sizeof(char));
@@ -415,9 +424,10 @@ nco_fl_lst_mk /* [fnc] Create file list from command line positional arguments *
} /* endelse */
/* Allocate temporary space for input buffer */
-#define FL_NM_IN_MAX_LNG 256 /* [nbr] Maximum length of input file name */
-#define FL_LST_IN_MAX_LNG 10000000 /* [nbr] Maximum length of input file list */
- /* 20121207: 10 MB is per user request of S. McGinnis on 20121130 */
+#define FL_NM_IN_MAX_LNG 256 /* [nbr] Maximum length of single input file name */
+#define FL_LST_IN_MAX_LNG 504576001 /* [nbr] Maximum length of input file list */
+ /* 20121207: 10 MB per request of S. McGinnis 20121130
+ 20140711: 50 MB per request of Christine Smit 20140711 for 30 years of hourly data files each 192 characters long */
bfr_in=(char *)nco_malloc((FL_NM_IN_MAX_LNG+1L)*sizeof(char));
(void)sprintf(fmt_sng,"%%%ds\n",FL_NM_IN_MAX_LNG);
@@ -532,6 +542,7 @@ nco_fl_mk_lcl /* [fnc] Retrieve input file and return local filename */
const char fnc_nm[]="nco_fl_mk_lcl()"; /* [sng] Function name */
const char ftp_url_sng[]="ftp://";
const char http_url_sng[]="http://";
+ const char https_url_sng[]="https://";
const char sftp_url_sng[]="sftp://";
#ifdef ENABLE_DAP
@@ -571,8 +582,8 @@ nco_fl_mk_lcl /* [fnc] Retrieve input file and return local filename */
fl_nm_lcl=(char *)nco_malloc(strlen(fl_pth_lcl_tmp)+1UL);
(void)strcpy(fl_nm_lcl,fl_pth_lcl_tmp);
fl_nm_lcl_tmp=(char *)nco_free(fl_nm_lcl_tmp);
- }else if(strstr(fl_nm_lcl,http_url_sng) == fl_nm_lcl){
- /* Filename starts with "http://": Try DAP first (if available), then wget */
+ }else if((strstr(fl_nm_lcl,http_url_sng) == fl_nm_lcl) || (strstr(fl_nm_lcl,https_url_sng) == fl_nm_lcl)){
+ /* Filename starts with "http://" or "https://" so try DAP first (if available), then wget */
#ifdef ENABLE_DAP
/* Filename has http:// prefix so try DAP access to unadulterated filename */
@@ -1161,8 +1172,8 @@ nco_fl_mv /* [fnc] Move first file to second */
/* 20131227 Allow for whitespace characters in fl_dst
Assume CDL translation results in acceptable name for shell commands */
- fl_src_cdl=nm2sng_cdl(fl_src);
- fl_dst_cdl=nm2sng_cdl(fl_dst);
+ fl_src_cdl=nm2sng_fl(fl_src);
+ fl_dst_cdl=nm2sng_fl(fl_dst);
/* Construct and execute move command */
cmd_mv=(char *)nco_malloc((strlen(cmd_mv_fmt)+strlen(fl_src_cdl)+strlen(fl_dst_cdl)-fmt_chr_nbr+1UL)*sizeof(char));
@@ -1364,8 +1375,12 @@ nco_fl_open /* [fnc] Open file using appropriate buffer size hints and verbosity
if(flg_rqs_vrb_xpl) (void)fprintf(stderr,"%s: INFO %s reports nc__open() will request file buffer size = %lu bytes\n",nco_prg_nm_get(),fnc_nm,(unsigned long)*bfr_sz_hnt);
/* Pass local copy of size hint otherwise user-specified value is overwritten on first call */
+#ifdef ENABLE_MPI
+ rcd=nco_open_par(fl_nm,md_open|NC_MPIIO,MPI_COMM_WORLD,MPI_INFO_NULL,nc_id);
+#else /* !ENABLE_MPI */
rcd=nco__open(fl_nm,md_open,&bfr_sz_hnt_lcl,nc_id);
-
+#endif /* !ENABLE_MPI */
+
/* Print results using same verbosity criteria
NB: bfr_sz_hnt_lcl is never NULL because nco__open() always returns a valid size */
if(flg_rqs_vrb_mpl || flg_rqs_vrb_xpl) (void)fprintf(stderr,"%s: INFO %s reports nc__open() opened file with buffer size = %lu bytes\n",nco_prg_nm_get(),fnc_nm,(unsigned long)bfr_sz_hnt_lcl);
@@ -1568,7 +1583,11 @@ nco_fl_out_open /* [fnc] Open output file subject to availability and user input
bfr_sz_hnt_lcl= (bfr_sz_hnt) ? *bfr_sz_hnt : NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
if(FORCE_OVERWRITE){
+#ifdef ENABLE_MPI
+ rcd+=nco_create_par(fl_out_tmp,md_create,MPI_COMM_WORLD,MPI_INFO_NULL,out_id);
+#else /* !ENABLE_MPI */
rcd+=nco__create(fl_out_tmp,md_create,NC_SIZEHINT_DEFAULT,&bfr_sz_hnt_lcl,out_id);
+#endif /* !ENABLE_MPI */
return fl_out_tmp;
} /* end if */
@@ -1654,8 +1673,12 @@ nco_fl_out_open /* [fnc] Open output file subject to availability and user input
break;
case 'O':
case 'o':
- rcd+=nco__create(fl_out_tmp,md_create,NC_SIZEHINT_DEFAULT,&bfr_sz_hnt_lcl,out_id);
- break;
+#ifdef ENABLE_MPI
+ rcd+=nco_create_par(fl_out_tmp,md_create,MPI_COMM_WORLD,MPI_INFO_NULL,out_id);
+#else /* !ENABLE_MPI */
+ rcd+=nco__create(fl_out_tmp,md_create,NC_SIZEHINT_DEFAULT,&bfr_sz_hnt_lcl,out_id);
+#endif /* !ENABLE_MPI */
+ break;
case 'A':
case 'a':
/* Incur expense of copying current file to temporary file */
@@ -1670,7 +1693,11 @@ nco_fl_out_open /* [fnc] Open output file subject to availability and user input
md_create=NC_NOCLOBBER;
md_create=nco_create_mode_mrg(md_create,fl_out_fmt);
if(RAM_CREATE) md_create|=NC_DISKLESS|NC_WRITE;
+#ifdef ENABLE_MPI
+ rcd+=nco_create_par(fl_out_tmp,md_create,MPI_COMM_WORLD,MPI_INFO_NULL,out_id);
+#else /* !ENABLE_MPI */
rcd+=nco__create(fl_out_tmp,md_create,NC_SIZEHINT_DEFAULT,&bfr_sz_hnt_lcl,out_id);
+#endif /* !ENABLE_MPI */
} /* end if output file does not already exist */
if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
diff --git a/src/nco/nco_fl_utl.h b/src/nco/nco_fl_utl.h
index 711a173..6f688bb 100644
--- a/src/nco/nco_fl_utl.h
+++ b/src/nco/nco_fl_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_fl_utl.h,v 1.76 2014/02/04 20:58:53 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_fl_utl.h,v 1.77 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: File manipulation */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_fl_utl.h" *//* File manipulation */
diff --git a/src/nco/nco_grp_trv.c b/src/nco/nco_grp_trv.c
index 1fadda2..37d677d 100644
--- a/src/nco/nco_grp_trv.c
+++ b/src/nco/nco_grp_trv.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_trv.c,v 1.297 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_trv.c,v 1.298 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: netCDF4 traversal storage */
-/* Copyright (C) 2011--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* This file contains the API for low level group data structures:
Group Traversal Table (GTT): functions prefixed with "trv_tbl_"
diff --git a/src/nco/nco_grp_trv.h b/src/nco/nco_grp_trv.h
index 83e2ad4..5c40ed0 100644
--- a/src/nco/nco_grp_trv.h
+++ b/src/nco/nco_grp_trv.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_trv.h,v 1.117 2014/04/17 06:13:38 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_trv.h,v 1.118 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: netCDF4 traversal storage */
-/* Copyright (C) 2011--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_grp_trv.h" *//* Group traversal */
diff --git a/src/nco/nco_grp_utl.c b/src/nco/nco_grp_utl.c
index 6a8b75e..38a4873 100644
--- a/src/nco/nco_grp_utl.c
+++ b/src/nco/nco_grp_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_utl.c,v 1.1437 2014/05/27 01:23:41 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_utl.c,v 1.1457 2014/08/26 20:10:16 zender Exp $ */
/* Purpose: Group utilities */
-/* Copyright (C) 2011--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Testing:
eos52nc4 ~/nco/data/in.he5 ~/in.nc4
@@ -440,7 +441,7 @@ nco_prn_att_trv /* [fnc] Traverse tree to print all group and global attributes
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
trv_sct trv=trv_tbl->lst[idx_tbl];
if(trv.nco_typ == nco_obj_typ_grp && trv.flg_xtr){
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,trv.nm_fll,&grp_id);
/* Obtain info for group */
@@ -981,11 +982,11 @@ nco_xtr_xcl /* [fnc] Convert extraction list to exclusion list */
Consider, e.g., ncks -x -g g1
In this case g1 and all descendents should be excluded
- ncdismember needs to create extraction lists like: *g1*, ~(/g1/v1)
+ ncdismember needs to create extraction lists like: *g1*, ~(/g1/v1); or *g1*, ~v1;
Potential avenues to implement this include
1. ncks -x -g g1 -v v1
2. ncks -x -g g1 -v /g1/v1
- 3. ncks --grp_xtr_var_xcl -g g1 -v v1
+ 3. ncks --grp_xtr_var_xcl -g g1 -v v1 (method implemented in NCO 4.4.4 in 201405)
Given that, here is how this routine and NCO actually uses flg_xcl:
For variables, -x sets the exclusion flag and is "permanent", i.e., removes variable from extraction list
@@ -1051,12 +1052,12 @@ nco_xtr_crd_add /* [fnc] Add all coordinates to extraction
void
nco_xtr_cf_add /* [fnc] Add to extraction list variables associated with CF convention */
(const int nc_id, /* I [ID] netCDF file ID */
- const char * const cf_nm, /* I [sng] CF convention ("coordinates" or "bounds") */
+ const char * const cf_nm, /* I [sng] CF convention ("ancillary_variables", "bounds", or "coordinates") */
trv_tbl_sct * const trv_tbl) /* I/O [sct] GTT (Group Traversal Table) */
{
/* Add to extraction list all variables associated with specified CF convention
Driver routine for nco_xtr_cf_prv_add()
- Detect associated coordinates specified by CF "bounds" and "coordinates" conventions
+ Detect associated coordinates specified by CF "ancillary_variables", "bounds", and "coordinates" conventions
http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#coordinate-system */
const char fnc_nm[]="nco_xtr_cf_add()"; /* [sng] Function name */
@@ -1064,10 +1065,7 @@ nco_xtr_cf_add /* [fnc] Add to extraction list variables
/* Search for and add CF-compliant bounds and coordinates to extraction list */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
trv_sct trv_obj=trv_tbl->lst[idx_tbl];
- /* Filter extracted variables */
- if(trv_obj.nco_typ == nco_obj_typ_var && trv_obj.flg_xtr){
- (void)nco_xtr_cf_prv_add(nc_id,&trv_obj,cf_nm,trv_tbl);
- } /* Filter extracted variables */
+ if(trv_obj.nco_typ == nco_obj_typ_var && trv_obj.flg_xtr) (void)nco_xtr_cf_prv_add(nc_id,&trv_obj,cf_nm,trv_tbl);
} /* end loop over table */
/* Print extraction list in debug mode */
@@ -1077,15 +1075,16 @@ nco_xtr_cf_add /* [fnc] Add to extraction list variables
} /* nco_xtr_cf_add() */
void
-nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordinates of specified variable to extraction list */
+nco_xtr_cf_prv_add /* [fnc] Add variables associated (via CF) with specified variable to extraction list */
(const int nc_id, /* I [ID] netCDF file ID */
const trv_sct * const var_trv, /* I [sct] Variable (object) */
- const char * const cf_nm, /* I [sng] CF convention ( "coordinates" or "bounds") */
+ const char * const cf_nm, /* I [sng] CF convention ("ancillary_variables", "bounds", or "coordinates") */
trv_tbl_sct * const trv_tbl) /* I/O [sct] GTT (Group Traversal Table) */
{
- /* Detect associated coordinates specified by CF "bounds" or "coordinates" convention for single variable
- Private routine called by nco_xtr_cf_add()
- http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#coordinate-system */
+ /* Detect associated variables specified by CF "ancillary_variables", "bounds", or "coordinates" convention
+ Private routine called by nco_xtr_cf_add()
+ http://cfconventions.org/1.6.html#ancillary-data
+ http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#coordinate-system */
char **cf_lst; /* [sng] 1D array of list elements */
char att_nm[NC_MAX_NAME+1]; /* [sng] Attribute name */
@@ -1094,12 +1093,12 @@ nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordi
int grp_id; /* [id] Group ID */
int nbr_att; /* [nbr] Number of attributes */
- int nbr_cf; /* [nbr] Number of coordinates specified in "bounds" or "coordinates" attribute */
+ int nbr_cf; /* [nbr] Number of variables specified in CF attribute ("ancillary_variables", "bounds", or "coordinates") */
int var_id; /* [id] Variable ID */
assert(var_trv->nco_typ == nco_obj_typ_var);
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
/* Obtain variable ID */
@@ -1125,8 +1124,7 @@ nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordi
/* Yes, get list of specified attributes */
(void)nco_inq_att(grp_id,var_id,att_nm,&att_typ,&att_sz);
if(att_typ != NC_CHAR){
- (void)fprintf(stderr,"%s: WARNING \"%s\" attribute for variable %s is type %s, not %s. This violates CF convention for specifying additional attributes. Therefore will skip this attribute.\n",
- nco_prg_nm_get(),att_nm,var_trv->nm_fll,nco_typ_sng(att_typ),nco_typ_sng(NC_CHAR));
+ (void)fprintf(stderr,"%s: WARNING \"%s\" attribute for variable %s is type %s, not %s. This violates CF convention for specifying additional attributes. Therefore will skip this attribute. If you want CF to support NC_STRING attributes, please tell them and CC: NCO.\n",nco_prg_nm_get(),att_nm,var_trv->nm_fll,nco_typ_sng(att_typ),nco_typ_sng(NC_CHAR));
return;
} /* end if */
att_val=(char *)nco_malloc((att_sz+1L)*sizeof(char));
@@ -1135,9 +1133,9 @@ nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordi
att_val[att_sz]='\0';
/* Split list into separate coordinate names
- Use nco_lst_prs_sgl_2D() not nco_lst_prs_2D() to avert TODO nco944 */
+ Use nco_lst_prs_sgl_2D() not nco_lst_prs_2D() to avert TODO nco944 */
cf_lst=nco_lst_prs_sgl_2D(att_val,dlm_sng,&nbr_cf);
- /* ...for each coordinate in CF convention attribute, i.e., "bounds" or "coordinate"... */
+ /* ...for each coordinate in CF convention attribute, i.e., "ancillary_variables", "bounds", or "coordinate"... */
for(int idx_cf=0;idx_cf<nbr_cf;idx_cf++){
char *cf_lst_var=cf_lst[idx_cf];
if(!cf_lst_var) continue;
@@ -1148,7 +1146,7 @@ nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordi
char *ptr_chr; /* [sng] Pointer to character '/' in full name */
int psn_chr; /* [nbr] Position of character '/' in in full name */
- /* Construct full name of 'CF' variable to find using the full group name where variable resides */
+ /* Construct full name of CF variable */
cf_lst_var_nm_fll=(char *)nco_malloc(strlen(var_trv->grp_nm_fll)+strlen(cf_lst_var)+2L);
strcpy(cf_lst_var_nm_fll,var_trv->grp_nm_fll);
if(strcmp(var_trv->grp_nm_fll,sls_sng)) strcat(cf_lst_var_nm_fll,sls_sng);
@@ -1161,14 +1159,11 @@ nco_xtr_cf_prv_add /* [fnc] Add specified CF-compliant coordi
/* If variable is on list */
if(trv_tbl_fnd_var_nm_fll(cf_lst_var_nm_fll,trv_tbl)){
-
/* Mark it for extraction */
(void)trv_tbl_mrk_xtr(cf_lst_var_nm_fll,True,trv_tbl);
-
- /* Exclude ancestor with lower scope (closer to root) variables, add only the most in scope (usually in same group) */
+ /* Exclude ancestor (greater scope, closer to root) variables, add only most in-scope (usually in same group) */
break;
-
- } /* If variable is on list, mark it for extraction */
+ } /* end if */
cf_lst_var_nm_fll[psn_chr]='\0';
ptr_chr=strrchr(cf_lst_var_nm_fll,sls_chr);
@@ -1235,9 +1230,9 @@ nco_trv_tbl_nm_id /* [fnc] Create extraction list of nm_id_s
grp_out_fll=(char *)nco_free(grp_out_fll);
/* 20130213: Necessary to allow MM3->MM4 and MM4->MM3 workarounds
- Store in/out group IDs as determined in nco_xtr_dfn()
- In MM3/4 cases, either grp_in_id or grp_out_id are always root
- Other is always root unless GPE is used */
+ Store in/out group IDs as determined in nco_xtr_dfn()
+ In MM3/4 cases, either grp_in_id or grp_out_id are always root
+ Other is always root unless GPE is used */
xtr_lst[nbr_tbl].grp_id_in=grp_id_in;
xtr_lst[nbr_tbl].grp_id_out=grp_id_out;
xtr_lst[nbr_tbl].id=var_id;
@@ -1276,10 +1271,10 @@ nco_xtr_crd_ass_add /* [fnc] Add to extraction list all coordi
/* Filter variables to extract */
if(var_trv.nco_typ == nco_obj_typ_var && var_trv.flg_xtr){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Get number of dimensions for *variable* */
@@ -1399,33 +1394,27 @@ nco_xtr_crd_ass_add /* [fnc] Add to extraction list all coordi
void
nco_get_prg_info(void) /* [fnc] Get program info */
{
- /* Purpose: Return a numeric code depending on netCDF library version */
-
+ /* Purpose: Return numeric code depending on netCDF library version */
char lbr_sng[NC_MAX_NAME+1];
int rcd=3;
-
strcpy(lbr_sng,nc_inq_libvers());
-#if defined(ENABLE_NETCDF4) && defined(ENABLE_NETCDF4)
- rcd=40;
- /* Used to detect buggy netCDF version 4.1; other versions are irrelavant */
- if (lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '1' )
- {
- rcd=41;
- }
- else if (lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '3' && lbr_sng[3] == '.' && lbr_sng[4] == '1' )
- {
- rcd=43;
- }
+#if defined(ENABLE_NETCDF4) && defined(HAVE_NETCDF4_H)
+ rcd=400;
+ /* Detect buggy netCDF version 4.1; other versions are irrelevant */
+ if(lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '1'){rcd=410;}
+ else if(lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '3' && lbr_sng[3] == '.' && lbr_sng[4] == '0' ){rcd=430;}
+ else if(lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '3' && lbr_sng[3] == '.' && lbr_sng[4] == '1' ){rcd=431;}
+ else if(lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '3' && lbr_sng[3] == '.' && lbr_sng[4] == '2' ){rcd=432;}
+ else if(lbr_sng[0] == '4' && lbr_sng[1] == '.' && lbr_sng[2] == '3' && lbr_sng[3] == '.' && lbr_sng[4] == '3' ){rcd=433;}
#endif /* HAVE_NETCDF4_H */
-
exit(rcd);
} /* end nco_get_prg_info() */
void
-nco_xtr_lst_prn /* [fnc] Print name-ID structure list */
-(nm_id_sct * const nm_id_lst, /* I [sct] Name-ID structure list */
- const int nm_id_nbr) /* I [nbr] Number of name-ID structures in list */
+nco_xtr_lst_prn /* [fnc] Print name-ID structure list */
+(nm_id_sct * const nm_id_lst, /* I [sct] Name-ID structure list */
+ const int nm_id_nbr) /* I [nbr] Number of name-ID structures in list */
{
(void)fprintf(stdout,"%s: INFO List: %d extraction variables\n",nco_prg_nm_get(),nm_id_nbr);
for(int idx=0;idx<nm_id_nbr;idx++) (void)fprintf(stdout,"[%d] %s\n",idx,nm_id_lst[idx].nm);
@@ -1450,10 +1439,10 @@ nco_prn_xtr_mtd /* [fnc] Print variable metadata */
int grp_id; /* [id] Group ID */
int var_id; /* [id] Variable ID */
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Print variable attributes */
@@ -1697,42 +1686,35 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
/* Isolate extra complexity of copying group metadata */
if(CPY_GRP_METADATA){
/* Extraction flag for groups was set in nco_xtr_grp_mrk()
- This loop defines those groups in output file and copies their metadata */
+ This loop defines those groups in output file and copies their metadata */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
trv_sct grp_trv=trv_tbl->lst[idx_tbl];
/* If object is group ancestor of extracted variable */
if(grp_trv.nco_typ == nco_obj_typ_grp && grp_trv.flg_xtr){
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_trv.grp_nm_fll,&grp_id);
- /* ncge case */
- if(nco_prg_id_get() == ncge){
-
- if(grp_trv.flg_nsm_prn){
- /* Ensemble parent groups */
- if(trv_tbl->nsm_sfx){
- /* Define new name by appending suffix (e.g., /cesm + _avg) */
- char *nm_fll_sfx=nco_bld_nsm_sfx(grp_trv.grp_nm_fll_prn,trv_tbl);
- /* Use then delete new name */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,nm_fll_sfx); else grp_out_fll=(char *)strdup(nm_fll_sfx);
- nm_fll_sfx=(char *)nco_free(nm_fll_sfx);
- }else{
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll_prn); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll_prn);
- } /* !nsm_sfx */
- }else if(grp_trv.flg_nsm_mbr){
- /* If group is ensemble member, do not create it in same location as input */
- continue;
- }else{
- /* Regular group */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll);
- } /* !flg_nsm_prn */
-
- }else{
- /* Non ncge case: Edit group name for output */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll);
- } /* !ncge */
+ /* ncge groups require special handling */
+ if(nco_prg_id == ncge && grp_trv.flg_nsm_prn){
+ /* Ensemble parent groups */
+ if(trv_tbl->nsm_sfx){
+ /* Define new name by appending suffix (e.g., /cesm + _avg) */
+ char *nm_fll_sfx=nco_bld_nsm_sfx(grp_trv.grp_nm_fll_prn,trv_tbl);
+ /* Use then delete new name */
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,nm_fll_sfx); else grp_out_fll=(char *)strdup(nm_fll_sfx);
+ nm_fll_sfx=(char *)nco_free(nm_fll_sfx);
+ }else{
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll_prn); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll_prn);
+ } /* !nsm_sfx */
+ }else if(nco_prg_id == ncge && grp_trv.flg_nsm_mbr){
+ /* Ensemble member groups are not written to output */
+ continue;
+ }else{
+ /* Regular (non-ensemble-related) group (within ncge or any other operator) */
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll);
+ } /* !flg_nsm */
/* If output group does not exist, create it */
if(nco_inq_grp_full_ncid_flg(nc_out_id,grp_out_fll,&grp_out_id)) nco_def_grp_full(nc_out_id,grp_out_fll,&grp_out_id);
@@ -1741,14 +1723,13 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
if(grp_trv.nbr_att){
PCK_ATT_CPY=True;
(void)nco_att_cpy(grp_id,grp_out_id,NC_GLOBAL,NC_GLOBAL,PCK_ATT_CPY);
- } /* Copy group attributes */
+ } /* grp_trv.nbr_att */
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
} /* end if group and flg_xtr */
- } /* end loop to define group attributes */
-
+ } /* end loop over traversal table */
} /* !CPY_GRP_METADATA */
/* Define variables */
@@ -1758,45 +1739,38 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
/* If object is an extracted variable... */
if(var_trv.nco_typ == nco_obj_typ_var && var_trv.flg_xtr){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* ncge */
- if(nco_prg_id_get() == ncge){
- /* If variable is in an ensemble member, do not create it in same location as input */
- if(var_trv.flg_nsm_mbr){
- if(trv_tbl->nsm_sfx){
- /* Define new name by appending suffix (e.g., /cesm + _avg) */
- char *nm_fll_sfx=nco_bld_nsm_sfx(var_trv.grp_nm_fll_prn,trv_tbl);
- /* Use then delete new name */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,nm_fll_sfx); else grp_out_fll=(char *)strdup(nm_fll_sfx);
- nm_fll_sfx=(char *)nco_free(nm_fll_sfx);
- }else{ /* Non suffix case */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv.nsm_nm); else grp_out_fll=(char *)strdup(var_trv.nsm_nm);
- } /* !trv_tbl->nsm_sfx */
-
- }else{
- /* Edit group name for output */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv.grp_nm_fll);
- } /* !flg_nsm_mbr */
+ /* Transform ensemble member group paths as above */
+ if(nco_prg_id == ncge && var_trv.flg_nsm_mbr){
+ if(trv_tbl->nsm_sfx){
+ /* Define new name by appending suffix (e.g., /cesm + _avg) */
+ char *nm_fll_sfx=nco_bld_nsm_sfx(var_trv.grp_nm_fll_prn,trv_tbl);
+ /* Use then delete new name */
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,nm_fll_sfx); else grp_out_fll=(char *)strdup(nm_fll_sfx);
+ nm_fll_sfx=(char *)nco_free(nm_fll_sfx);
+ }else{ /* Non-suffix case */
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv.nsm_nm); else grp_out_fll=(char *)strdup(var_trv.nsm_nm);
+ } /* !trv_tbl->nsm_sfx */
}else{
- /* Edit group name for output */
- if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv.grp_nm_fll);
+ /* Variable not in ensembles */
+ if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv.grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv.grp_nm_fll);
} /* !ncge */
/* If output group does not exist, create it */
if(nco_inq_grp_full_ncid_flg(nc_out_id,grp_out_fll,&grp_out_id)) nco_def_grp_full(nc_out_id,grp_out_fll,&grp_out_id);
- /* ncge */
- if(nco_prg_id_get() == ncge){
- /* Is requested variable in output file? */
+ if(nco_prg_id == ncge){
+ /* Is requested variable already in output file?
+ fxm: Seems wasteful. Can ncge restrict definition to only variables in template group? i.e., satifying both flg_xtr and flg_nsm_tpl */
int rcd=nco_inq_varid_flg(grp_out_id,var_trv.nm,&var_out_id);
/* Yes, get outta' Dodge... avoid GPE failure on duplicate definition */
- if(rcd == 0) continue;
+ if(rcd == NC_NOERR) continue;
} /* ncge */
/* Detect duplicate GPE names in advance, then exit() with helpful error */
- if(gpe) nco_gpe_chk(grp_out_fll,var_trv.nm,&gpe_nm,&nbr_gpe_nm);
+ if(gpe) nco_gpe_chk(grp_out_fll,var_trv.nm,&gpe_nm,&nbr_gpe_nm);
/* Define variable in output file */
var_out_id=nco_cpy_var_dfn_trv(nc_id,nc_out_id,cnk,grp_out_fll,dfl_lvl,gpe,rec_dmn_nm,&var_trv,&dmn_cmn_out,&nbr_dmn_cmn_out,trv_tbl);
@@ -1807,7 +1781,7 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
var_sct *var_prc; /* [sct] Variable to process */
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -1823,7 +1797,7 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
for(int idx_dmn=0;idx_dmn<var_prc->nbr_dim;idx_dmn++){
var_prc->dim[idx_dmn]->xrf=(dmn_sct *)nco_dmn_free(var_prc->dim[idx_dmn]->xrf);
var_prc->dim[idx_dmn]=(dmn_sct *)nco_dmn_free(var_prc->dim[idx_dmn]);
- }
+ } /* end loop over dimensions */
var_prc=(var_sct *)nco_var_free(var_prc);
} /* !CPY_VAR_METADATA */
@@ -1850,17 +1824,13 @@ nco_xtr_dfn /* [fnc] Define extracted groups, variables
} /* end if variable and flg_xtr */
} /* end loop over idx_tbl */
- /* Retain all dimensions */
- if (RETAIN_ALL_DIMS){
- (void)nco_rad(nc_out_id,nbr_dmn_cmn_out,dmn_cmn_out,trv_tbl);
- }
+ /* Retain all dimensions */
+ if(RETAIN_ALL_DIMS) (void)nco_rad(nc_out_id,nbr_dmn_cmn_out,dmn_cmn_out,trv_tbl);
/* Memory management for GPE names */
for(int idx=0;idx<nbr_gpe_nm;idx++) gpe_nm[idx].var_nm_fll=(char *)nco_free(gpe_nm[idx].var_nm_fll);
- for(int idx=0;idx<nbr_dmn_cmn_out;idx++){
- dmn_cmn_out[idx].nm_fll=(char *)nco_free(dmn_cmn_out[idx].nm_fll);
- }
+ for(int idx=0;idx<nbr_dmn_cmn_out;idx++) dmn_cmn_out[idx].nm_fll=(char *)nco_free(dmn_cmn_out[idx].nm_fll);
dmn_cmn_out=(dmn_cmn_sct *)nco_free(dmn_cmn_out);
/* Print extraction list in developer mode */
@@ -1982,7 +1952,7 @@ nco_prn_dmn /* [fnc] Print dimensions for a group */
long dmn_sz; /* [nbr] Dimension size */
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_nm_fll,&grp_id);
(void)nco_inq_unlimdims(grp_id,&nbr_dmn_ult,NULL);
@@ -2246,7 +2216,7 @@ nco_grp_itr /* [fnc] Populate traversal table by exam
if(grp_nm_fll_prn) trv_tbl->lst[idx].grp_nm_fll_prn=strdup(grp_nm_fll_prn); /* [sng] (ncge) Parent group full name */
else trv_tbl->lst[idx].grp_nm_fll_prn=NULL;
trv_tbl->lst[idx].flg_nsm_prn=False; /* [flg] (ncge) Group is, or variable is in, ensemble parent group */
- trv_tbl->lst[idx].flg_nsm_mbr=False; /* [flg] (ncge ) Group is, or variable is in, ensemble member group */
+ trv_tbl->lst[idx].flg_nsm_mbr=False; /* [flg] (ncge) Group is, or variable is in, ensemble member group */
trv_tbl->lst[idx].flg_nsm_tpl=False; /* [flg] Group is, or variable is in, template member group */
trv_tbl->lst[idx].nsm_nm=NULL; /* [sng] (ncge) Ensemble parent group name i.e., full path to ensemble parent */
@@ -2343,8 +2313,7 @@ nco_grp_itr /* [fnc] Populate traversal table by exam
trv_tbl->lst[idx].var_typ=var_typ;
trv_tbl->lst[idx].enm_prc_typ=err_typ;
trv_tbl->lst[idx].var_typ_out=(nc_type)err_typ;
- if(grp_nm_fll_prn) trv_tbl->lst[idx].grp_nm_fll_prn=strdup(grp_nm_fll_prn); /* [sng] (ncge) Parent group full name */
- else trv_tbl->lst[idx].grp_nm_fll_prn=NULL;
+ if(grp_nm_fll_prn) trv_tbl->lst[idx].grp_nm_fll_prn=strdup(grp_nm_fll_prn); else trv_tbl->lst[idx].grp_nm_fll_prn=NULL;
trv_tbl->lst[idx].flg_nsm_prn=False;
trv_tbl->lst[idx].flg_nsm_mbr=False;
trv_tbl->lst[idx].flg_nsm_tpl=False;
@@ -2670,11 +2639,9 @@ nco_bld_crd_var_trv /* [fnc] Build GTT "crd_sct" coordinate va
trv_tbl->lst_dmn[idx_dmn].crd[crd_idx]->lmt_msa.lmt_crr=0;
trv_tbl->lst_dmn[idx_dmn].crd[crd_idx]->lmt_msa.lmt_dmn=NULL;
-
if(nco_dbg_lvl_get() == nco_dbg_old){
crd_sct *crd=trv_tbl->lst_dmn[idx_dmn].crd[crd_idx];
- (void)fprintf(stdout,"%s: INFO %s variable <%s> has coordinate <%s> from dimension <%s>\n",nco_prg_nm_get(),fnc_nm,
- var_trv.nm_fll,crd->crd_nm_fll,crd->dmn_nm_fll);
+ (void)fprintf(stdout,"%s: INFO %s variable <%s> has coordinate <%s> from dimension <%s>\n",nco_prg_nm_get(),fnc_nm,var_trv.nm_fll,crd->crd_nm_fll,crd->dmn_nm_fll);
}
/* Limits are initialized in build limits function */
@@ -2900,10 +2867,7 @@ nco_has_crd_dmn_scp /* [fnc] Is there a variable with same name
} /* Unique dimension list */
/* Unique dimension list */
- for(unsigned idx_dmn=0;idx_dmn<trv_tbl->nbr_dmn;idx_dmn++){
- dmn_trv_sct dmn_trv=trv_tbl->lst_dmn[idx_dmn];
- assert(dmn_trv.has_crd_scp != nco_obj_typ_err);
- } /* Unique dimension list */
+ for(unsigned idx_dmn=0;idx_dmn<trv_tbl->nbr_dmn;idx_dmn++) assert(trv_tbl->lst_dmn[idx_dmn].has_crd_scp != nco_obj_typ_err);
} /* nco_has_crd_dmn_scp() */
@@ -3316,8 +3280,7 @@ nco_wrt_trv_tbl /* [fnc] Obtain file information from GTT (
(void)fprintf(stdout,"%s: INFO %s variable <%s>",nco_prg_nm_get(),fnc_nm,var_trv.nm_fll);
} /* endif dbg */
-
- /* Obtain group ID where variable is located using full group name */
+ /* Obtain group ID where variable is located */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* Obtain variable ID */
@@ -3332,9 +3295,7 @@ nco_wrt_trv_tbl /* [fnc] Obtain file information from GTT (
/* Get dimension IDs for variable */
(void)nco_inq_vardimid(grp_id,var_id,dmn_id_var);
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout," %d dimensions: ",nbr_dmn_var);
- } /* endif dbg */
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout," %d dimensions: ",nbr_dmn_var);
/* Variable dimensions */
for(int idx_dmn_var=0;idx_dmn_var<nbr_dmn_var;idx_dmn_var++){
@@ -3344,23 +3305,14 @@ nco_wrt_trv_tbl /* [fnc] Obtain file information from GTT (
/* Get dimension name */
(void)nco_inq_dim(grp_id,dmn_id_var[idx_dmn_var],dmn_nm_var,&dmn_sz_var);
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"#%d'%s' ",dmn_id_var[idx_dmn_var],dmn_nm_var);
+ } /* end for */
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"#%d'%s' ",
- dmn_id_var[idx_dmn_var],dmn_nm_var);
- }
- }
-
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"\n");
- }
-
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"\n");
dmn_id_var=(int *)nco_free(dmn_id_var);
} /* endif */
-
} /* end loop over idx_tbl */
-
} /* nco_wrt_trv_tbl() */
void
@@ -3494,7 +3446,7 @@ nco_fll_var_trv /* [fnc] Fill-in variable structure list f
if(trv_tbl->lst[tbl_idx].nco_typ == nco_obj_typ_var && trv_tbl->lst[tbl_idx].flg_xtr){
trv_sct var_trv=trv_tbl->lst[tbl_idx];
- /* Obtain group ID from API using full group name */
+ /* Obtain group ID from API */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -3552,7 +3504,7 @@ nco_var_trv /* [fnc] Fill-in variable structure list f
int grp_id; /* [ID] Group ID */
int var_id; /* [ID] Variable ID */
- /* Obtain group ID from API using full group name */
+ /* Obtain group ID from API */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -3598,7 +3550,7 @@ nco_cpy_fix_var_trv /* [fnc] Copy fixed variables from input t
continue;
}
- /* Obtain group IDs using full group name */
+ /* Obtain group IDs */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id_in);
/* Edit group name for output */
@@ -3691,7 +3643,7 @@ nco_prc_cmn /* [fnc] Process objects (ncbo only) */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,trv_2->grp_nm_fll); else grp_out_fll=(char *)strdup(trv_2->grp_nm_fll);
} /* !flg_grp_1 */
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id_1,trv_1->grp_nm_fll,&grp_id_1);
(void)nco_inq_grp_full_ncid(nc_id_2,trv_2->grp_nm_fll,&grp_id_2);
@@ -3935,7 +3887,7 @@ nco_cpy_fix /* [fnc] Copy fixed object (ncbo only) */
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,trv_1->grp_nm_fll); else grp_out_fll=(char *)strdup(trv_1->grp_nm_fll);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id_1,trv_1->grp_nm_fll,&grp_id_1);
/* Get variable ID */
@@ -4204,12 +4156,12 @@ nco_var_fll_trv /* [fnc] Allocate variable structure and f
assert(strcmp(dmn_nm,dmn_trv->nm) == 0);
/* Get hyperslabbed count */
- dmn_cnt=-1;
+ dmn_cnt=-1L;
if(var_trv->var_dmn[idx_dmn].crd) dmn_cnt=var_trv->var_dmn[idx_dmn].crd->lmt_msa.dmn_cnt;
else if(var_trv->var_dmn[idx_dmn].ncd) dmn_cnt=var_trv->var_dmn[idx_dmn].ncd->lmt_msa.dmn_cnt;
var->cnt[idx_dmn]=dmn_cnt;
- var->end[idx_dmn]=dmn_cnt-1;
+ var->end[idx_dmn]=dmn_cnt-1L;
var->srt[idx_dmn]=0L;
var->srd[idx_dmn]=1L;
var->sz*=dmn_cnt;
@@ -4318,22 +4270,19 @@ nco_var_fll_trv /* [fnc] Allocate variable structure and f
/* Get enm_prc_typ from GTT */
for(unsigned idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
if(!strcmp(var->nm_fll,trv_tbl->lst[idx_tbl].nm_fll)){
- if(trv_tbl->lst[idx_tbl].enm_prc_typ == prc_typ){
- var->is_fix_var=0;
- }else if(trv_tbl->lst[idx_tbl].enm_prc_typ == fix_typ){
- var->is_fix_var=1;
- }
+ if(trv_tbl->lst[idx_tbl].enm_prc_typ == prc_typ) var->is_fix_var=False;
+ else if(trv_tbl->lst[idx_tbl].enm_prc_typ == fix_typ) var->is_fix_var=True;
break;
- }
- }
+ } /* endif */
+ }
var->undefined=False; /* [flg] Used by ncap parser */
dmn_in_id_var=(int *)nco_free(dmn_in_id_var);
+
return var;
} /* nco_var_fll_trv() */
-
int /* O [id] Output file variable ID */
nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output file */
(const int nc_in_id, /* I [ID] netCDF input file ID */
@@ -4366,6 +4315,7 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
char *rec_dmn_nm=NULL; /* [sng] User-specified record dimension name */
char *rec_dmn_nm_mlc=NULL; /* [sng] Local copy of rec_dmn_nm_cst, which may be encoded */
char *grp_dmn_out_fll=NULL; /* [sng] Group name of dimension in output */
+ char *dmn_nm_fll_out=NULL; /* [sng] Full name of dimension in output */
char dmn_nm[NC_MAX_NAME+1]; /* [sng] Dimension name */
char dmn_nm_grp[NC_MAX_NAME+1]; /* [sng] Dimension name for group */
@@ -4407,7 +4357,7 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
dmn_trv_sct *dmn_trv; /* [sct] Unique dimension object */
- dmn_cmn_sct dmn_cmn[NC_MAX_DIMS]; /* [sct] Dimension information on output (for a variable ) */
+ dmn_cmn_sct dmn_cmn[NC_MAX_DIMS]; /* [sct] Dimension information on output (for a variable) */
rec_dmn_out_id=NCO_REC_DMN_UNDEFINED;
@@ -4614,7 +4564,6 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
} /* strcmp() */
} /* Loop group defined dimensions */
-
dmn_out_id_grp=(int *)nco_free(dmn_out_id_grp);
/* Define dimension in output file if necessary */
@@ -4713,7 +4662,7 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
In other words, there is no good way to "fix" a record dimension for a variable with no records/data
Workaround is to arbitrarily assign such dimensions a size of 1 so they are fixed output, and still have no data
This ugly hack seems to work and is only invoked in this extreme corner case so may be OK */
- if(dmn_cnt == 0) dmn_cnt=1;
+ if(dmn_cnt == 0) dmn_cnt=1L;
/* Update GTT dimension */
(void)nco_dmn_set_msa(var_dim_id,dmn_cnt,trv_tbl);
} /* !DFN_CRR_DMN_AS_REC_IN_OUTPUT */
@@ -4735,29 +4684,63 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
if(var_trv->var_dmn[idx_dmn].flg_rdd){
found_dim=True;
/* If dimension was to be record keep it that way, otherwise define degenerate size of 1 */
- if(DFN_CRR_DMN_AS_REC_IN_OUTPUT) dmn_cnt=NC_UNLIMITED; else dmn_cnt=1;
+ if(DFN_CRR_DMN_AS_REC_IN_OUTPUT) dmn_cnt=NC_UNLIMITED; else dmn_cnt=1L;
}
if(!found_dim){
DEFINE_DIM[idx_dmn]=False;
nbr_dmn_var_out--;
} /* found_dim */
- } /* ncwa */
+ } /* !ncwa */
/* Always define, except maybe for ncwa */
if(DEFINE_DIM[idx_dmn]){
/* Define dimension and obtain dimension ID */
(void)nco_def_dim(grp_dmn_out_id,dmn_nm,dmn_cnt,&dmn_id_out);
- if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"%s: DEBUG %s Defined dimension <%s><%s>#%d\n",nco_prg_nm_get(),fnc_nm,grp_dmn_out_fll,dmn_nm,dmn_id_out);
+ if(nco_dbg_lvl_get() == nco_dbg_dev){
+ (void)fprintf(stdout,"%s: DEBUG %s Defined dimension <%s><%s>#%d\n",nco_prg_nm_get(),fnc_nm,grp_dmn_out_fll,dmn_nm,dmn_id_out);
+ }
- /* Redefine output dimension array for this dimension */
- (void)nco_dfn_dmn(dmn_nm,dmn_cnt,dmn_id_out,dmn_cmn,var_trv->nbr_dmn);
/* Assign defined ID to dimension ID array for the variable */
dmn_out_id[idx_dmn]=dmn_id_out;
} /* !DEFINE_DIM */
} /* end if dimension is not yet defined */
+ /* pvn 20140824 Always redefine output dimension array; repeat logic above regarding value of "dmn_cnt"
+ for both non ncwa and ncwa cases */
+ if(nco_prg_id != ncwa){
+ if(var_trv->var_dmn[idx_dmn].is_crd_var){
+ dmn_cnt=var_trv->var_dmn[idx_dmn].crd->lmt_msa.dmn_cnt;
+ }else{ /* !is_crd_var */
+ dmn_cnt=var_trv->var_dmn[idx_dmn].ncd->lmt_msa.dmn_cnt;
+ } /* !is_crd_var */
+ } else if(nco_prg_id == ncwa){
+ /* Degenerate dimensions */
+ for(int idx_dmn_dgn=0;idx_dmn_dgn<trv_tbl->nbr_dmn_dgn;idx_dmn_dgn++){
+ /* Compare ID */
+ if(trv_tbl->dmn_dgn[idx_dmn_dgn].id == var_dim_id){
+ dmn_cnt=trv_tbl->dmn_dgn[idx_dmn_dgn].cnt;
+ /* If dimension is record keep it that way */
+ if(dmn_trv->is_rec_dmn) dmn_cnt=NC_UNLIMITED;
+ break;
+ } /* Compare ID */
+ } /* !Degenerate */
+ if(var_trv->var_dmn[idx_dmn].flg_rdd){
+ /* If dimension was to be record keep it that way, otherwise define degenerate size of 1 */
+ if(DFN_CRR_DMN_AS_REC_IN_OUTPUT) dmn_cnt=NC_UNLIMITED; else dmn_cnt=1L;
+ }
+ } /* !ncwa */
+
+ /* Construct full dimension name using the full group name */
+ dmn_nm_fll_out=(char *)nco_malloc(strlen(grp_dmn_out_fll)+strlen(dmn_nm)+2L);
+ strcpy(dmn_nm_fll_out,grp_dmn_out_fll);
+ if(strcmp(grp_dmn_out_fll,"/")) strcat(dmn_nm_fll_out,"/");
+ strcat(dmn_nm_fll_out,dmn_nm);
+
+ /* Redefine output dimension array for this dimension */
+ (void)nco_dfn_dmn(dmn_nm_fll_out,dmn_cnt,dmn_id_out,dmn_cmn,var_trv->nbr_dmn);
+
/* Die informatively if record dimension is not first dimension in netCDF3 output */
if(idx_dmn > 0 && dmn_out_id[idx_dmn] == rec_dmn_out_id && fl_fmt != NC_FORMAT_NETCDF4 && DEFINE_DIM[idx_dmn]){
(void)fprintf(stdout,"%s: ERROR User defined the output record dimension to be \"%s\". Yet in the variable \"%s\" this is dimension number %d. The output file adheres to the netCDF3 API which only supports the record dimension as the first (i.e., least rapidly varying) dimension. Consider using ncpdq to permute the location of the record dimension in the output file.\n",nco_prg_nm_get(),rec_dmn_nm,var_nm,idx_dmn+1);
@@ -4766,6 +4749,7 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
/* Memory management after defining current output dimension */
if(grp_dmn_out_fll) grp_dmn_out_fll=(char *)nco_free(grp_dmn_out_fll);
+ if(dmn_nm_fll_out) dmn_nm_fll_out=(char *)nco_free(dmn_nm_fll_out);
} /* End of the very important dimension loop */
@@ -4860,18 +4844,16 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
(void)nco_def_var(grp_out_id,var_nm,var_typ_out,nbr_dmn_var_out,dmn_out_id,&var_out_id);
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"%s: DEBUG %s Defined variable <%s><%s> : ",nco_prg_nm_get(),fnc_nm,grp_out_fll,var_nm);
- for(int idx_dmn=0;idx_dmn<nbr_dmn_var;idx_dmn++){
- (void)fprintf(stdout,"<%s>#%d : ",dmn_cmn[idx_dmn].nm_fll,dmn_out_id[idx_dmn]);
- }
- (void)fprintf(stdout,"\n");
- }
-
} /* !ncwa */
+ if(nco_dbg_lvl_get() == nco_dbg_dev){
+ (void)fprintf(stdout,"%s: DEBUG %s Defined variable <%s><%s> : ",nco_prg_nm_get(),fnc_nm,grp_out_fll,var_nm);
+ for(int idx_dmn=0;idx_dmn<nbr_dmn_var;idx_dmn++) (void)fprintf(stdout,"<%s>#%d SIZE=%ld : ",dmn_cmn[idx_dmn].nm_fll,dmn_out_id[idx_dmn],dmn_cmn[idx_dmn].sz);
+ (void)fprintf(stdout,"\n");
+ } /* endif dbg */
+
/* If output dimensions array exists */
- if (dmn_cmn_out!=NULL && nco_prg_id == ncks){
+ if(dmn_cmn_out != NULL && nco_prg_id == ncks){
nco_bool dmn_flg=False;
@@ -4882,7 +4864,7 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
for(int idx_dmn_out=0;idx_dmn_out<*nbr_dmn_cmn_out;idx_dmn_out++){
/* Match by ID */
- if( (*dmn_cmn_out)[idx_dmn_out].id==dmn_cmn[idx_dmn].id){
+ if((*dmn_cmn_out)[idx_dmn_out].id == dmn_cmn[idx_dmn].id){
dmn_flg=True;
break;
} /* Match by ID */
@@ -4907,12 +4889,9 @@ nco_cpy_var_dfn_trv /* [fnc] Define specified variable in output
nbr_dmn_out_tmp++;
*nbr_dmn_cmn_out=nbr_dmn_out_tmp;
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"%s: DEBUG %s Inserted dimension #%d to output list\n",nco_prg_nm_get(),fnc_nm,
- dmn_cmn[idx_dmn].id);
- }
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"%s: DEBUG %s Inserted dimension #%d to output list\n",nco_prg_nm_get(),fnc_nm,dmn_cmn[idx_dmn].id);
- } /* If this dimension is not in output array */
+ } /* If this dimension is not in output array */
} /* Loop over each dimension in variable */
} /* If output dimensions array exists */
@@ -5018,21 +4997,11 @@ nco_dmn_swap /* [fnc] Swap dimensions */
dmn_cmn_sct dmn_cmn_tmp;
- /* Loop dimensions */
- for(int idx_dmn=0;idx_dmn<nbr_dmn;idx_dmn++){
- /* Find index of name 1 */
- if(strcmp(dmn_nm_1,dmn_cmn[idx_dmn].nm) == 0){
- dmn_nm_1_idx=idx_dmn;
- } /* Find index of name 1 */
- } /* Loop dimensions */
+ for(int idx_dmn=0;idx_dmn<nbr_dmn;idx_dmn++)
+ if(!strcmp(dmn_nm_1,dmn_cmn[idx_dmn].nm)) dmn_nm_1_idx=idx_dmn;
- /* Loop dimensions */
- for(int idx_dmn=0;idx_dmn<nbr_dmn;idx_dmn++){
- /* Find index of name 2 */
- if(strcmp(dmn_nm_2,dmn_cmn[idx_dmn].nm) == 0){
- dmn_nm_2_idx=idx_dmn;
- } /* Find index of name 2 */
- } /* Loop dimensions */
+ for(int idx_dmn=0;idx_dmn<nbr_dmn;idx_dmn++)
+ if(!strcmp(dmn_nm_2,dmn_cmn[idx_dmn].nm)) dmn_nm_2_idx=idx_dmn;
/* Swap */
dmn_cmn_tmp=dmn_cmn[dmn_nm_1_idx];
@@ -5043,18 +5012,18 @@ nco_dmn_swap /* [fnc] Swap dimensions */
void
nco_dfn_dmn /* [fnc] Define dimension size and ID in array */
-(const char * const dmn_nm, /* I [sng] Name of dimension */
+(const char * const dmn_nm_fll_out, /* I [sng] Full name of dimension in output */
const long dmn_sz, /* I [nbr] Size of dimension */
- const int dmn_id, /* I [id] ID of dimension */
+ const int dmn_id_out, /* I [id] ID of dimension in output */
dmn_cmn_sct *dmn_cmn, /* I/O [sct] Dimension structure array */
const int nbr_dmn) /* I [nbr] Number of dimensions (size of above array) */
{
/* Loop dimensions */
for(int idx_dmn=0;idx_dmn<nbr_dmn;idx_dmn++){
/* Find dimension */
- if(strcmp(dmn_nm,dmn_cmn[idx_dmn].nm) == 0){
+ if(!strcmp(dmn_nm_fll_out,dmn_cmn[idx_dmn].nm_fll)){
dmn_cmn[idx_dmn].sz=dmn_sz;
- dmn_cmn[idx_dmn].id=dmn_id;
+ dmn_cmn[idx_dmn].id=dmn_id_out;
return;
} /* Find dimension */
} /* Loop dimensions */
@@ -5333,24 +5302,20 @@ nco_var_dmn_rdr_mtd_trv /* [fnc] Determine and set new dimensional
nco_var_prc_idx_trv(var_trv_mrk.nm_fll,var_prc_out,nbr_var_prc,&idx_var_prc_out);
/* Transfer dimension structures to be re-ordered *from* GTT (opposite of above) */
- for(int idx_dmn=0;idx_dmn<var_trv_mrk.nbr_dmn;idx_dmn++){
+ for(int idx_dmn=0;idx_dmn<var_trv_mrk.nbr_dmn;idx_dmn++)
dmn_idx_out_in[idx_dmn]=var_trv_mrk.dmn_idx_out_in[idx_dmn];
- }
int dmn_out_idx;
/* Search all dimensions in variable for new record dimension */
- for(dmn_out_idx=0;dmn_out_idx<var_prc_out[idx_var_prc_out]->nbr_dim;dmn_out_idx++){
- if(!strcmp(var_prc_out[idx_var_prc_out]->dim[dmn_out_idx]->nm,rec_dmn_nm_out)){
- break;
- }
- }
+ for(dmn_out_idx=0;dmn_out_idx<var_prc_out[idx_var_prc_out]->nbr_dim;dmn_out_idx++)
+ if(!strcmp(var_prc_out[idx_var_prc_out]->dim[dmn_out_idx]->nm,rec_dmn_nm_out)) break;
+
/* ...Will variable be record variable in output file?... */
if(dmn_out_idx == var_prc_out[idx_var_prc_out]->nbr_dim){
/* ...No. Variable will be non-record---does this change its status?... */
- if(nco_dbg_lvl_get() >= nco_dbg_var){
- if(var_prc_out[idx_var_prc_out]->is_rec_var) (void)fprintf(stdout,"%s: INFO Requested re-order will change variable %s from record to non-record variable\n",
- nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm);
- }
+ if(nco_dbg_lvl_get() >= nco_dbg_var)
+ if(var_prc_out[idx_var_prc_out]->is_rec_var)
+ (void)fprintf(stdout,"%s: INFO Requested re-order will change variable %s from record to non-record variable\n",nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm);
/* Assign record flag dictated by re-order */
var_prc_out[idx_var_prc_out]->is_rec_var=False;
}else{ /* ...otherwise variable will be record variable... */
@@ -5360,16 +5325,14 @@ nco_var_dmn_rdr_mtd_trv /* [fnc] Determine and set new dimensional
int dmn_dpl_idx;
for(dmn_dpl_idx=1;dmn_dpl_idx<var_prc_out[idx_var_prc_out]->nbr_dim;dmn_dpl_idx++){ /* NB: loop starts from 1 */
if(var_prc_out[idx_var_prc_out]->dmn_id[0] == var_prc_out[idx_var_prc_out]->dmn_id[dmn_dpl_idx]){
- (void)fprintf(stdout,"%s: ERROR Requested re-order turns duplicate non-record dimension %s in variable %s into output record dimension. netCDF does not support duplicate record dimensions in a single variable.\n%s: HINT: Exclude variable %s from extraction list with \"-x -v %s\".\n",
- nco_prg_nm_get(),rec_dmn_nm_out,var_prc_out[idx_var_prc_out]->nm,nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm,var_prc_out[idx_var_prc_out]->nm);
+ (void)fprintf(stdout,"%s: ERROR Requested re-order turns duplicate non-record dimension %s in variable %s into output record dimension. netCDF does not support duplicate record dimensions in a single variable.\n%s: HINT: Exclude variable %s from extraction list with \"-x -v %s\".\n",nco_prg_nm_get(),rec_dmn_nm_out,var_prc_out[idx_var_prc_out]->nm,nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm,var_prc_out[idx_var_prc_out]->nm);
nco_exit(EXIT_FAILURE);
} /* endif err */
} /* end loop over dmn_out */
} /* endif has_dpl_dmn */
/* ...Will becoming record variable change its status?... */
if(!var_prc_out[idx_var_prc_out]->is_rec_var){
- if(nco_dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: INFO Requested re-order will change variable %s from non-record to record variable\n",
- nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm);
+ if(nco_dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: INFO Requested re-order will change variable %s from non-record to record variable\n",nco_prg_nm_get(),var_prc_out[idx_var_prc_out]->nm);
/* Change record flag to status dictated by re-order */
var_prc_out[idx_var_prc_out]->is_rec_var=True;
/* ...Swap dimension information for multi-dimensional variables... */
@@ -5392,9 +5355,8 @@ nco_var_dmn_rdr_mtd_trv /* [fnc] Determine and set new dimensional
dmn_idx_out_in[dmn_idx_rec_in]=dmn_idx_swp;
/* Transfer dimension structures (re-ordered again) into GTT */
- for(int idx_dmn=0;idx_dmn<var_trv_mrk.nbr_dmn;idx_dmn++){
+ for(int idx_dmn=0;idx_dmn<var_trv_mrk.nbr_dmn;idx_dmn++)
trv_tbl->lst[ idx_var_mrk ].dmn_idx_out_in[idx_dmn]=dmn_idx_out_in[idx_dmn];
- }
/* Swap dimensions in list */
dmn_swp=var_prc_out[idx_var_prc_out]->dim[dmn_idx_rec_out];
@@ -5763,9 +5725,9 @@ nco_aed_prc_trv /* [fnc] Process single attribute edit for
trv_sct var_trv=trv_tbl->lst[idx_tbl];
/* Filter variables */
if(var_trv.nco_typ == nco_obj_typ_var){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Edit attribute */
(void)nco_aed_prc(grp_id,var_id,aed_lst[idx_aed]);
@@ -5783,9 +5745,9 @@ nco_aed_prc_trv /* [fnc] Process single attribute edit for
trv_sct var_trv=trv_tbl->lst[idx_tbl];
/* Filter variables */
if(var_trv.nco_typ == nco_obj_typ_var ){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Edit attribute */
(void)nco_aed_prc(grp_id,var_id,aed_lst[idx_aed]);
@@ -5803,9 +5765,9 @@ nco_aed_prc_trv /* [fnc] Process single attribute edit for
trv_sct var_trv=trv_tbl->lst[idx_tbl];
/* Filter variables */
if(var_trv.nco_typ == nco_obj_typ_var && strcmp(aed_lst[idx_aed].var_nm,var_trv.nm) == 0){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Edit attribute */
(void)nco_aed_prc(grp_id,NC_GLOBAL,aed_lst[idx_aed]);
@@ -5822,9 +5784,9 @@ nco_aed_prc_trv /* [fnc] Process single attribute edit for
trv_sct var_trv=trv_tbl->lst[idx_tbl];
/* Filter variables */
if(var_trv.nco_typ == nco_obj_typ_var && strcmp(aed_lst[idx_aed].var_nm,var_trv.nm) == 0){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Edit attribute */
(void)nco_aed_prc(grp_id,var_id,aed_lst[idx_aed]);
@@ -5854,7 +5816,7 @@ nco_dmn_trv_msa_tbl /* [fnc] Update all GTT dimensions with hy
/* If object is an extracted variable... */
if(var_trv.nco_typ == nco_obj_typ_var && var_trv.flg_xtr){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* Update for this variable */
@@ -5950,12 +5912,8 @@ nco_dmn_msa_tbl /* [fnc] Update all GTT dimensions with hy
/* If variable has a re-defined record dimension. NOTE: this implies passing NULL as User-specified record dimension parameter */
if(var_trv->rec_dmn_nm_out){
-
- /* Must be ncpdq */
assert(nco_prg_id == ncpdq);
-
rec_dmn_nm=(char *)strdup(var_trv->rec_dmn_nm_out);
-
} /* If variable has a re-defined record dimension */
/* Is requested record dimension in input file? */
@@ -6589,7 +6547,7 @@ nco_bld_rec_dmn /* [fnc] Build record dimensions array */
(*lmt_rec)=(lmt_sct **)nco_realloc((*lmt_rec),(rec_nbr+1)*sizeof(lmt_sct *));
(*lmt_rec)[rec_nbr]=(lmt_sct *)nco_malloc(sizeof(lmt_sct));
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
/* a) case where the dimension has coordinate variables */
@@ -6827,9 +6785,10 @@ nco_bld_trv_tbl /* [fnc] Construct GTT, Group Traversal Ta
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(nc_id);
if(CNV_CCM_CCSM_CF && EXTRACT_ASSOCIATED_COORDINATES){
- /* Implement CF "coordinates" and "bounds" conventions */
- (void)nco_xtr_cf_add(nc_id,"coordinates",trv_tbl);
+ /* Implement CF "ancillary_variables", "bounds", and "coordinates" */
+ (void)nco_xtr_cf_add(nc_id,"ancillary_variables",trv_tbl);
(void)nco_xtr_cf_add(nc_id,"bounds",trv_tbl);
+ (void)nco_xtr_cf_add(nc_id,"coordinates",trv_tbl);
} /* CNV_CCM_CCSM_CF */
/* Mark extracted dimensions */
@@ -6868,7 +6827,7 @@ nco_chk_dmn /* [fnc] Check valid dimension names */
(const int lmt_nbr, /* I [nbr] number of dimensions with limits */
nco_dmn_dne_t * flg_dne) /* I/O [lst] Flag to check if input dimension -d "does not exist" */
{
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
for(int lmt_idx=0;lmt_idx<lmt_nbr;lmt_idx++){
/* Check this flag */
if(flg_dne[lmt_idx].flg_dne){
@@ -6876,7 +6835,7 @@ nco_chk_dmn /* [fnc] Check valid dimension names */
flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
nco_exit(EXIT_FAILURE);
} /* Check this flag */
- } /* Check if all input -d dimensions were found */
+ } /* Were all user-specified dimensions found? */
} /* nco_chk_dmn() */
void
@@ -7261,8 +7220,8 @@ nco_msa_var_get_lmn_trv /* [fnc] Read a used defined limit */
/* And set start,count,stride to match current record ...Jesuzz */
var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->srt=idx_rec_crr_in;
var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->end=idx_rec_crr_in;
- var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->cnt=1;
- var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->srd=1;
+ var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->cnt=1L;
+ var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[idx_lmt]->srd=1L;
} /* Loop limits */
/* ! Case of previously existing limits */
@@ -7277,8 +7236,8 @@ nco_msa_var_get_lmn_trv /* [fnc] Read a used defined limit */
/* And set start, count, stride to match current record ... */
var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->srt=idx_rec_crr_in;
var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->end=idx_rec_crr_in;
- var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->cnt=1;
- var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->srd=1;
+ var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->cnt=1L;
+ var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->srd=1L;
var_trv->var_dmn[idx_dmn].crd->lmt_msa.lmt_dmn[0]->nm=strdup("record_limit");
} /* ! Case of previously existing limits */
} /* Case of dimension being coordinate variable */
@@ -7297,8 +7256,8 @@ nco_msa_var_get_lmn_trv /* [fnc] Read a used defined limit */
/* And set start,count,stride to match current record ...Jesuzz */
var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->srt=idx_rec_crr_in;
var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->end=idx_rec_crr_in;
- var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->cnt=1;
- var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->srd=1;
+ var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->cnt=1L;
+ var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[idx_lmt]->srd=1L;
} /* Loop limits */
/* ! Case of previously existing limits */
@@ -7313,8 +7272,8 @@ nco_msa_var_get_lmn_trv /* [fnc] Read a used defined limit */
/* And set start,count,stride to match current record ...Jesuzz */
var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->srt=idx_rec_crr_in;
var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->end=idx_rec_crr_in;
- var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->cnt=1;
- var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->srd=1;
+ var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->cnt=1L;
+ var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->srd=1L;
var_trv->var_dmn[idx_dmn].ncd->lmt_msa.lmt_dmn[0]->nm=strdup("record_limit");
} /* ! Case of previously existing limits */
} /* Case of dimension not being coordinate variable */
@@ -7409,7 +7368,7 @@ nco_var_get_wgt_trv /* [fnc] Retrieve weighting or mask variab
var_sct *wgt_var;
- /* Obtain group ID from API using full group name */
+ /* Obtain group ID from API */
(void)nco_inq_grp_full_ncid(nc_id,wgt_trv->grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -7464,7 +7423,7 @@ nco_var_get_wgt_trv /* [fnc] Retrieve weighting or mask variab
if(!strcmp(wgt_trv[idx_wgt]->grp_nm_fll,var_trv.grp_nm_fll)){
var_sct *wgt_var;
- /* Obtain group ID from API using full group name */
+ /* Obtain group ID from API */
(void)nco_inq_grp_full_ncid(nc_id,wgt_trv[idx_wgt]->grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -7892,14 +7851,14 @@ nco_grp_var_lst /* [fnc] Export list of variable names fo
} /* end nco_grp_var_lst() */
char * /* O [sng] Name of variable */
-nco_var_has_cf /* [fnc] Variable has CF-compliant information ("coordinates" or "bounds") */
+nco_var_has_cf /* [fnc] Variable has CF-compliant attributes ("ancillary_variables", "bounds", or "coordinates") */
(const int nc_id, /* I [ID] netCDF file ID */
const trv_sct * const var_trv, /* I [sct] Variable (object) */
- const char * const cf_nm, /* I [sng] CF convention ( "coordinates" or "bounds") */
+ const char * const cf_nm, /* I [sng] CF convention ("ancillary_variables", "bounds", or "coordinates") */
nco_bool *flg_cf_fnd) /* I/O [flg] CF variable was found */
{
- /* Detect associated coordinates specified by CF "bounds" or "coordinates" convention for single variable
- http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#coordinate-system */
+ /* Detect associated variables specified by CF "ancillary_variables", "bounds", or "coordinates" convention
+ http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#coordinate-system */
const char dlm_sng[]=" "; /* [sng] Delimiter string */
@@ -7916,7 +7875,7 @@ nco_var_has_cf /* [fnc] Variable has CF-compliant informa
/* Initialize return value */
*flg_cf_fnd=False;
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
/* Obtain variable ID */
@@ -7954,15 +7913,15 @@ nco_var_has_cf /* [fnc] Variable has CF-compliant informa
att_val[att_sz]='\0';
/* Split list into separate coordinate names
- Use nco_lst_prs_sgl_2D() not nco_lst_prs_2D() to avert TODO nco944 */
+ Use nco_lst_prs_sgl_2D() not nco_lst_prs_2D() to avert TODO nco944 */
cf_lst=nco_lst_prs_sgl_2D(att_val,dlm_sng,&nbr_cf);
- /* ...for each coordinate in CF convention attribute, i.e., "bounds" or "coordinate"... */
+ /* ...for each associated variable in CF convention attribute, i.e., "ancillary_variables", "bounds", or "coordinates"... */
for(int idx_cf=0;idx_cf<nbr_cf;idx_cf++){
char *cf_lst_var=cf_lst[idx_cf];
if(!cf_lst_var) continue;
} /* end loop over idx_cf */
- /* Return cf_lst_var, associated name (e.g., "lat_bounds"). NB: Assumption only 1 associated name */
+ /* Return cf_lst_var, associated name (e.g., "lat_bounds"). NB: Assumption only one associated name */
char *cf_lst_var=strdup(cf_lst[0]);
/* Free allocated memory */
@@ -7970,7 +7929,6 @@ nco_var_has_cf /* [fnc] Variable has CF-compliant informa
cf_lst=nco_sng_lst_free(cf_lst,nbr_cf);
return cf_lst_var;
-
} /* end strcmp() */
} /* end loop over attributes */
@@ -8538,7 +8496,7 @@ nco_dmn_malloc /* [fnc] Inquire about number of dimension
int grp_id; /* [ID] Group ID */
int nbr_dmn; /* [nbr] Number of dimensions */
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_nm_fll,&grp_id);
/* Obtain number of dimensions for group */
@@ -8558,37 +8516,6 @@ nco_dmn_malloc /* [fnc] Inquire about number of dimension
}
void
-nco_prn_var /* [fnc] Print variable (debug only) */
-(const int nc_id, /* I [ID] netCDF file ID (Input or output file) */
- trv_tbl_sct * const trv_tbl) /* I/O [sct] Traversal table */
-{
- const char fnc_nm[]="nco_prn_var()"; /* [sng] Function name */
-
- int grp_id;
- int var_id;
- int nbr_dmn;
-
- nc_type var_typ;
-
- /* Loop table */
- for(unsigned int idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
-
- trv_sct var_trv=trv_tbl->lst[idx_tbl];
-
- /* Is variable */
- if(var_trv.nco_typ == nco_obj_typ_var){
-
- (void)nco_inq_grp_full_ncid(nc_id,var_trv.grp_nm_fll,&grp_id);
- (void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
- (void)nco_inq_var(grp_id,var_id,(char *)NULL,&var_typ,&nbr_dmn,(int *)NULL,(int *)NULL);
-
- if(nco_dbg_lvl_get() >= nco_dbg_dev) (void)fprintf(stdout,"%s: DEBUG %s variable <%s> Type: %d\n",nco_prg_nm_get(),fnc_nm,var_trv.nm_fll,var_typ);
-
- } /* Is variable */
- } /* Loop table */
-} /* nco_prn_var() */
-
-void
nco_dmn_lmt /* [fnc] Convert a lmt_sct array to dmn_sct (name only) */
(lmt_sct **lmt, /* I [lst] lmt_sct array */
const int nbr_lmt, /* I [nbr] Size of lmt_sct array */
@@ -8603,13 +8530,13 @@ nco_dmn_lmt /* [fnc] Convert a lmt_sct array to dmn_s
(*dmn)[idx]->xrf=NULL;
(*dmn)[idx]->val.vp=NULL;
(*dmn)[idx]->is_rec_dmn=lmt[idx]->is_rec_dmn;
- (*dmn)[idx]->cnt=-1;
- (*dmn)[idx]->sz=-1;
- (*dmn)[idx]->srt=-1;
- (*dmn)[idx]->end=-1;
- (*dmn)[idx]->srd=-1;
+ (*dmn)[idx]->cnt=-1L;
+ (*dmn)[idx]->sz=-1L;
+ (*dmn)[idx]->srt=-1L;
+ (*dmn)[idx]->end=-1L;
+ (*dmn)[idx]->srd=-1L;
(*dmn)[idx]->cid=-1;
- (*dmn)[idx]->cnk_sz=-1;
+ (*dmn)[idx]->cnk_sz=-1L;
(*dmn)[idx]->type=(nc_type)-1;
}
@@ -8932,7 +8859,6 @@ nco_nsm_dfn_wrt /* [fnc] Define OR write ensemble fixed var
for(int idx_nsm=0;idx_nsm<trv_tbl->nsm_nbr;idx_nsm++){
/* Get output group */
-
if(trv_tbl->nsm_sfx){
/* Define new name by appending suffix (e.g., /cesm + _avg) */
char *nm_fll_sfx=nco_bld_nsm_sfx(trv_tbl->nsm[idx_nsm].grp_nm_fll_prn,trv_tbl);
@@ -8943,27 +8869,23 @@ nco_nsm_dfn_wrt /* [fnc] Define OR write ensemble fixed var
if(gpe) grp_out_fll=nco_gpe_evl(gpe,trv_tbl->nsm[idx_nsm].grp_nm_fll_prn); else grp_out_fll=(char *)strdup(trv_tbl->nsm[idx_nsm].grp_nm_fll_prn);
} /* !trv_tbl->nsm_sfx */
-
- /* List of fixed templates */
+ /* List of fixed templates */
for(int idx_skp=0;idx_skp<trv_tbl->nsm[idx_nsm].skp_nbr;idx_skp++){
/* Get variable */
trv_sct *var_trv=trv_tbl_var_nm_fll(trv_tbl->nsm[idx_nsm].skp_nm_fll[idx_skp],trv_tbl);
/* Define variable */
- if (flg_def == True) (void)nco_cpy_var_dfn_trv(nc_id,nc_out_id,cnk,grp_out_fll,dfl_lvl,gpe,NULL,var_trv,NULL,0,trv_tbl);
+ if(flg_def) (void)nco_cpy_var_dfn_trv(nc_id,nc_out_id,cnk,grp_out_fll,dfl_lvl,gpe,NULL,var_trv,NULL,0,trv_tbl);
- /* Obtain group IDs using full group name */
+ /* Obtain group IDs */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id_in);
(void)nco_inq_grp_full_ncid(nc_out_id,grp_out_fll,&grp_id_out);
- /* Copy variable data */
- if (flg_def == False) (void)nco_cpy_var_val_mlt_lmt_trv(grp_id_in,grp_id_out,(FILE *)NULL,NULL,var_trv);
+ /* Copy variable data */
+ if(!flg_def) (void)nco_cpy_var_val_mlt_lmt_trv(grp_id_in,grp_id_out,(FILE *)NULL,NULL,var_trv);
- if(nco_dbg_lvl_get() >= nco_dbg_vrb && nco_dbg_lvl_get() != nco_dbg_dev){
- (void)fprintf(stdout,"%s: INFO creating fixed variables <%s> in ensemble parent group <%s>\n",nco_prg_nm_get(),
- trv_tbl->nsm[idx_nsm].skp_nm_fll[idx_skp],grp_out_fll);
- }
+ if(nco_dbg_lvl_get() >= nco_dbg_vrb && nco_dbg_lvl_get() != nco_dbg_dev) (void)fprintf(stdout,"%s: INFO creating fixed variables <%s> in ensemble parent group <%s>\n",nco_prg_nm_get(),trv_tbl->nsm[idx_nsm].skp_nm_fll[idx_skp],grp_out_fll);
} /* List of fixed templates */
@@ -9006,7 +8928,7 @@ nco_nsm_ncr /* [fnc] Increase ensembles (more than 1 f
(void)fprintf(stdout,"%s: DEBUG %s <ensemble %d> <%s>\n",nco_prg_nm_get(),fnc_nm,idx_nsm,trv_tbl->nsm[idx_nsm].grp_nm_fll_prn);
}
- /* Obtain group ID of current ensemble using full group name */
+ /* Obtain group ID of current ensemble */
rcd+=nco_inq_grp_full_ncid_flg(nc_id,trv_tbl->nsm[idx_nsm].grp_nm_fll_prn,&grp_id);
/* Group must exist (file # call > 1 ), if not exit */
@@ -9928,7 +9850,7 @@ nco_fix_dfn_wrt /* [fnc] Define/write fixed variables (nc
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,trv->grp_nm_fll); else grp_out_fll=(char *)strdup(trv->grp_nm_fll);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,trv->grp_nm_fll,&grp_id);
/* Get variable ID */
@@ -9952,7 +9874,6 @@ nco_fix_dfn_wrt /* [fnc] Define/write fixed variables (nc
}else{ /* !flg_dfn */
/* Write mode */
-
md5_sct *md5=NULL; /* [sct] MD5 configuration */
/* Get group ID */
@@ -10176,7 +10097,7 @@ nco_chk_nsm /* [fnc] Check if ensembles are valid */
if(nco_dbg_lvl_get() >= nco_dbg_dev) (void)fprintf(stdout,"%s: DEBUG %s <ensemble %d> <%s>\n",nco_prg_nm_get(),fnc_nm,
idx_nsm,trv_tbl->nsm[idx_nsm].grp_nm_fll_prn);
- /* Obtain group ID of current ensemble using full group name */
+ /* Obtain group ID of current ensemble */
rcd+=nco_inq_grp_full_ncid_flg(in_id,trv_tbl->nsm[idx_nsm].grp_nm_fll_prn,&grp_id);
/* Group must exist, if not exit */
@@ -10260,7 +10181,7 @@ nco_chk_nsm /* [fnc] Check if ensembles are valid */
size_t tpl_sz; /* [nbr] Size of template dimension */
long dmn_sz; /* [nbr] Size of dimension */
- long dmn_cnt_gtt; /* [nbr] Hyperslabbed size of dimension of GTT variable (first file only) */
+ long dmn_cnt_gtt=-1; /* [nbr] Hyperslabbed size of dimension of GTT variable (first file only) */
nco_bool flg_has_lmt; /* [flg] Dimension has hyperslab */
@@ -10387,7 +10308,7 @@ nco_nsm_att /* [fnc] Inquire if ensemble parent group
trv_sct trv=trv_tbl->lst[idx_tbl];
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(nc_id,trv.grp_nm_fll,&grp_id);
/* Does attribute "ensemble_source" exist? (saved in ncge); string is hard coded and duplicated */
@@ -10608,10 +10529,10 @@ nco_prt_dmn /* [fnc] Print dimensions (debug) */
long dmn_sz; /* [nbr] Dimension size */
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_nm_fll,&grp_id);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_nm,&var_id);
/* Get number of dimensions for variable */
@@ -10643,7 +10564,7 @@ nco_prt_dmn /* [fnc] Print dimensions (debug) */
/* Loop over dimensions of variable */
for(int idx_var_dim=0;idx_var_dim<var_trv->nbr_dmn;idx_var_dim++){
- int dmn_id;
+ int dmn_id=-1;
if (var_trv->var_dmn[idx_var_dim].crd){
dmn_sz=var_trv->var_dmn[idx_var_dim].crd->sz;
@@ -10683,7 +10604,7 @@ nco_nsm_wrt_att /* [fnc] Save ncge metadata attribute */
/* If object is group */
if(grp_trv.nco_typ == nco_obj_typ_grp){
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_trv.grp_nm_fll,&grp_id);
if(grp_trv.flg_nsm_prn){
@@ -10701,7 +10622,7 @@ nco_nsm_wrt_att /* [fnc] Save ncge metadata attribute */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,grp_trv.grp_nm_fll_prn); else grp_out_fll=(char *)strdup(grp_trv.grp_nm_fll_prn);
} /* !nsm_sfx */
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
aed.att_nm=strdup("ensemble_source");
diff --git a/src/nco/nco_grp_utl.h b/src/nco/nco_grp_utl.h
index d5de0d8..580c0ee 100644
--- a/src/nco/nco_grp_utl.h
+++ b/src/nco/nco_grp_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_utl.h,v 1.511 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_grp_utl.h,v 1.514 2014/08/26 17:53:43 pvicente Exp $ */
/* Purpose: Group utilities */
-/* Copyright (C) 2011--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_utl.h" *//* Group utilities */
@@ -671,9 +672,9 @@ nco_dmn_swap /* [fnc] Swap dimensions */
void
nco_dfn_dmn /* [fnc] Define dimension size and ID in array */
-(const char * const dmn_nm, /* I [sng] Name of dimension */
+(const char * const dmn_nm_fll_out, /* I [sng] Full name of dimension in output */
const long dmn_sz, /* I [nbr] Size of dimension */
- const int dmn_id, /* I [id] ID of dimension */
+ const int dmn_id_out, /* I [id] ID of dimension in output */
dmn_cmn_sct *dmn_cmn, /* I/O [sct] Dimension structure array */
const int nbr_dmn); /* I [nbr] Number of dimensions (size of above array) */
@@ -726,19 +727,13 @@ nco_lmt_aux /* [fnc] Apply auxiliary -X limits (Auxili
trv_tbl_sct * const trv_tbl); /* I/O [sct] GTT (Group Traversal Table) */
void
-nco_prn_var /* [fnc] Print variable (debug only) */
-(const int nc_id, /* I [ID] netCDF file ID (Input or output file) */
- trv_tbl_sct * const trv_tbl); /* I/O [sct] Traversal table */
-
-void
nco_dmn_lmt /* [fnc] Convert a lmt_sct array to dmn_sct (name only) */
(lmt_sct **lmt, /* I [lst] lmt_sct array */
const int nbr_lmt, /* I [nbr] Size of lmt_sct array */
dmn_sct ***dmn); /* O [sct] dmn_sct array */
void
-nco_prn_nsm /* [fnc] Print ensembles */
-(const trv_tbl_sct * const trv_tbl); /* I [sct] Traversal table */
+nco_prn_nsm /* [fnc] Print ensembles */ (const trv_tbl_sct * const trv_tbl); /* I [sct] Traversal table */
void
nco_bld_nsm /* [fnc] Build ensembles */
diff --git a/src/nco/nco_lmt.c b/src/nco/nco_lmt.c
index 7c76f9f..0d396c2 100644
--- a/src/nco/nco_lmt.c
+++ b/src/nco/nco_lmt.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_lmt.c,v 1.208 2014/02/14 05:22:17 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_lmt.c,v 1.210 2014/07/15 18:48:55 zender Exp $ */
/* Purpose: Hyperslab limits */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_lmt.h" /* Hyperslab limits */
@@ -1368,7 +1369,7 @@ nco_lmt_evl_dmn_crd /* [fnc] Parse user-specified limits into hypersl
lmt.srd=1L;
lmt.flg_input_complete=False;
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,grp_nm_fll,&grp_id);
/* Use parameter to inquire about coordinate.
@@ -1378,7 +1379,7 @@ nco_lmt_evl_dmn_crd /* [fnc] Parse user-specified limits into hypersl
ncks -O -v ts -d time,0,1 -d Latitude,40.0 -d Longitude,-105.0 http://hydro1.sci.gsfc.nasa.gov/opendap/hyrax/ncml/LPRM_AMSRE_D_SOILM3_timeSeries.ncml amsre.nc */
if(is_crd){
- /* Obtain coordinate variable ID using group ID */
+ /* Obtain coordinate variable ID */
(void)nco_inq_varid(grp_id,nm,&var_id);
/* Get coordinate type */
@@ -1492,7 +1493,7 @@ nco_lmt_evl_dmn_crd /* [fnc] Parse user-specified limits into hypersl
/* If there is a coordinate variable */
if(is_crd){
- /* Get variable ID of coordinate. NOTE: using group ID */
+ /* Get variable ID of coordinate */
(void)nco_inq_varid(grp_id,lmt.nm,&dim.cid);
char *cln_sng=NULL_CEWI;
diff --git a/src/nco/nco_lmt.h b/src/nco/nco_lmt.h
index e07795a..d830521 100644
--- a/src/nco/nco_lmt.h
+++ b/src/nco/nco_lmt.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_lmt.h,v 1.69 2014/01/28 07:15:55 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_lmt.h,v 1.70 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Hyperslab limits */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_lmt.h" *//* Hyperslab limits */
diff --git a/src/nco/nco_lst_utl.c b/src/nco/nco_lst_utl.c
index 95a4821..1d8fdd3 100644
--- a/src/nco/nco_lst_utl.c
+++ b/src/nco/nco_lst_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_lst_utl.c,v 1.84 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_lst_utl.c,v 1.85 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: List utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_lst_utl.h" /* List utilities */
diff --git a/src/nco/nco_lst_utl.h b/src/nco/nco_lst_utl.h
index 3f35ae3..9229f46 100644
--- a/src/nco/nco_lst_utl.h
+++ b/src/nco/nco_lst_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_lst_utl.h,v 1.54 2014/01/06 06:46:05 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_lst_utl.h,v 1.55 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: List utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_lst_utl.h" *//* List utilities */
diff --git a/src/nco/nco_md5.c b/src/nco/nco_md5.c
index 578d911..e21baeb 100644
--- a/src/nco/nco_md5.c
+++ b/src/nco/nco_md5.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_md5.c,v 1.21 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_md5.c,v 1.22 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: NCO utilities for MD5 digests */
-/* Copyright (C) 2012--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
ncecat -O -D 1 --md5 -p ~/nco/data in.nc in.nc ~/foo.nc
@@ -197,7 +198,7 @@ nco_md5_chk_ram /* [fnc] Perform MD5 digest on hyperslab in RAM */
L. Peter Deutsch
ghost at aladdin.com
*/
-/* $Id: nco_md5.c,v 1.21 2013/12/31 05:14:02 zender Exp $ */
+/* $Id: nco_md5.c,v 1.22 2014/06/15 21:06:23 zender Exp $ */
/*
Independent implementation of MD5 (RFC 1321).
diff --git a/src/nco/nco_md5.h b/src/nco/nco_md5.h
index 79f0135..c969ba3 100644
--- a/src/nco/nco_md5.h
+++ b/src/nco/nco_md5.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_md5.h,v 1.15 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_md5.h,v 1.16 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Description (definition) of MD5 digest functions */
-/* Copyright (C) 2012--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_md5.h" *//* MD5 digests */
@@ -93,7 +94,7 @@ extern "C" {
ghost at aladdin.com
*/
-/* $Id: nco_md5.h,v 1.15 2013/12/31 05:14:02 zender Exp $ */
+/* $Id: nco_md5.h,v 1.16 2014/06/15 21:06:23 zender Exp $ */
/*
Independent implementation of MD5 (RFC 1321).
diff --git a/src/nco/nco_mmr.c b/src/nco/nco_mmr.c
index 700902b..95c909b 100644
--- a/src/nco/nco_mmr.c
+++ b/src/nco/nco_mmr.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_mmr.c,v 1.64 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_mmr.c,v 1.66 2014/07/10 22:33:02 zender Exp $ */
/* Purpose: Memory management */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage of NCO memory allocation routines nco_malloc(), nco_malloc_flg(), and nco_malloc_dbg():
nco_malloc(): Use this for small memory requests
@@ -572,6 +573,9 @@ nco_mmr_usg_prn /* [fnc] Print rusage memory usage statistics */
#if (defined LINUX) || (defined LINUXAMD64)
(void)fprintf(stdout,"%s: INFO %s reports system type is LINUX so getrusage() does implement ru_maxrss [kB] and DOES NOT implement ru_ixrss, ru_idrss, and ru_idrss. Page size is %d B.\n",nco_prg_nm_get(),fnc_nm,sz_pg);
#endif /* !LINUX */
+#ifdef MACOSX
+ (void)fprintf(stdout,"%s: INFO %s reports system type is MACOSX so rusage structure elements ru_utime and ru_stime are of type 'int' not 'long int'.\n",nco_prg_nm_get(),fnc_nm);
+#endif /* !MACOSX */
#ifdef NECSX
(void)fprintf(stdout,"%s: INFO %s reports system type is NECSX so getrusage() units for page size and time are unknown.\n",nco_prg_nm_get(),fnc_nm);
#endif /* !NECSX */
@@ -586,7 +590,8 @@ nco_mmr_usg_prn /* [fnc] Print rusage memory usage statistics */
rcd_sys=rusage_who;
/* fxm: use input argument rusage_who instead of RUSAGE_SELF */
rcd_sys=0*rcd_sys+getrusage(RUSAGE_SELF,&usg);
- if(nco_dbg_lvl_get() > nco_dbg_io) (void)fprintf(stdout,"%s: INFO %s reports: rusage.ru_utime.tv_sec = user time used = %li s, rusage.ru_utime.tv_usec = user time used = %li us, rusage.ru_stime.tv_sec = system time used = %li s, rusage.ru_stime.tv_usec = system time used = %li us, rusage.ru_maxrss = maximum resident set size = %li [sz], rusage.ru_ixrss = integral shared memory size = %li [sz tm], rusage.ru_idrss = integral unshared data size = %li [sz], rusage.ru_isrss = integral unsh [...]
+ /* MACOSX rusage structure elements ru_utime and ru_stime are of type 'int' not 'long int' */
+ if(nco_dbg_lvl_get() > nco_dbg_io) (void)fprintf(stdout,"%s: INFO %s reports: rusage.ru_utime.tv_sec = user time used = %li s, rusage.ru_utime.tv_usec = user time used = %li us, rusage.ru_stime.tv_sec = system time used = %li s, rusage.ru_stime.tv_usec = system time used = %li us, rusage.ru_maxrss = maximum resident set size = %li [sz], rusage.ru_ixrss = integral shared memory size = %li [sz tm], rusage.ru_idrss = integral unshared data size = %li [sz], rusage.ru_isrss = integral unsh [...]
return (long)usg.ru_maxrss; /* [B] Maximum resident set size */
#else /* !HAVE_GETRUSAGE */
diff --git a/src/nco/nco_mmr.h b/src/nco/nco_mmr.h
index bdb30b6..e718cd2 100644
--- a/src/nco/nco_mmr.h
+++ b/src/nco/nco_mmr.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_mmr.h,v 1.37 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_mmr.h,v 1.38 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Memory management */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_mmr.h" *//* Memory management */
diff --git a/src/nco/nco_mpi.h b/src/nco/nco_mpi.h
index 544da82..6720b26 100644
--- a/src/nco/nco_mpi.h
+++ b/src/nco/nco_mpi.h
@@ -1,21 +1,22 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_mpi.h,v 1.22 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_mpi.h,v 1.24 2014/07/11 02:13:51 zender Exp $ */
/* Purpose: MPI utilities */
/* NB: Currently this header is only accessed by main() MPI programs
Hence it is not (yet) part of libnco.a
- Header assumes its inclusion is already conditional on ENABLE_MPI
+ Header assumes its inclusion depends on ENABLE_MPI
Header is currently mostly for file-scope constants needed by MPI routines
No functions (yet) but some will eventually live here after MPI functionalization
Adding functions will require creating a corresponding *.c file
*.c files must reside in libnco.a or link separately to MPI executables
The latter would slightly complicate the build procedure
- I am not yet sure I want _any_ MPI dependencies in libnco.a
- Cross-platform link weirdness (e.g., AIX) makes avoiding this desirable */
+ Should _any_ MPI dependencies be in libnco.a?
+ Cross-platform link weirdness (e.g., AIX) makes MPI dependencies in libnco.a fragile */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_mpi.h" *//* MPI utilities */
diff --git a/src/nco/nco_msa.c b/src/nco/nco_msa.c
index 176d4f8..f323723 100644
--- a/src/nco/nco_msa.c
+++ b/src/nco/nco_msa.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_msa.c,v 1.246 2014/05/23 20:37:23 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_msa.c,v 1.250 2014/08/27 04:44:01 zender Exp $ */
/* Purpose: Multi-slabbing algorithm */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_msa.h" /* Multi-slabbing algorithm */
@@ -780,10 +781,7 @@ nco_msa_wrp_splt_trv /* [fnc] Split wrapped dimensions (GTT version) */
if(dmn_trv->lmt_msa.lmt_dmn[idx]->srt > dmn_trv->lmt_msa.lmt_dmn[idx]->end){
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"%s: INFO %s dimension <%s> has wrapped limits (%li->%li):\n",
- nco_prg_nm_get(),fnc_nm,dmn_trv->nm_fll,dmn_trv->lmt_msa.lmt_dmn[idx]->srt,dmn_trv->lmt_msa.lmt_dmn[idx]->end);
- }
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"%s: INFO %s dimension <%s> has wrapped limits (%li->%li):\n",nco_prg_nm_get(),fnc_nm,dmn_trv->nm_fll,dmn_trv->lmt_msa.lmt_dmn[idx]->srt,dmn_trv->lmt_msa.lmt_dmn[idx]->end);
lmt_wrp=(lmt_sct *)nco_malloc(2*sizeof(lmt_sct));
@@ -831,7 +829,6 @@ nco_msa_wrp_splt_trv /* [fnc] Split wrapped dimensions (GTT version) */
(void)fprintf(stdout,"%d:\n",dmn_trv->lmt_msa.lmt_dmn_nbr);
}
-
/* "trv": Insert 2 non-wrapped limits */
/* Current number of dimension limits for this table dimension */
@@ -859,19 +856,13 @@ nco_msa_wrp_splt_trv /* [fnc] Split wrapped dimensions (GTT version) */
/* Update current index of dimension limits for this table dimension */
dmn_trv->lmt_msa.lmt_crr++;
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"%s: INFO %s dimension <%s> new limits inserted (%li->%li) - (%li->%li):\n",
- nco_prg_nm_get(),fnc_nm,dmn_trv->nm_fll,dmn_trv->lmt_msa.lmt_dmn[idx]->srt,dmn_trv->lmt_msa.lmt_dmn[idx]->end,
- dmn_trv->lmt_msa.lmt_dmn[lmt_new_idx]->srt,dmn_trv->lmt_msa.lmt_dmn[lmt_new_idx]->end);
- }
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"%s: INFO %s dimension <%s> new limits inserted (%li->%li) - (%li->%li):\n",nco_prg_nm_get(),fnc_nm,dmn_trv->nm_fll,dmn_trv->lmt_msa.lmt_dmn[idx]->srt,dmn_trv->lmt_msa.lmt_dmn[idx]->end,dmn_trv->lmt_msa.lmt_dmn[lmt_new_idx]->srt,dmn_trv->lmt_msa.lmt_dmn[lmt_new_idx]->end);
} /* endif srt > end */
} /* end loop over size */
/* Check if genuine wrapped co-ordinate */
- if(size==1 && dmn_trv->lmt_msa.lmt_dmn_nbr==2){
- dmn_trv->lmt_msa.WRP=True;
- }
+ if(size == 1 && dmn_trv->lmt_msa.lmt_dmn_nbr == 2) dmn_trv->lmt_msa.WRP=True;
} /* End nco_msa_wrp_splt_trv() */
@@ -921,7 +912,6 @@ nco_msa_clc_cnt_trv /* [fnc] Calculate size of multiple hyperslab (GTT vers
} /* end else */
return;
-
} /* End nco_msa_clc_cnt_trv() */
void
@@ -942,8 +932,6 @@ nco_msa_qsort_srt_trv /* [fnc] Sort limits by srt values (GTT version) */
} /* End nco_msa_qsort_srt_trv() */
-
-
nco_bool /* O [flg] Return true if limits overlap (GTT version) */
nco_msa_ovl_trv /* [fnc] See if limits overlap */
(dmn_trv_sct *dmn_trv) /* [sct] Dimension structure from GTT */
@@ -1030,7 +1018,6 @@ nco_msa_wrp_splt /* [fnc] Split wrapped dimensions */
if(size==1 && lmt_lst->lmt_dmn_nbr==2) lmt_lst->WRP=True;
} /* end nco_msa_wrp_splt() */
-
void
nco_msa_wrp_splt_cpy /* [fnc] Split wrapped dimensions (make deep copy of new wrapped limits) */
(lmt_msa_sct *lmt_lst) /* [sct] MSA */
@@ -1113,7 +1100,6 @@ nco_msa_wrp_splt_cpy /* [fnc] Split wrapped dimensions (make deep copy of new
(void)fprintf(stdout,"current limits=%d:\n",lmt_lst->lmt_dmn_nbr);
}
-
/* "trv": Insert 2 non-wrapped limits */
/* Current number of dimension limits for this table dimension */
@@ -1141,11 +1127,7 @@ nco_msa_wrp_splt_cpy /* [fnc] Split wrapped dimensions (make deep copy of new
/* Update current index of dimension limits for this table dimension */
lmt_lst->lmt_crr++;
- if(nco_dbg_lvl_get() == nco_dbg_old){
- (void)fprintf(stdout,"%s: INFO %s dimension <%s> new limits inserted (%li->%li) - (%li->%li):\n",
- nco_prg_nm_get(),fnc_nm,lmt_lst->dmn_nm,lmt_lst->lmt_dmn[idx]->srt,lmt_lst->lmt_dmn[idx]->end,
- lmt_lst->lmt_dmn[lmt_new_idx]->srt,lmt_lst->lmt_dmn[lmt_new_idx]->end);
- }
+ if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"%s: INFO %s dimension <%s> new limits inserted (%li->%li) - (%li->%li):\n",nco_prg_nm_get(),fnc_nm,lmt_lst->dmn_nm,lmt_lst->lmt_dmn[idx]->srt,lmt_lst->lmt_dmn[idx]->end,lmt_lst->lmt_dmn[lmt_new_idx]->srt,lmt_lst->lmt_dmn[lmt_new_idx]->end);
} /* endif srt > end */
} /* end loop over size */
@@ -1165,7 +1147,8 @@ nco_cpy_var_val_mlt_lmt_trv /* [fnc] Copy variable data from input to ou
{
/* Purpose: Copy variable data from input netCDF file to output netCDF file
Routine truncates dimensions in variable definition in output file according to user-specified limits
- Routine copies variable-by-variable, old-style, used only by ncks
+ Routine copies variable-by-variable, old-style, used only by ncks
+ Routine does not handle strides (srd)
"GTT" changes from the original nco_cpy_var_val_mlt_lmt():
Object to write (variable) is passed as parameter */
@@ -1367,9 +1350,8 @@ nco_cpy_msa_lmt /* [fnc] Copy MSA struct from table to local
} /* End Loop needed limits */
-
/* No limits? ...Make a limit to read all */
- if ( (*lmt_msa)[dmn_idx_var]->lmt_dmn_nbr == 0){
+ if ((*lmt_msa)[dmn_idx_var]->lmt_dmn_nbr == 0){
if(nco_dbg_lvl_get() == nco_dbg_old) (void)fprintf(stdout,"Warning...no limit zone\n ");
@@ -1382,9 +1364,9 @@ nco_cpy_msa_lmt /* [fnc] Copy MSA struct from table to local
(void)nco_lmt_init((*lmt_msa)[dmn_idx_var]->lmt_dmn[0]);
/* And set start,count,stride to read everything ...major success */
- (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srt=0;
+ (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srt=0L;
(*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->cnt=(*lmt_msa)[dmn_idx_var]->dmn_sz_org;
- (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srd=1;
+ (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srd=1L;
} /* Make a limit to read all */
} /* If there are limits for this variable dimension, get MSA from table */
@@ -1436,9 +1418,9 @@ nco_cpy_msa_lmt /* [fnc] Copy MSA struct from table to local
(void)nco_lmt_init((*lmt_msa)[dmn_idx_var]->lmt_dmn[0]);
/* And set start,count,stride to read everything ...major success */
- (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srt=0;
+ (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srt=0L;
(*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->cnt=(*lmt_msa)[dmn_idx_var]->dmn_sz_org;
- (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srd=1;
+ (*lmt_msa)[dmn_idx_var]->lmt_dmn[0]->srd=1L;
} /* Make a limit to read all */
} /* If there are limits for this variable dimension, get MSA from table */
@@ -1476,7 +1458,7 @@ nco_msa_var_get_trv /* [fnc] Get variable data from disk taking
var_trv=trv_tbl_var_nm_fll(var_in->nm_fll,trv_tbl);
assert(var_trv);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
nbr_dim=var_in->nbr_dim;
diff --git a/src/nco/nco_msa.h b/src/nco/nco_msa.h
index 413d0da..bbe9c38 100644
--- a/src/nco/nco_msa.h
+++ b/src/nco/nco_msa.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_msa.h,v 1.81 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_msa.h,v 1.82 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Multi-slabbing algorithm */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_msa.h" *//* Multi-slabbing algorithm */
diff --git a/src/nco/nco_mss_val.c b/src/nco/nco_mss_val.c
index 31ecaec..42c1717 100644
--- a/src/nco/nco_mss_val.c
+++ b/src/nco/nco_mss_val.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_mss_val.c,v 1.55 2014/05/27 02:55:26 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_mss_val.c,v 1.56 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Missing value utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_mss_val.h" /* Missing value utilities */
diff --git a/src/nco/nco_mss_val.h b/src/nco/nco_mss_val.h
index 620a350..d6df1c1 100644
--- a/src/nco/nco_mss_val.h
+++ b/src/nco/nco_mss_val.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_mss_val.h,v 1.35 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_mss_val.h,v 1.36 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Missing value utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_mss_val.h" *//* Missing value utilities */
diff --git a/src/nco/nco_netcdf.c b/src/nco/nco_netcdf.c
index b178f51..75c1be3 100644
--- a/src/nco/nco_netcdf.c
+++ b/src/nco/nco_netcdf.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_netcdf.c,v 1.242 2014/05/20 17:17:03 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_netcdf.c,v 1.252 2014/07/11 02:13:51 zender Exp $ */
/* Purpose: NCO wrappers for netCDF C library */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_netcdf.h" /* NCO wrappers for netCDF C library */
@@ -77,7 +78,7 @@ nco_err_exit /* [fnc] Print netCDF error message, routine name, then exit */
switch(rcd){
case NC_EBADTYPE: (void)fprintf(stdout,"ERROR NC_BADTYPE Not a netCDF data type\nHINT: NC_EBADTYPE errors can occur when NCO tries to write netCDF4 features to a netCDF3 file. Features that cannot be defined in a netCDF3 file, and that thus will trigger this error, include groups and netCDF4 atomic types (e.g., NC_STRING, NC_UBYTE). The workaround is to remove all netCDF4 features before attempting the conversion, or to just give up and write a netCDF4 output file instead of a netCDF3 [...]
case NC_ECANTWRITE: (void)fprintf(stdout,"ERROR NC_ECANTWRITE Can't write file\nHINT: NC_ECANTWRITE errors can occur when NCO tries to write to an HDF5 file that is not netCDF4-compliant. One workaround is translate the file to a netCDF4-compliant file first, e.g., with \'ncks in.h5 out.nc\'.\n"); break;
- case NC_EINVAL: (void)fprintf(stdout,"ERROR NC_EINVAL Invalid argument\nHINT: NC_EINVAL errors can occur for many reasons. Three common ones are described here. 1. When NCO operators attempt to open netCDF4 files using the diskless option, usually invoked with --diskless_all, --ram_all, or --open_ram. Is your input file netCDF4 format? (http://nco.sf.net/nco.html#fmt_inq shows how to tell.) If so then omitting the diskless option may solve this problem. 2. When HDF4-enabled NCO attem [...]
+ case NC_EINVAL: (void)fprintf(stdout,"ERROR NC_EINVAL Invalid argument\nHINT: NC_EINVAL errors can occur for many reasons. Three common ones are described here. 1. When NCO operators attempt to open netCDF4 files using the diskless option, usually invoked with --diskless_all, --ram_all, or --open_ram. Is your input file netCDF4 format? (http://nco.sf.net/nco.html#fmt_inq shows how to tell.) If so then omitting the diskless option may solve this problem. 2. When HDF4-enabled NCO attem [...]
case NC_ELATEFILL: /* netcdf.h replaced NC_EFILLVALUE by NC_ELATEFILL after about netCDF ~4.2.1 */
(void)fprintf(stdout,"ERROR NC_ELATEFILL (formerly NC_EFILLVALUE) Attempt to define fill value when data already exists\nHINT: NC_ELATEFILL errors can occur when ncap2 attempts to define a variable with a _FillValue attribute in a netCDF4 file. We believe this is an NCO bug (fxm TODO nco1089) and are working to fix it. Does your output file need to be netCDF4 or netCDF4_classic format? If so, then wait for us to fix the bug. If not, change the output format to netCDF3 (e.g., with - [...]
#ifdef ENABLE_NETCDF4
@@ -89,7 +90,7 @@ nco_err_exit /* [fnc] Print netCDF error message, routine name, then exit */
#else /* !ENABLE_NETCDF4 */
(void)fprintf(stdout,"Are your input files netCDF4 format? (http://nco.sf.net/nco.html#fmt_inq shows how to tell.) If so then installing or re-building a netCDF4-compatible version of NCO should solve this problem. First upgrade netCDF to version 4.x, then install NCO using those netCDF 4.x libraries.\n2. NC_ENOTNC can occur when users attempt to utilize diskless (i.e., RAM) files. In this case remove the diskless switches (e.g., --ram or --diskless) and then re-issue the command. \n");
#endif /* !ENABLE_NETCDF4 */
- (void)fprintf(stdout,"2. NCO attempts to utilize diskless (i.e., RAM) files. In this case remove the diskless switches (e.g., --ram or --diskless) and then re-issue the command.\n3. NCO attempts to read other non-supported filetypes, e.g., HDF4, HDF-EOS2. In this case it may be possible to access the input files using NCO if NCO is first re-linked to a version of netCDF configured with the --enable-hdf4 option. This is a non-standard netCDF build option described here: http://www.u [...]
+ (void)fprintf(stdout,"2. NCO attempts to utilize diskless (i.e., RAM) files. In this case remove the diskless switches (e.g., --ram or --diskless) and then re-issue the command.\n3. NCO attempts to read other filetypes (HDF4, HDF-EOS2, pnetCDF) for which support must be (but was not) enabled at netCDF build-time. In this case it may be possible to access the input files using NCO if NCO is first re-linked to a version of netCDF configured with the --enable-hdf4 option. This is a no [...]
case NC_ERANGE: (void)fprintf(stdout,"ERROR NC_ERANGE Result not representable in output file\nHINT: NC_ERANGE errors typically occur after an arithmetic operation results in a value not representible by the output variable type when NCO attempts to write those values to an output file. Possible workaround: Promote the variable to higher precision before attempting arithmetic. For example,\nncap2 -O -s \'foo=double(foo);\' in.nc in.nc\nFor more details, see http://nco.sf.net/nco.html [...]
case NC_EUNLIMIT: (void)fprintf(stdout,"ERROR NC_UNLIMIT NC_UNLIMITED size already in use\nHINT: NC_EUNLIMIT errors can occur when attempting to convert netCDF4 classic files that contain multiple record dimensions into a netCDF3 file that allows only one record dimension. In this case, try first fixing the excess record dimension(s) (with, e.g., ncks --fix_rec_dmn) and then convert to netCDF3. For more details, see http://nco.sf.net/nco.html#fix_rec_dmn\n"); break;
case NC_EVARSIZE: (void)fprintf(stdout,"ERROR NC_EVARSIZE One or more variable sizes violate format constraints\nHINT: NC_EVARSIZE errors can occur when attempting to aggregate netCDF3 classic files together into outputs that exceed the capacity of the netCDF3 classic file format, e.g., a variable with size in excess of 2^31 bytes. In this case, try altering the output file type to netCDF3 classic with 64-bit offsets (with --64) or to netCDF4 (with -4). For more details, see http://nco [...]
@@ -450,6 +451,8 @@ nco_fmt_sng /* [fnc] Convert netCDF file format enum to string */
return "NC_FORMAT_NETCDF4";
case NC_FORMAT_NETCDF4_CLASSIC:
return "NC_FORMAT_NETCDF4_CLASSIC";
+ case NC_FORMAT_CDF5:
+ return "NC_FORMAT_CDF5";
default: nco_dfl_case_nc_type_err(); break;
} /* end switch */
@@ -472,6 +475,8 @@ nco_fmt_hdn_sng /* [fnc] Convert netCDF file format enum to string for hidden at
return "netCDF-4";
case NC_FORMAT_NETCDF4_CLASSIC:
return "netCDF-4 classic model";
+ case NC_FORMAT_CDF5:
+ return "64-bit-variable";
default: nco_dfl_case_nc_type_err(); break;
} /* end switch */
@@ -651,11 +656,22 @@ nco_open_flg(const char * const fl_nm,const int mode,int * const nc_id)
return rcd;
} /* end nco_open */
-#if 0
-#ifdef HAVE_NETCDF4_H
+#ifdef ENABLE_MPI
+# ifdef HAVE_NETCDF4_H
/* netCDF4 routines defined by Unidata netCDF4 Library libnetcdf.a
20051129: nc_*_par() routines require that netCDF4 be configured for parallel filesystems */
int
+nco_create_par(const char * const fl_nm,const int cmode,MPI_Comm mpi_cmm,MPI_Info mpi_nfo,int * const nc_id)
+{
+ /* Purpose: Wrapper for nc_create_par() */
+ const char fnc_nm[]="nco_create_par()";
+ int rcd;
+ rcd=nc_create_par(fl_nm,cmode,mpi_cmm,mpi_nfo,nc_id);
+ if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
+ return rcd;
+} /* end nco_create_par */
+
+int
nco_open_par(const char * const fl_nm,const int mode,MPI_Comm mpi_cmm,MPI_Info mpi_nfo,int * const nc_id)
{
/* Purpose: Wrapper for nc_open_par() */
@@ -665,22 +681,48 @@ nco_open_par(const char * const fl_nm,const int mode,MPI_Comm mpi_cmm,MPI_Info m
if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
return rcd;
} /* end nco_open_par */
-#endif /* !HAVE_NETCDF4_H */
-#endif /* !0 */
-#ifdef ENABLE_PNETCDF
-/* pnetCDF routines defined by ANL Parallel netCDF Library libpnetcdf.a */
+int
+nco_var_par_access(const int nc_id,const int var_id,const int par_access)
+{
+ /* Purpose: Wrapper for nc_var_par_access()
+ NB: HDF5 allows per-variable setting of access type
+ PnetCDF sets all variables to same access type */
+ const char fnc_nm[]="nco_var_par_access()";
+ int rcd;
+ rcd=nc_var_par_access(nc_id,var_id,par_access);
+ if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
+ return rcd;
+} /* end nco_var_par_access */
+# endif /* !HAVE_NETCDF4_H */
+
+# ifdef PNETCDF_EXPOSED_API
+/* PnetCDF routines defined by ANL Parallel netCDF Library libpnetcdf.a
+ NB: netCDF4 versions 4.3.x automagically call PnetCDF internally, yet do not expose its API
+ These sample prototypes will never be used until/unless someone exposes the PnetCDF API to NCO (unlikely)
+ Until then, the token ENABLE_PNETCDF means that netCDF4 was built with --enable-pnetcdf */
int
-ncompi_open(MPI_Comm mpi_cmm,const char * const fl_nm,const int mode,MPI_Info mpi_nfo,int * const nc_id)
+ncompi_create(MPI_Comm mpi_cmm,const char * const fl_nm,const int cmode,MPI_Info mpi_nfo,int * const nc_id)
+{
+ /* Purpose: Wrapper for ncmpi_create() */
+ const char fnc_nm[]="ncompi_create()";
+ int rcd;
+ rcd=ncmpi_create(mpi_cmm,fl_nm,cmode,mpi_nfo,nc_id);
+ if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
+ return rcd;
+} /* end ncompi_create */
+int
+ncompi_open(MPI_Comm mpi_cmm,const char * const fl_nm,const int omode,MPI_Info mpi_nfo,int * const nc_id)
{
/* Purpose: Wrapper for ncmpi_open() */
const char fnc_nm[]="ncompi_open()";
int rcd;
- rcd=ncmpi_open(mpi_cmm,fl_nm,mode,mpi_nfo,nc_id);
+ rcd=ncmpi_open(mpi_cmm,fl_nm,omode,mpi_nfo,nc_id);
if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
return rcd;
} /* end ncompi_open */
-#endif /* !ENABLE_PNETCDF */
+# endif /* !PNETCDF_EXPOSED_API */
+#endif /* !ENABLE_MPI */
int
nco_redef(const int nc_id)
@@ -1932,9 +1974,21 @@ int
nco_rename_att(const int nc_id,const int var_id,const char * const att_nm,const char * const att_new_nm)
{
/* Purpose: Wrapper for nc_rename_att() */
+ const char fnc_nm[]="nco_rename_att()";
int rcd;
rcd=nc_rename_att(nc_id,var_id,att_nm,att_new_nm);
- if(rcd != NC_NOERR) nco_err_exit(rcd,"nco_rename_att()");
+ if(rcd == NC_ENAMEINUSE){
+ if(var_id > NC_GLOBAL){
+ char var_nm[NC_MAX_NAME+1L];
+ (void)nco_inq_varname(nc_id,var_id,var_nm);
+ (void)fprintf(stdout,"ERROR: %s unable to rename variable \"%s\" attribute \"%s\" to \"%s\" because the variable already has an attribute of that name\n",fnc_nm,var_nm,att_nm,att_new_nm);
+ }else{
+ char grp_nm[NC_MAX_NAME+1L];
+ (void)nco_inq_grpname(nc_id,grp_nm);
+ (void)fprintf(stdout,"ERROR: %s unable to rename group \"%s\" attribute \"%s\" to \"%s\" because the group already has an attribute of that name\n",fnc_nm,grp_nm,att_nm,att_new_nm);
+ } /* endif */
+ } /* !NC_ENAMEINUSE */
+ if(rcd != NC_NOERR) nco_err_exit(rcd,fnc_nm);
return rcd;
} /* end nco_rename_att */
@@ -2150,7 +2204,7 @@ int NCO_PUT_ATT_UINT64(const int nc_id,const int var_id,const char *att_nm,const
int NCO_PUT_ATT_STRING(const int nc_id,const int var_id,const char *att_nm,const nc_type att_typ,size_t att_len,const char **sngp){return 1;}
#endif /* ENABLE_NETCDF4 */
#ifndef ENABLE_NETCDF4
-/* 20051119: netcdf4 library did not support these until alpha10, still does not support nco_put/get_att_ubyte() */
+/* 20051119: netCDF4 library did not support these until alpha10, still does not support nco_put/get_att_ubyte() */
int NCO_GET_ATT_UBYTE(const int nc_id,const int var_id,const char *att_nm,nco_ubyte *ubp){return 1;}
int NCO_GET_ATT_USHORT(const int nc_id,const int var_id,const char *att_nm,nco_ushort *usp){return 1;}
int NCO_GET_ATT_UINT(const int nc_id,const int var_id,const char *att_nm,nco_uint *uip){return 1;}
diff --git a/src/nco/nco_netcdf.h b/src/nco/nco_netcdf.h
index 2141603..43c291d 100644
--- a/src/nco/nco_netcdf.h
+++ b/src/nco/nco_netcdf.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_netcdf.h,v 1.114 2014/04/14 04:54:12 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_netcdf.h,v 1.120 2014/07/10 23:36:22 zender Exp $ */
/* Purpose: NCO wrappers for netCDF C library */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_netcdf.h" *//* NCO wrappers for netCDF C library */
@@ -47,10 +48,10 @@
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
-#ifdef ENABLE_PNETCDF
-#include <mpi.h> /* MPI definitions */
-#include <pnetcdf.h> /* ANL Parallel netCDF definitions and C library */
-#endif /* !ENABLE_PNETCDF */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+#endif /* !ENABLE_MPI */
/* Personal headers */
#include "nco_typ.h" /* Type definitions, opaque types */
@@ -114,6 +115,18 @@
# define NC_FORMAT_DAP4 (6)
#endif
+/* Three compatibility tokens from pnetcdf.h introduced to NCO 20140604
+ None are used yet */
+#ifndef NC_64BIT_DATA
+# define NC_64BIT_DATA 0x0010 /* CDF-5 format, (64-bit) supported */
+#endif
+#ifndef NC_FORMAT_CDF5
+# define NC_FORMAT_CDF5 5 /* CDF-5 format, with NC_64BIT_DATA. */
+#endif
+#ifndef NC_FORMAT_64BIT_DATA
+# define NC_FORMAT_64BIT_DATA NC_FORMAT_CDF5
+#endif
+
/* Some netCDF3 stubs for netCDF4 routines need netCDF4-only return codes
These netCDF4 tokens are never defined in netCDF3-only netcdf.h */
#ifndef HAVE_NETCDF4_H
@@ -221,16 +234,19 @@ char * /* O [sng] netCDF-compatible name */
nm2sng_nc /* [fnc] Turn group/variable/dimension/attribute name into legal netCDF */
(const char * const nm_sng); /* I [sng] Name to netCDF-ize */
-#if 0
-#ifdef HAVE_NETCDF4_H
+#ifdef ENABLE_MPI
+# ifdef HAVE_NETCDF4_H
/* netCDF4 routines defined by Unidata netCDF4 Library libnetcdf.a */
-int nco_open_par(const char * const fl_nm,const int mode,MPI_Comm mpi_cmm,MPI_Info mpi_nfo,int * const nc_id);
-#endif /* !HAVE_NETCDF4_H */
-#endif /* !0 */
-#ifdef ENABLE_PNETCDF
+int nco_create_par(const char * const fl_nm,const int cmode,MPI_Comm mpi_cmm,MPI_Info mpi_nfo,int * const nc_id);
+int nco_open_par (const char * const fl_nm,const int mode,MPI_Comm mpi_cmm,MPI_Info mpi_nfo,int * const nc_id);
+int nco_var_par_access(const int nc_id,const int var_id,const int par_access);
+# endif /* !HAVE_NETCDF4_H */
+# ifdef PNETCDF_EXPOSED_API
/* pnetCDF routines defined by ANL Parallel netCDF Library libpnetcdf.a */
-int ncompi_open(MPI_Comm mpi_cmm,const char * const fl_nm,const int mode,MPI_Info mpi_nfo,int * const nc_id);
-#endif /* !ENABLE_PNETCDF */
+int ncompi_create(MPI_Comm mpi_cmm,const char * const fl_nm,const int cmode,MPI_Info mpi_nfo,int * const nc_id);
+int ncompi_open (MPI_Comm mpi_cmm,const char * const fl_nm,const int omode,MPI_Info mpi_nfo,int * const nc_id);
+# endif /* !PNETCDF_EXPOSED_API */
+#endif /* !ENABLE_MPI */
/* Begin file-level routines */
int nco_create(const char * const fl_nm,const int cmode,int * const nc_id);
diff --git a/src/nco/nco_omp.c b/src/nco/nco_omp.c
index a90a241..83db90d 100644
--- a/src/nco/nco_omp.c
+++ b/src/nco/nco_omp.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_omp.c,v 1.70 2014/03/16 06:29:43 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_omp.c,v 1.71 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: OpenMP utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_omp.h" /* OpenMP utilities */
diff --git a/src/nco/nco_omp.h b/src/nco/nco_omp.h
index 630e451..842f4f0 100644
--- a/src/nco/nco_omp.h
+++ b/src/nco/nco_omp.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_omp.h,v 1.31 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_omp.h,v 1.32 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: OpenMP utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_omp.h" *//* OpenMP utilities */
diff --git a/src/nco/nco_pck.c b/src/nco/nco_pck.c
index b20b07b..bf80730 100644
--- a/src/nco/nco_pck.c
+++ b/src/nco/nco_pck.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_pck.c,v 1.98 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_pck.c,v 1.99 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: NCO utilities for packing and unpacking variables */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_pck.h" /* Packing and unpacking variables */
diff --git a/src/nco/nco_pck.h b/src/nco/nco_pck.h
index 3be4c7c..0b0e21c 100644
--- a/src/nco/nco_pck.h
+++ b/src/nco/nco_pck.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_pck.h,v 1.52 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_pck.h,v 1.53 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Description (definition) of packing/unpacking functions */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_pck.h" *//* Packing and unpacking variables */
diff --git a/src/nco/nco_prn.c b/src/nco/nco_prn.c
index 3b1cb86..93e2af4 100644
--- a/src/nco/nco_prn.c
+++ b/src/nco/nco_prn.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_prn.c,v 1.220 2014/04/16 18:00:08 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_prn.c,v 1.222 2014/07/15 18:48:55 zender Exp $ */
/* Purpose: Print variables, attributes, metadata */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_prn.h" /* Print variables, attributes, metadata */
@@ -1159,10 +1160,10 @@ nco_prn_var_dfn /* [fnc] Print variable metadata */
size_t cnk_sz[NC_MAX_DIMS]; /* [nbr] Chunk sizes */
size_t dmn_sz[NC_MAX_DIMS]; /* [nbr] Dimension sizes */
- /* Obtain group ID from netCDF API using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
- /* Obtain variable ID from netCDF API using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv->nm,&var_id);
/* Get number of dimensions, type, and number of attributes for variable */
@@ -1397,7 +1398,7 @@ nco_prn_var_val_trv /* [fnc] Print variable data (GTT version) */
if(prn_flg->new_fmt && CDL_OR_TRD) prn_ndn=prn_flg->ndn+prn_flg->var_fst;
if(XML) prn_ndn=prn_flg->ndn;
- /* Obtain group ID where variable is located using full group name */
+ /* Obtain group ID where variable is located */
(void)nco_inq_grp_full_ncid(nc_id,var_trv->grp_nm_fll,&grp_id);
/* Set defaults */
@@ -1788,10 +1789,10 @@ nco_prn_var_val_trv /* [fnc] Print variable data (GTT version) */
/* Get coordinate from table */
crd_sct *crd=var_trv->var_dmn[idx].crd;
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(nc_id,crd->crd_grp_nm_fll,&var_crd.nc_id);
- /* Obtain variable ID using group ID and name */
+ /* Obtain variable ID and name */
(void)nco_inq_varid(var_crd.nc_id,crd->nm,&var_crd.id);
/* Store "var_sct" members for MSA read */
@@ -2222,7 +2223,7 @@ nco_grp_prn /* [fnc] Recursively print group contents */
/* Print variable metadata */
if(prn_flg->PRN_VAR_METADATA || CDL_OR_XML) (void)nco_prn_var_dfn(nc_id,prn_flg,&var_trv);
- /* Obtain variable ID using group ID */
+ /* Obtain variable ID */
(void)nco_inq_varid(grp_id,var_trv.nm,&var_id);
/* Print variable attributes */
diff --git a/src/nco/nco_prn.h b/src/nco/nco_prn.h
index 8c81b69..92223d3 100644
--- a/src/nco/nco_prn.h
+++ b/src/nco/nco_prn.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_prn.h,v 1.52 2014/02/06 00:48:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_prn.h,v 1.53 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Print variables, attributes, metadata */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_prn.h" *//* Print variables, attributes, metadata */
diff --git a/src/nco/nco_rec_var.c b/src/nco/nco_rec_var.c
index 746b51b..c281948 100644
--- a/src/nco/nco_rec_var.c
+++ b/src/nco/nco_rec_var.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rec_var.c,v 1.29 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rec_var.c,v 1.30 2014/06/15 21:06:23 zender Exp $ */
/* Purpose: Record variable utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_rec_var.h" /* Record variable utilities */
diff --git a/src/nco/nco_rec_var.h b/src/nco/nco_rec_var.h
index 75ca0a6..62c18e9 100644
--- a/src/nco/nco_rec_var.h
+++ b/src/nco/nco_rec_var.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rec_var.h,v 1.21 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rec_var.h,v 1.22 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Record variable utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_rec_var.h" *//* Record variable utilities */
diff --git a/src/nco/nco_rth_flt.c b/src/nco/nco_rth_flt.c
index ca4b5bf..17b3b76 100644
--- a/src/nco/nco_rth_flt.c
+++ b/src/nco/nco_rth_flt.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_flt.c,v 1.38 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_flt.c,v 1.39 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Float-precision arithmetic, MSVC macros */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_rth_flt.h" /* Float-precision arithmetic, MSVC macros */
diff --git a/src/nco/nco_rth_flt.h b/src/nco/nco_rth_flt.h
index cd434d4..ffc5886 100644
--- a/src/nco/nco_rth_flt.h
+++ b/src/nco/nco_rth_flt.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_flt.h,v 1.51 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_flt.h,v 1.52 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Float-precision arithmetic, MSVC macros */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_rth_flt.h" *//* Float-precision arithmetic, MSVC macros */
diff --git a/src/nco/nco_rth_utl.c b/src/nco/nco_rth_utl.c
index 7443403..bd7be01 100644
--- a/src/nco/nco_rth_utl.c
+++ b/src/nco/nco_rth_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_utl.c,v 1.69 2014/02/17 23:12:38 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_utl.c,v 1.70 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Arithmetic controls and utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_rth_utl.h" /* Arithmetic controls and utilities */
diff --git a/src/nco/nco_rth_utl.h b/src/nco/nco_rth_utl.h
index ad988a4..e50446e 100644
--- a/src/nco/nco_rth_utl.h
+++ b/src/nco/nco_rth_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_utl.h,v 1.43 2014/01/03 19:44:44 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_rth_utl.h,v 1.44 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Arithmetic controls and utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_rth_utl.h" *//* Arithmetic controls and utilities */
diff --git a/src/nco/nco_scl_utl.c b/src/nco/nco_scl_utl.c
index 098a023..b496a15 100644
--- a/src/nco/nco_scl_utl.c
+++ b/src/nco/nco_scl_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_scl_utl.c,v 1.31 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_scl_utl.c,v 1.32 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Scalar utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_scl_utl.h" /* Scalar utilities */
diff --git a/src/nco/nco_scl_utl.h b/src/nco/nco_scl_utl.h
index 169317a..14afbb8 100644
--- a/src/nco/nco_scl_utl.h
+++ b/src/nco/nco_scl_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_scl_utl.h,v 1.24 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_scl_utl.h,v 1.25 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Scalar utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_scl_utl.h" *//* Scalar utilities */
diff --git a/src/nco/nco_scm.c b/src/nco/nco_scm.c
index a6e585f..07bae6d 100644
--- a/src/nco/nco_scm.c
+++ b/src/nco/nco_scm.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_scm.c,v 1.53 2014/03/04 16:59:24 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_scm.c,v 1.57 2014/08/21 18:22:44 zender Exp $ */
/* Purpose: Software configuration management */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_scm.h" /* Software configuration management */
@@ -30,7 +31,7 @@ cvs_vrs_prs(void) /* [fnc] Return CVS version string */
/* Unexpanded cvs keywords in cvs_Name trigger GCC 4.0+ warning
"./src/nco/nco_scm.c:81: warning: offset outside bounds of constant string"
because routine looks for cvs_Name+7 later on */
- char cvs_Name[]="$Name: nco-4_4_4 $";
+ char cvs_Name[]="$Name: nco-4_4_5 $";
const char dlr_nm_cln_spc[]="$Name: "; /* [sng] Dollar name colon space */
const char nco_sng[]="nco";
const char spc_dlr[]=" $"; /* [sng] Space dollar */
@@ -124,7 +125,7 @@ cvs_vrs_prs(void) /* [fnc] Return CVS version string */
(void)sprintf(cvs_vrs_sng,"%li.%li",cvs_mjr_vrs,cvs_mnr_vrs);
}/* end else */
- if(nco_dbg_lvl_get() >= nco_dbg_sbr){
+ if(nco_dbg_lvl_get() >= nco_dbg_vrb){
(void)fprintf(stderr,"NCO version %s\n",cvs_vrs_sng);
(void)fprintf(stderr,"cvs_nm_sng %s\n",cvs_nm_sng);
(void)fprintf(stderr,"cvs_mjr_vrs_sng %s\n",cvs_mjr_vrs_sng);
@@ -148,7 +149,7 @@ nco_cpy_prn(void) /* [fnc] Print copyright notice */
{
/* Purpose: Print copyright notice */
(void)fprintf(stderr,"Copyright (C) 1995--2014 Charlie Zender\n");
- (void)fprintf(stdout,"NCO is free software and comes with a BIG FAT KISS and ABOLUTELY NO WARRANTY\nLicense: GNU General Public License (GPL) Version 3\n");
+ (void)fprintf(stdout,"This program is part of NCO, the netCDF Operators.\nNCO is free software and comes with a BIG FAT KISS and ABOLUTELY NO WARRANTY\nYou can redistribute and/or modify NCO under the terms of the\nGNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file\nGPL: http://www.gnu.org/copyleft/gpl.html\nLICENSE: http://nco.cvs.sf.net/nco/nco/LICENSE\n");
} /* end copyright_prn() */
void
diff --git a/src/nco/nco_scm.h b/src/nco/nco_scm.h
index 4b72e3a..c959818 100644
--- a/src/nco/nco_scm.h
+++ b/src/nco/nco_scm.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_scm.h,v 1.25 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_scm.h,v 1.26 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Software configuration management */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_scm.h" *//* Software configuration management */
diff --git a/src/nco/nco_sng_utl.c b/src/nco/nco_sng_utl.c
index 960496f..d0cd4c5 100644
--- a/src/nco/nco_sng_utl.c
+++ b/src/nco/nco_sng_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_sng_utl.c,v 1.75 2014/04/13 07:56:41 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_sng_utl.c,v 1.77 2014/08/22 20:27:48 zender Exp $ */
/* Purpose: String utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_sng_utl.h" /* String utilities */
@@ -172,14 +173,14 @@ nm2sng_cdl /* [fnc] Turn variable/dimension/attribute name into legal CDL */
if(nm_sng == NULL) return NULL;
- /* Otherwise name contains special character(s)... */
+ /* Otherwise name may contain special character(s)... */
nm_lng=strlen(nm_sng);
/* Maximum conceivable length of CDL-ized name */
chr_out_ptr=nm_cdl=(char *)nco_malloc(4*nm_lng+1L);
/* Copy to preserve const-ness */
chr_in_ptr=nm_cpy=(char *)strdup(nm_sng);
/* NUL-terminate in case input string is empty so will be output string */
- chr_out_ptr[0]='0';
+ chr_out_ptr[0]='\0';
/* Search and replace special characters */
@@ -241,7 +242,7 @@ nm2sng_cdl /* [fnc] Turn variable/dimension/attribute name into legal CDL */
chr_in_ptr++;
} /* end while loop */
/* NUL-terminate */
- *chr_out_ptr=0;
+ *chr_out_ptr='\0';
/* Free memory */
nm_cpy=(char *)nco_free(nm_cpy);
@@ -249,6 +250,98 @@ nm2sng_cdl /* [fnc] Turn variable/dimension/attribute name into legal CDL */
return nm_cdl;
} /* end nm2sng_cdl() */
+char * /* O [sng] CDL-compatible name */
+nm2sng_fl /* [fnc] Turn file name into legal string for shell commands */
+(const char * const nm_sng) /* I [sng] Name to sanitize */
+{
+ /* Purpose: Turn file name into legal string for shell commands
+ Currently this means protecting special characters with backslash so shell is not confused
+ Based on nm2sng_cdl()
+ NB: Calling function must free() memory containing sanitized string */
+
+ char *chr_in_ptr; /* [sng] Pointer to current character in input name */
+ char *chr_out_ptr; /* [sng] Pointer to current character in output name */
+ char *nm_fl; /* [sng] CDL-compatible name */
+ char *nm_cpy; /* [sng] Copy of input */
+
+ int nm_lng; /* [nbr] Length of original name */
+
+ if(nm_sng == NULL) return NULL;
+
+ /* Otherwise name may contain special character(s)... */
+ nm_lng=strlen(nm_sng);
+ /* Maximum conceivable length of sanitized name */
+ chr_out_ptr=nm_fl=(char *)nco_malloc(4*nm_lng+1L);
+ /* Copy to preserve const-ness */
+ chr_in_ptr=nm_cpy=(char *)strdup(nm_sng);
+ /* NUL-terminate in case input string is empty so will be output string */
+ chr_out_ptr[0]='\0';
+
+ /* Search and replace special characters */
+
+ /* This block stolen from: ncdump/utils.c/escaped_name() */
+
+ if((*chr_in_ptr >= 0x01 && *chr_in_ptr <= 0x20) || (*chr_in_ptr == 0x7f)){
+ (void)fprintf(stderr,"%s: ERROR name begins with space or control-character: %c\n",nco_prg_nm_get(),*chr_in_ptr);
+ nco_exit(EXIT_FAILURE);
+ } /* endif error */
+
+ while(*chr_in_ptr){
+ if(isascii(*chr_in_ptr)){
+ if(iscntrl(*chr_in_ptr)){ /* Render control chars as two hex digits, \%xx */
+ snprintf(chr_out_ptr,4,"\\%%%.2x",*chr_in_ptr);
+ chr_out_ptr+=4;
+ }else{
+ switch(*chr_in_ptr){
+ case ' ':
+ case '!':
+ case '"':
+ case '#':
+ case '$':
+ case '&':
+ case '\'':
+ case '(':
+ case ')':
+ case '*':
+ case ',':
+ // case ':': /* 20140822: Protecting colon with backslash causes Windows error parsing volume names, e.g., "C:\foo" */
+ case ';':
+ case '<':
+ case '=':
+ case '>':
+ case '?':
+ case '[':
+ case ']':
+ case '\\':
+ case '^':
+ case '`':
+ case '{':
+ case '|':
+ case '}':
+ case '~':
+ *chr_out_ptr++='\\';
+ *chr_out_ptr++=*chr_in_ptr;
+ break;
+ default: /* NB: includes '/' */
+ *chr_out_ptr++=*chr_in_ptr;
+ break;
+ } /* end switch */
+ } /* not a control character */
+ }else{ /* not ascii, assume just UTF-8 byte */
+ *chr_out_ptr++=*chr_in_ptr;
+ } /* end else not ascii */
+ /* Advance character */
+ chr_in_ptr++;
+ } /* end while loop */
+ /* NUL-terminate */
+ *chr_out_ptr='\0';
+
+ /* Free memory */
+ nm_cpy=(char *)nco_free(nm_cpy);
+
+ return nm_fl;
+} /* end nm2sng_fl() */
+
char * /* O [sng] String containing printable result */
chr2sng_cdl /* [fnc] Translate C language character to printable, visible ASCII bytes */
(const char chr_val, /* I [chr] Character to process */
diff --git a/src/nco/nco_sng_utl.h b/src/nco/nco_sng_utl.h
index 0b77292..3116151 100644
--- a/src/nco/nco_sng_utl.h
+++ b/src/nco/nco_sng_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_sng_utl.h,v 1.46 2014/04/14 04:54:12 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_sng_utl.h,v 1.48 2014/08/22 20:27:48 zender Exp $ */
/* Purpose: String utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_sng_utl.h" *//* String utilities */
@@ -81,6 +82,10 @@ char * /* O [sng] CDL-compatible name */
nm2sng_cdl /* [fnc] Turn variable/dimension/attribute name into legal CDL */
(const char * const nm_sng); /* I [sng] Name to CDL-ize */
+char * /* O [sng] CDL-compatible name */
+nm2sng_fl /* [fnc] Turn file name into legal string for shell commands */
+(const char * const nm_sng); /* I [sng] Name to sanitize */
+
char * /* O [sng] String containing printable result */
chr2sng_cdl /* [fnc] Translate C language character to printable, visible ASCII bytes */
(const char chr_val, /* I [chr] Character to process */
diff --git a/src/nco/nco_srm.c b/src/nco/nco_srm.c
index f68adad..f5a7e18 100644
--- a/src/nco/nco_srm.c
+++ b/src/nco/nco_srm.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_srm.c,v 1.2 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_srm.c,v 1.3 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Streams */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_srm.h" /* Streams */
diff --git a/src/nco/nco_srm.h b/src/nco/nco_srm.h
index 8590352..8ad97af 100644
--- a/src/nco/nco_srm.h
+++ b/src/nco/nco_srm.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_srm.h,v 1.2 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_srm.h,v 1.3 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Streams */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_srm.h" *//* Streams */
diff --git a/src/nco/nco_typ.h b/src/nco/nco_typ.h
index 5dd1e3e..15225fe 100644
--- a/src/nco/nco_typ.h
+++ b/src/nco/nco_typ.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_typ.h,v 1.38 2014/05/27 02:04:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_typ.h,v 1.39 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Type definitions, opaque types */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_typ.h" *//* Type definitions, opaque types */
diff --git a/src/nco/nco_var_avg.c b/src/nco/nco_var_avg.c
index ead95a2..ac8563b 100644
--- a/src/nco/nco_var_avg.c
+++ b/src/nco/nco_var_avg.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_avg.c,v 1.79 2014/02/13 03:21:49 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_avg.c,v 1.80 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Average variables */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_var_avg.h" /* Average variables */
diff --git a/src/nco/nco_var_avg.h b/src/nco/nco_var_avg.h
index 4948e5c..64fb322 100644
--- a/src/nco/nco_var_avg.h
+++ b/src/nco/nco_var_avg.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_avg.h,v 1.27 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_avg.h,v 1.28 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Average variables */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_avg.h" *//* Average variables */
diff --git a/src/nco/nco_var_lst.c b/src/nco/nco_var_lst.c
index 0562c6f..6d5181c 100644
--- a/src/nco/nco_var_lst.c
+++ b/src/nco/nco_var_lst.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_lst.c,v 1.168 2014/03/27 18:25:16 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_lst.c,v 1.169 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable list utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_var_lst.h" /* Variable list utilities */
diff --git a/src/nco/nco_var_lst.h b/src/nco/nco_var_lst.h
index c8d5257..57de992 100644
--- a/src/nco/nco_var_lst.h
+++ b/src/nco/nco_var_lst.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_lst.h,v 1.75 2014/03/27 18:25:16 pvicente Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_lst.h,v 1.76 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable list utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_lst.h" *//* Variable list utilities */
diff --git a/src/nco/nco_var_rth.c b/src/nco/nco_var_rth.c
index a6b369e..0181168 100644
--- a/src/nco/nco_var_rth.c
+++ b/src/nco/nco_var_rth.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_rth.c,v 1.69 2014/02/13 04:38:12 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_rth.c,v 1.70 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable arithmetic */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_var_rth.h" /* Variable arithmetic */
diff --git a/src/nco/nco_var_rth.h b/src/nco/nco_var_rth.h
index eaae65d..320e396 100644
--- a/src/nco/nco_var_rth.h
+++ b/src/nco/nco_var_rth.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_rth.h,v 1.38 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_rth.h,v 1.39 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable arithmetic */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_rth.h" *//* Variable arithmetic */
diff --git a/src/nco/nco_var_scv.c b/src/nco/nco_var_scv.c
index fc547b8..c143b99 100644
--- a/src/nco/nco_var_scv.c
+++ b/src/nco/nco_var_scv.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_scv.c,v 1.39 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_scv.c,v 1.40 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Arithmetic between variables and scalar values */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_var_scv.h" /* Arithmetic between variables and scalar values */
diff --git a/src/nco/nco_var_scv.h b/src/nco/nco_var_scv.h
index 8c2439b..71ac7c5 100644
--- a/src/nco/nco_var_scv.h
+++ b/src/nco/nco_var_scv.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_scv.h,v 1.28 2013/12/31 05:14:02 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_scv.h,v 1.29 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Arithmetic between variables and scalar values */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_scv.h" *//* Arithmetic between variables and scalar values */
diff --git a/src/nco/nco_var_utl.c b/src/nco/nco_var_utl.c
index d0980db..d09ad97 100644
--- a/src/nco/nco_var_utl.c
+++ b/src/nco/nco_var_utl.c
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_utl.c,v 1.358 2014/03/04 22:44:16 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_utl.c,v 1.359 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include "nco_var_utl.h" /* Variable utilities */
diff --git a/src/nco/nco_var_utl.h b/src/nco/nco_var_utl.h
index 500de37..5b0f4f7 100644
--- a/src/nco/nco_var_utl.h
+++ b/src/nco/nco_var_utl.h
@@ -1,10 +1,11 @@
-/* $Header: /cvsroot/nco/nco/src/nco/nco_var_utl.h,v 1.103 2014/02/14 05:22:17 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/nco_var_utl.h,v 1.104 2014/06/15 21:06:24 zender Exp $ */
/* Purpose: Variable utilities */
/* Copyright (C) 1995--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* Usage:
#include "nco_var_utl.h" *//* Variable utilities */
diff --git a/src/nco/ncpdq.c b/src/nco/ncpdq.c
index b5d68b3..2e384b9 100644
--- a/src/nco/ncpdq.c
+++ b/src/nco/ncpdq.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncpdq.c,v 1.395 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncpdq.c,v 1.401 2014/08/21 18:22:44 zender Exp $ */
/* ncpdq -- netCDF pack, re-dimension, query */
/* Purpose: Pack, re-dimension, query single netCDF file and output to a single file */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -61,8 +59,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
-/* 3rd party vendors */
-#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
+/* 3rd party vendors */
+#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
#define MAIN_PROGRAM_FILE
@@ -121,8 +137,8 @@ main(int argc,char **argv)
char scl_fct_sng[]="scale_factor"; /* [sng] Unidata standard string for scale factor */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncpdq.c,v 1.395 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.395 $";
+ const char * const CVS_Id="$Id: ncpdq.c,v 1.401 2014/08/21 18:22:44 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.401 $";
const char * const opt_sht_lst="3467Aa:CcD:d:Fg:G:hL:l:M:Oo:P:p:Rrt:v:UxZ-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -202,6 +218,13 @@ main(int argc,char **argv)
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -316,6 +339,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -409,6 +440,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -542,7 +574,7 @@ main(int argc,char **argv)
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Create reversed dimension list */
@@ -556,49 +588,41 @@ main(int argc,char **argv)
/* Loop table */
for(unsigned int idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
trv_sct var_trv=trv_tbl->lst[idx_tbl];
- /* Is variable to extract */
+
+ /* Is variable to extract */
if(var_trv.nco_typ == nco_obj_typ_var && var_trv.flg_xtr){
+
/* Loop variable dimensions */
for(int idx_dmn=0;idx_dmn<var_trv.nbr_dmn;idx_dmn++){
- nco_bool flg_is_rvr=False;
- optarg_lcl=NULL;
-
/* Loop input -a names */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
- /* Does it have a '-' ? */
+ /* Is dimension to be reversed? i.e., does it have a '-'? */
if(dmn_rdr_lst_in[idx_rdr][0] == '-'){
- optarg_lcl=(char *)strdup(dmn_rdr_lst_in[idx_rdr]+1);
- flg_is_rvr=True;
- } /* !flg_is_rvr */
-
- /* Compare with dimension name */
- if(optarg_lcl && !strcmp(optarg_lcl,var_trv.var_dmn[idx_dmn].dmn_nm)) dmn_rdr_nbr_trv++;
-
- if(flg_is_rvr){
- assert(optarg_lcl);
- dmn_rvr_rdr[idx_dmn_rdr_nbr_trv]=True;
+ optarg_lcl=(char *)strdup(dmn_rdr_lst_in[idx_rdr]+1L);
+ if(!strcmp(optarg_lcl,var_trv.var_dmn[idx_dmn].dmn_nm)) dmn_rdr_nbr_trv++;
optarg_lcl=(char *)nco_free(optarg_lcl);
- }else{
+ dmn_rvr_rdr[idx_dmn_rdr_nbr_trv]=True;
+ }else{
dmn_rvr_rdr[idx_dmn_rdr_nbr_trv]=False;
- } /* !flg_is_rvr */
+ } /* !flg_is_rvr */
idx_dmn_rdr_nbr_trv++;
} /* Loop input -a names */
} /* Loop variable dimensions */
- } /* Is variable to extract */
+ } /* Is variable to extract */
} /* Loop table */
- /* Strip all '-' */
+ /* Strip all '-' */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
if(dmn_rdr_lst_in[idx_rdr][0] == '-'){
/* Copy string to new memory one past negative sign to avoid losing byte */
optarg_lcl=dmn_rdr_lst_in[idx_rdr];
- dmn_rdr_lst_in[idx_rdr]=(char *)strdup(optarg_lcl+1);
+ dmn_rdr_lst_in[idx_rdr]=(char *)strdup(optarg_lcl+1L);
optarg_lcl=(char *)nco_free(optarg_lcl);
} /* endif */
- } /* Strip all '-' */
+ } /* Strip all '-' */
} /* Create reversed dimension list */
/* Get number of variables, dimensions, and global attributes in file, file format */
@@ -781,7 +805,7 @@ main(int argc,char **argv)
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
@@ -840,7 +864,7 @@ main(int argc,char **argv)
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
@@ -949,11 +973,15 @@ main(int argc,char **argv)
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncra.c b/src/nco/ncra.c
index 074c6d1..2ef3aa9 100644
--- a/src/nco/ncra.c
+++ b/src/nco/ncra.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncra.c,v 1.538 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncra.c,v 1.545 2014/07/15 18:48:55 zender Exp $ */
/* This single source file compiles into three separate executables:
ncra -- netCDF record averager
@@ -10,17 +10,15 @@
to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
of the GPL, but in addition obeying the extra stipulations of the
HDF, netCDF, OPeNDAP, and UDUnits licenses.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
@@ -76,8 +74,8 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
-/* Internationalization i18n, Linux Journal 200211 p. 57--59 */
#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
# include <libintl.h> /* Internationalization i18n */
# include <locale.h> /* Locale setlocale() */
# define _(sng) gettext (sng)
@@ -89,8 +87,13 @@
# define gettext(foo) foo
#endif /* _LIBINTL_H */
-/* 3rd party vendors */
-#include <netcdf.h> /* netCDF definitions and C library */
+/* 3rd party vendors */
+#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* Personal headers */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
@@ -137,8 +140,8 @@ main(int argc,char **argv)
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncra.c,v 1.538 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.538 $";
+ const char * const CVS_Id="$Id: ncra.c,v 1.545 2014/07/15 18:48:55 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.545 $";
const char * const opt_sht_lst="3467ACcD:d:FG:g:HhL:l:n:Oo:p:P:rRt:v:X:xY:y:-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -267,6 +270,13 @@ main(int argc,char **argv)
lmt_sct **lmt_rec=NULL; /* [lst] (ncra) Record dimensions */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -380,7 +390,7 @@ main(int argc,char **argv)
setlocale(LC_ALL,""); /* LC_ALL sets all localization tokens to same value */
bindtextdomain("nco","/home/zender/share/locale"); /* ${LOCALEDIR} is e.g., /usr/share/locale */
/* MO files should be in ${LOCALEDIR}/es/LC_MESSAGES */
- textdomain("nco"); /* PACKAGE is name of program */
+ textdomain("nco"); /* PACKAGE is name of program or library */
#endif /* not _LIBINTL_H */
/* Start timer and save command line */
@@ -392,6 +402,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -499,6 +517,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -635,7 +654,7 @@ main(int argc,char **argv)
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,var_lst_in_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Store ncge ensemble suffix in table */
@@ -812,7 +831,7 @@ main(int argc,char **argv)
for(idx=0;idx<nbr_var_prc;idx++){
/* Obtain variable GTT object using full variable name */
trv_sct *trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,trv->grp_nm_fll,&grp_id);
(void)nco_var_mtd_refresh(grp_id,var_prc[idx]);
} /* end loop over variables */
@@ -823,7 +842,7 @@ main(int argc,char **argv)
/* Loop over number of different record variables in file */
for(idx_rec=0;idx_rec<nbr_rec;idx_rec++){
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,lmt_rec[idx_rec]->grp_nm_fll,&grp_id);
/* Fill record array */
@@ -854,7 +873,7 @@ main(int argc,char **argv)
/* This file may be superfluous though valid data will be found in upcoming files */
if(nco_dbg_lvl >= nco_dbg_std)
if((lmt_rec[idx_rec]->srt > lmt_rec[idx_rec]->end) && (lmt_rec[idx_rec]->rec_rmn_prv_ssc == 0L))
- (void)fprintf(fp_stdout,gettext("%s: INFO %s (input file %d) is superfluous\n"),nco_prg_nm_get(),fl_in,fl_idx);
+ (void)fprintf(fp_stdout,"%s: INFO %s (input file %d) is superfluous\n",nco_prg_nm_get(),fl_in,fl_idx);
rec_dmn_sz=lmt_rec[idx_rec]->rec_dmn_sz;
rec_rmn_prv_ssc=lmt_rec[idx_rec]->rec_rmn_prv_ssc; /* Local copy may be decremented later */
@@ -890,7 +909,7 @@ main(int argc,char **argv)
if(rec_rmn_prv_ssc == 1L) REC_LST_GRP=True; else REC_LST_GRP=False;
/* Process all variables in current record */
- if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(fp_stdout,gettext("%s: INFO Record %ld of %s contributes to output record %ld\n"),nco_prg_nm_get(),idx_rec_crr_in,fl_in,idx_rec_out[idx_rec]);
+ if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(fp_stdout,"%s: INFO Record %ld of %s contributes to output record %ld\n",nco_prg_nm_get(),idx_rec_crr_in,fl_in,idx_rec_out[idx_rec]);
#ifdef _OPENMP
#pragma omp parallel for default(none) private(idx,in_id) shared(CNV_ARM,base_time_crr,base_time_srt,nco_dbg_lvl,fl_in,fl_out,idx_rec_crr_in,idx_rec_out,rec_usd_cml,in_id_arr,REC_FRS_GRP,REC_LST_DSR,md5,nbr_var_prc,nco_op_typ,FLG_BFR_NRM,FLG_MRO,out_id,nco_prg_id,rcd,var_prc,var_prc_out,nbr_dmn_fl,trv_tbl,var_trv,grp_id,gpe,grp_out_fll,grp_out_id,var_out_id,idx_rec,flg_skp1,flg_skp2,lmt_rec,nbr_rec)
@@ -907,12 +926,12 @@ main(int argc,char **argv)
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,var_trv->grp_nm_fll,&grp_id);
/* Edit group name for output */
grp_out_fll=NULL;
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=var_trv->grp_nm_fll;
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
@@ -1015,7 +1034,7 @@ main(int argc,char **argv)
var_trv=trv_tbl_var_nm_fll(var_prc_out[idx]->nm_fll,trv_tbl);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
@@ -1071,11 +1090,11 @@ main(int argc,char **argv)
rec_nbr_trn=max_int(rec_nbr_spn_max-rec_nbr_spn_act,0L);
/* Records requested is maximum minus any truncated in last group */
rec_nbr_rqs=rec_nbr_rqs_max-rec_nbr_trn;
- if(rec_nbr_rqs != rec_usd_cml[idx_rec]) (void)fprintf(fp_stdout,gettext("%s: WARNING User requested %li records but only %li were found and used\n"),nco_prg_nm_get(),rec_nbr_rqs,rec_usd_cml[idx_rec]);
+ if(rec_nbr_rqs != rec_usd_cml[idx_rec]) (void)fprintf(fp_stdout,"%s: WARNING User requested %li records but only %li were found and used\n",nco_prg_nm_get(),rec_nbr_rqs,rec_usd_cml[idx_rec]);
} /* end if */
/* ... and die if no records were read ... */
if(rec_usd_cml[idx_rec] <= 0){
- (void)fprintf(fp_stdout,gettext("%s: ERROR No records lay within specified hyperslab\n"),nco_prg_nm_get());
+ (void)fprintf(fp_stdout,"%s: ERROR No records lay within specified hyperslab\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
} /* end if */
} /* end if */
@@ -1096,11 +1115,11 @@ main(int argc,char **argv)
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,var_trv->grp_nm_fll,&grp_id);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
@@ -1135,7 +1154,7 @@ main(int argc,char **argv)
/* Construct GTT using current file ID */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,var_lst_in_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl1);
- /* Check if all input -d dimensions were found */
+ /* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Loop over ensembles in current file */
@@ -1168,7 +1187,7 @@ main(int argc,char **argv)
var_prc[idx_prc]->nm_fll=nco_bld_nm_fll(grp_nm_fll,var_prc[idx_prc]->nm);
if(nco_dbg_lvl > nco_dbg_std) (void)fprintf(fp_stdout,"%s:\t variable <%s>\n",nco_prg_nm_get(),var_prc[idx_prc]->nm_fll);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,grp_nm_fll,&grp_id);
(void)nco_var_mtd_refresh(grp_id,var_prc[idx_prc]);
@@ -1285,7 +1304,7 @@ main(int argc,char **argv)
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
} /* end else */
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Get output variable ID */
(void)nco_inq_varid(grp_out_id,var_prc_out[idx]->nm,&var_out_id);
@@ -1363,10 +1382,15 @@ main(int argc,char **argv)
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncrename.c b/src/nco/ncrename.c
index d3588f9..a133db8 100644
--- a/src/nco/ncrename.c
+++ b/src/nco/ncrename.c
@@ -1,15 +1,13 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncrename.c,v 1.193 2014/05/21 20:39:29 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncrename.c,v 1.198 2014/07/11 20:55:45 zender Exp $ */
/* ncrename -- netCDF renaming operator */
/* Purpose: Rename dimensions, variables, and attributes of a netCDF file */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -58,8 +56,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
/* 3rd party vendors */
#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
#define MAIN_PROGRAM_FILE
@@ -100,8 +116,8 @@ main(int argc,char **argv)
char var_nm[NC_MAX_NAME+1];
- const char * const CVS_Id="$Id: ncrename.c,v 1.193 2014/05/21 20:39:29 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.193 $";
+ const char * const CVS_Id="$Id: ncrename.c,v 1.198 2014/07/11 20:55:45 zender Exp $";
+ const char * const CVS_Revision="$Revision: 1.198 $";
const char * const opt_sht_lst="a:D:d:g:hl:Oo:p:rv:-:";
const char dlm_chr='@'; /* Character delimiting variable from attribute name */
const char opt_chr='.'; /* Character indicating presence of following variable/dimension/attribute in file is optional */
@@ -137,6 +153,13 @@ main(int argc,char **argv)
trv_tbl_sct *trv_tbl; /* [lst] Traversal table */
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[] =
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -192,6 +215,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -233,6 +264,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy argument for later processing */
dmn_rnm_arg[nbr_dmn_rnm]=(char *)strdup(optarg);
@@ -446,15 +478,13 @@ main(int argc,char **argv)
trv_obj=nco_obj_usr_sng(var_nm,trv_tbl,&is_opt);
/* If object is group, set NC_GLOBAL */
- if(trv_obj && trv_obj->nco_typ == nco_obj_typ_grp){
- var_id=NC_GLOBAL;
- }
+ if(trv_obj && trv_obj->nco_typ == nco_obj_typ_grp) var_id=NC_GLOBAL;
/* Object found that matches "var_nm" */
- if (trv_obj || IS_GLB_GRP_ATT){
+ if(trv_obj || IS_GLB_GRP_ATT){
/* If object found get group ID, else groud ID is root (cases of "global") */
- if (trv_obj) (void)nco_inq_grp_full_ncid(nc_id,trv_obj->grp_nm_fll,&grp_id); else grp_id=nc_id;
+ if(trv_obj) (void)nco_inq_grp_full_ncid(nc_id,trv_obj->grp_nm_fll,&grp_id); else grp_id=nc_id;
/* Get var_id of variable */
if(IS_GLB_GRP_ATT){
@@ -473,9 +503,7 @@ main(int argc,char **argv)
}else{ /* Variable name does not contain opt_chr so variable presence is required */
/* Get ID only if object is variable (not group). NB: use relative name found */
- if(trv_obj->nco_typ == nco_obj_typ_var){
- rcd=nco_inq_varid(grp_id,trv_obj->nm,&var_id);
- } /* Get ID only if object is variable (not group) */
+ if(trv_obj->nco_typ == nco_obj_typ_var) rcd=nco_inq_varid(grp_id,trv_obj->nm,&var_id);
} /* end if */
} /* !IS_GLB_GRP_ATT */
@@ -506,29 +534,22 @@ main(int argc,char **argv)
} /* Match variable by name */
+ }else{ /* ...or rename attribute for all variables and groups... */
- }else{ /* ...or rename attribute for all variables... */
-
- /* Loop table */
for(unsigned int idx_tbl=0;idx_tbl<trv_tbl->nbr;idx_tbl++){
(void)nco_inq_grp_full_ncid(nc_id,trv_tbl->lst[idx_tbl].grp_nm_fll,&grp_id);
- /* We are in NC_GLOBAL zone if group */
- if (trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_grp){
- var_id=NC_GLOBAL;
- }else {
- (void)nco_inq_varid(grp_id,trv_tbl->lst[idx_tbl].nm,&var_id);
- }
+ if(trv_tbl->lst[idx_tbl].nco_typ == nco_obj_typ_grp) var_id=NC_GLOBAL; else (void)nco_inq_varid(grp_id,trv_tbl->lst[idx_tbl].nm,&var_id);
if(att_rnm_lst[idx_att].old_nm[0] == opt_chr){
- /* Rename attribute if variable contains attribute else do nothing */
+ /* Rename attribute if variable/group contains attribute else do nothing */
rcd=nco_inq_attid_flg(grp_id,var_id,att_rnm_lst[idx_att].old_nm+1L,&att_rnm_lst[idx_att].id);
if(rcd == NC_NOERR){
(void)nco_rename_att(grp_id,var_id,att_rnm_lst[idx_att].old_nm+1L,att_rnm_lst[idx_att].new_nm);
nbr_rnm++;
/* Inform user which variable had attribute renamed */
if(var_id > NC_GLOBAL){
- if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stdout,"%s: Renamed attribute \'%s\' to \'%s\' for variable \'%s\'\n",nco_prg_nm,att_rnm_lst[idx_att].old_nm+1L,att_rnm_lst[idx_att].new_nm,var_nm);
+ if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stdout,"%s: Renamed attribute \'%s\' to \'%s\' for variable \'%s\'\n",nco_prg_nm,att_rnm_lst[idx_att].old_nm+1L,att_rnm_lst[idx_att].new_nm,trv_tbl->lst[idx_tbl].nm);
}else{
if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stdout,"%s: Renamed global or group attribute \'%s\' to \'%s\'\n",nco_prg_nm,att_rnm_lst[idx_att].old_nm+1L,att_rnm_lst[idx_att].new_nm);
} /* end else */
@@ -575,7 +596,7 @@ main(int argc,char **argv)
} /* nbr_rnm */
} /* end loop over attributes to rename */
- /* Catenate timestamped command line to "history" global attribute */
+ /* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(nc_id,cmd_ln);
#ifdef _OPENMP
@@ -623,11 +644,15 @@ main(int argc,char **argv)
(void)trv_tbl_free(trv_tbl);
} /* !flg_cln */
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
-
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco/ncwa.c b/src/nco/ncwa.c
index 2aeadee..eb4cfdc 100644
--- a/src/nco/ncwa.c
+++ b/src/nco/ncwa.c
@@ -1,4 +1,4 @@
-/* $Header: /cvsroot/nco/nco/src/nco/ncwa.c,v 1.420 2014/05/27 03:26:18 zender Exp $ */
+/* $Header: /cvsroot/nco/nco/src/nco/ncwa.c,v 1.425 2014/08/26 17:13:41 pvicente Exp $ */
/* ncwa -- netCDF weighted averager */
@@ -6,11 +6,9 @@
in a single input netCDF file and output them to a single file. */
/* Copyright (C) 1995--2014 Charlie Zender
-
- License: GNU General Public License (GPL) Version 3
- The full license text is at http://www.gnu.org/copyleft/gpl.html
- and in the file nco/doc/LICENSE in the NCO source distribution.
-
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3.
As a special exception to the terms of the GPL, you are permitted
to link the NCO source code with the HDF, netCDF, OPeNDAP, and UDUnits
libraries and to distribute the resulting executables under the terms
@@ -19,7 +17,7 @@
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details.
The original author of this software, Charlie Zender, seeks to improve
@@ -60,8 +58,26 @@
# endif /* !HAVE_GETOPT_H */
#endif /* HAVE_GETOPT_LONG */
-/* 3rd party vendors */
-#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef I18N
+# include <langinfo.h> /* nl_langinfo() */
+# include <libintl.h> /* Internationalization i18n */
+# include <locale.h> /* Locale setlocale() */
+# define _(sng) gettext (sng)
+# define gettext_noop(sng) (sng)
+# define N_(sng) gettext_noop(sng)
+#endif /* I18N */
+/* Supply stub gettext() function in case i18n failed */
+#ifndef _LIBINTL_H
+# define gettext(foo) foo
+#endif /* _LIBINTL_H */
+
+/* 3rd party vendors */
+#include <netcdf.h> /* netCDF definitions and C library */
+#ifdef ENABLE_MPI
+# include <mpi.h> /* MPI definitions */
+# include <netcdf_par.h> /* Parallel netCDF definitions */
+# include "nco_mpi.h" /* MPI utilities */
+#endif /* !ENABLE_MPI */
/* #define MAIN_PROGRAM_FILE MUST precede #include libnco.h */
#define MAIN_PROGRAM_FILE
@@ -135,8 +151,8 @@ main(int argc,char **argv)
char *wgt_nm=NULL;
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
- const char * const CVS_Id="$Id: ncwa.c,v 1.420 2014/05/27 03:26:18 zender Exp $";
- const char * const CVS_Revision="$Revision: 1.420 $";
+ const char * const CVS_Id="$Id: ncwa.c,v 1.425 2014/08/26 17:13:41 pvicente Exp $";
+ const char * const CVS_Revision="$Revision: 1.425 $";
const char * const opt_sht_lst="3467Aa:B:bCcD:d:Fg:G:hIL:l:M:m:nNOo:p:rRT:t:v:Ww:xy:-:";
cnk_sct cnk; /* [sct] Chunking structure */
@@ -222,6 +238,13 @@ main(int argc,char **argv)
prs_sct prs_arg; /* I/O [sct] Global information required in ncwa parser */
#endif
+#ifdef ENABLE_MPI
+ /* Declare all MPI-specific variables here */
+ MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
+ int prc_rnk; /* [idx] Process rank */
+ int prc_nbr=0; /* [nbr] Number of MPI processes */
+#endif /* !ENABLE_MPI */
+
static struct option opt_lng[]=
{ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
@@ -349,6 +372,14 @@ main(int argc,char **argv)
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
+#ifdef ENABLE_MPI
+ /* MPI Initialization */
+ if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
+ MPI_Init(&argc,&argv);
+ MPI_Comm_size(mpi_cmm,&prc_nbr);
+ MPI_Comm_rank(mpi_cmm,&prc_rnk);
+#endif /* !ENABLE_MPI */
+
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
@@ -457,6 +488,7 @@ main(int argc,char **argv)
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
+ nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
@@ -684,7 +716,7 @@ main(int argc,char **argv)
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc,nbr_var_fix,var_fix,trv_tbl);
/* We now have final list of variables to extract. Phew. */
- if(nco_dbg_lvl >= nco_dbg_var){
+ if(nco_dbg_lvl >= nco_dbg_var && nco_dbg_lvl != nco_dbg_dev){
for(idx=0;idx<xtr_nbr;idx++) (void)fprintf(stderr,"var[%d]->nm = %s, ->id=[%d]\n",idx,var[idx]->nm,var[idx]->id);
for(idx=0;idx<nbr_var_fix;idx++) (void)fprintf(stderr,"var_fix[%d]->nm = %s, ->id=[%d]\n",idx,var_fix[idx]->nm,var_fix[idx]->id);
for(idx=0;idx<nbr_var_prc;idx++) (void)fprintf(stderr,"var_prc[%d]->nm = %s, ->id=[%d]\n",idx,var_prc[idx]->nm,var_prc[idx]->id);
@@ -723,7 +755,7 @@ main(int argc,char **argv)
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
@@ -822,7 +854,7 @@ main(int argc,char **argv)
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
- /* Obtain group ID using full group name */
+ /* Obtain group ID */
(void)nco_inq_grp_full_ncid(in_id,var_trv->grp_nm_fll,&grp_id);
if(nco_dbg_lvl >= nco_dbg_var && nco_dbg_lvl < nco_dbg_nbr) rcd+=nco_var_prc_crr_prn(idx,var_prc[idx]->nm);
@@ -1051,7 +1083,7 @@ main(int argc,char **argv)
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
- /* Obtain output group ID using full group name */
+ /* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
@@ -1163,15 +1195,19 @@ main(int argc,char **argv)
var_out=(var_sct **)nco_free(var_out);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if (flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
+ /* Free traversal table */
+ trv_tbl_free(trv_tbl);
} /* !flg_cln */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
+ if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
- /* Free traversal table */
- trv_tbl_free(trv_tbl);
-
+#ifdef ENABLE_MPI
+ MPI_Finalize();
+#endif /* !ENABLE_MPI */
+
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
diff --git a/src/nco_c++/Makefile.old b/src/nco_c++/Makefile.old
index 95d5fad..b2f9147 100644
--- a/src/nco_c++/Makefile.old
+++ b/src/nco_c++/Makefile.old
@@ -1,4 +1,4 @@
-# $Header: /cvsroot/nco/nco/src/nco_c++/Makefile.old,v 1.106 2014/05/04 05:39:01 zender Exp $ -*-makefile-*-
+# $Header: /cvsroot/nco/nco/src/nco_c++/Makefile.old,v 1.110 2014/07/07 06:04:23 zender Exp $ -*-makefile-*-
# Purpose: Makefile for libnco_c++ module nco_c++
# Requires GNU Make---AT&T Make chokes on GNU syntax
@@ -93,12 +93,9 @@ endif
ifndef ${CCACHE}
CCACHE := N
endif # CCACHE
-ifndef DAP_NETCDF
- DAP_NETCDF := Y
-endif # DAP_NETCDF
-ifndef DAP_OPENDAP
- DAP_OPENDAP := N
-endif # DAP_OPENDAP
+ifndef DAP
+ DAP := Y
+endif # DAP
ifndef ${DBG}
# Debugging token N=No (default) Y=Yes
DBG := N
@@ -237,171 +234,25 @@ endif # endif PRC
# NB: CPP_TKN is recursively expanded variable, define only when components are ready
CPP_TKN = ${USR_TKN} -D${PVM_ARCH} -DNO_NETCDF_2 -DVERSION='${VRS_SNG}' -DHOSTNAME='${HOST}' -DUSER='${USER}' -DNCO_ABORT_ON_ERROR
-# Default NCO build. DAP, NETCDF4, and PNETCDF clauses may overwrite this
-NC_LDFLAGS := -L${NETCDF_LIB}
-NC_LIBS := -lnetcdf
-
-ifeq (${DAP_NETCDF},Y)
-# Build NCO as DAP-enabled clients with netCDF-provided DAP
-ifndef DAP_NETCDF_ROOT
-# Directory containing libcurl.a
- DAP_NETCDF_ROOT := /usr
-endif # DAP_NETCDF_ROOT
- NC_LDFLAGS := -L${DAP_NETCDF_ROOT}/lib
-# netCDF 4.0.1+:
- NC_LIBS += -lcurl
-endif # end DAP_NETCDF
-
-ifeq (${DAP_OPENDAP},Y)
-# Build NCO as DAP-enabled clients with OPeNDAP
-# fxm: OPeNDAP bloats executables, should automagically enable stripping?
-# http://www.opendap.org/user/guide-html/guide_28.html
-ifndef DAP_OPENDAP_ROOT
-# Directory containing libdap.a, libnc-dap.a
- DAP_OPENDAP_ROOT := /usr/local
-endif # DAP_OPENDAP_ROOT
- NC_LDFLAGS := -L${DAP_OPENDAP_ROOT}/lib
-# NB: nc-dods, dap++ prior to version 3.5.X must be linked twice!
-# Required libraries for
-# DODS 3.3-:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lwww -lz -lrx
-# DODS 3.4.X:
-# NC_LIBS := -lnc-dods -ldap++ -lnc-dods -ldap++ -lxml2 -lcurl -lpthread -ldl -lz
-# OPeNDAP 3.5.0-3.5.1:
-# NC_LIBS := -lnc-dap -ldap++ -lxml2 -lcurl
-# OPeNDAP 3.5+:
- NC_LIBS := -lnc-dap -ldap -lxml2 -lcurl
-# In addition, AIX OPeNDAP requires these libraries...
-ifneq (${null},$(findstring AIX,${PVM_ARCH}))
- NC_LIBS += -lcrypto -liconv -lssl -lz
-endif # end AIX
-# Get netCDF from OPeNDAP version
- NETCDF_INC=${DAP_OPENDAP_ROOT}/include/libnc-dap
- NETCDF_LIB=${DAP_OPENDAP_ROOT}/lib
-endif # end DAP_OPENDAP
-
-# Internationalize NCO with i18n features
-ifeq (${I18N},Y)
- MY_SHR_DIR := ${HOME}/share
- MY_ES_DIR := ${MY_SHR_DIR}/locale/es/LC_MESSAGES
- MY_FR_DIR := ${MY_SHR_DIR}/locale/fr/LC_MESSAGES
-endif
-
-ifeq (${NETCDF4},Y)
- CPPFLAGS += -DENABLE_NETCDF4 -DHAVE_NETCDF4_H
-endif
-# endif NETCDF4
-
-# Message Passing Interface (MPI)
-ifeq (${MPI_FAKE},Y)
-# MPI_FAKE instructs make to compile mpnc*.c operators without defining ENABLE_MPI
-# Resulting executables use UP or SMP code not MPI code
-# This tests compile, link, execution of MPI mpnc*.c code without using any MPI calls
- MPI := Y
-endif # !MPI_FAKE
-ifdef MPI_PRC
-# MPI_PRC tells test scripts how many MPI processes to spawn
-# Pass this MPI argument to nco_bm.pl
- MPI_PRC_SNG := "--mpi_prc=${MPI_PRC}"
-# MPI_PRC implies MPI
- MPI := Y
-else # !MPI_PRC
- MPI_PRC_SNG :=
-endif # !MPI_PRC
-
-ifeq (${NETCDF4},Y)
-# Enable netCDF4 functionality
-ifndef HDF5_ROOT
- HDF5_ROOT := ${NETCDF4_ROOT}
-endif
-ifndef HDF5_INC
- HDF5_INC := ${HDF5_ROOT}/include # Directory containing hdf5.h
-endif
-ifndef HDF5_LIB
- HDF5_LIB := ${HDF5_ROOT}/lib # Directory containing libhdf5.a
-endif
-# fxm: Temporary kludge: Machines with MPI_ROOT set are assumed to have parallel filesystems for NCO builds
-ifdef MPI_ROOT
- HDF5_INC += -I${MPI_ROOT}/include # Directory containing mpi.h
- HDF5_LIB += ${MPI_ROOT}/lib64 # Directory containing libmpi.a
-endif # !MPI_ROOT
- NETCDF_INC := ${NETCDF4_ROOT}/include
- NETCDF_LIB := ${NETCDF4_ROOT}/lib
- NC_LDFLAGS := -L${NETCDF_LIB} $(addprefix -L,${HDF5_LIB})
-# NC_LIBS := -lnetcdf -lhdf5_hl -lhdf5 -lz ${NC_LIBS}
- NC_LIBS := $(shell nc-config --libs) ${NC_LIBS}
-ifdef MPI_ROOT
- NC_LIBS += -lmpi
-endif # !MPI_ROOT
-ifdef CURL_LIB
- NC_LDFLAGS += -L${CURL_LIB}
-endif # end
-ifeq (${SZ},Y)
-ifndef SZ_LIB
- SZ_LIB := /usr/lib # Directory containing libsz.a
-endif
- NC_LDFLAGS += -L${SZ_LIB}
- NC_LIBS += -lsz
-endif # !SZ
-ifneq (${HDF5_INC},${NETCDF_INC})
- NETCDF_INC += -I${HDF5_INC}
-endif # end
-endif # endif NETCDF4
+# At this point we change NETCDF_INC from a directory to a flag
+NC_CFLAGS := $(shell nc-config --cflags)
+NC_LDFLAGS := $(shell nc-config --libs)
+NCO_LDFLAGS := -L${MY_LIB_DIR} -lnco -lnco++
ifeq (${PNETCDF},Y)
# Enable pnetCDF functionality
- NC_LDFLAGS := -L${NETCDF_LIB}
- NC_LIBS += -lpnetcdf
+ NC_CFLAGS := $(shell /usr/local/parallel/bin/nc-config --cflags)
+ NC_LDFLAGS := $(shell /usr/local/parallel/bin/nc-config --libs)
+ MPI_CFLAGS := -I/usr/include/openmpi-x86_64
+ MPI_LDFLAGS := -L/usr/lib64/openmpi/lib -lmpi
endif # endif PNETCDF
-ifeq (${UDUNITS2},Y)
- UDUNITS := Y
-endif # end if UDUNITS
-ifeq (${UDUNITS},Y)
-# Build UDUnits-enabled NCO
-# Place UDUNITS block after DAP blocks for both to work together
-ifndef UDUNITS_INC
- UDUNITS_INC := /usr/local/include # Directory containing udunits.h
-endif
-ifndef UDUNITS_LIB
- UDUNITS_LIB := /usr/local/lib # Directory containing libudunits.a
-endif
-ifneq (${UDUNITS_INC},${NETCDF_INC})
- NETCDF_INC += -I${UDUNITS_INC}
-endif # end
-ifneq (${UDUNITS_LIB},${NETCDF_LIB})
- NC_LDFLAGS += -L${UDUNITS_LIB}
-endif # end if
-ifeq (${UDUNITS2},Y)
-# 20130607: -lexpat needed on .deb systems, not on RPM systems
-UDUNITS_RPM_DRC := /usr/include/udunits2
-ifneq (${UDUNITS_INC},/usr/local/include)
-# UDUNITS_RPM_TST := $(shell ls ${UDUNITS_RPM_DRC}/udunits2.h)
- UDUNITS_RPM_TST := ${UDUNITS_RPM_DRC}/udunits2.h
-else
- UDUNITS_RPM_TST := /usr/include/udunits2.h
-endif # end if
-ifeq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NETCDF_INC += -I${UDUNITS_RPM_DRC}
-endif # end if
-ifneq (${UDUNITS_RPM_TST},${UDUNITS_RPM_DRC}/udunits2.h)
- NC_LIBS += -ludunits2 -lexpat
-else # end if UDUNITS2 Fedora
- NC_LIBS += -ludunits2
-endif # end if UDUNITS2 Fedora
-else
- NC_LIBS += -ludunits
-endif # end if UDUNITS2
-endif # end if UDUNITS
+ifdef LIB_NCAR
+ NC_LDFLAGS := ${LIB_NCAR} ${NC_LDFLAGS}
+endif
-# TMP_* and NCO_* are required to play nicely with DAP flags
-NCO_LDFLAGS := -L${MY_LIB_DIR}
-NCO_LIBS := -lnco_c++
-TMP_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS}
-TMP_LIBS := ${NCO_LIBS} ${NC_LIBS}
-# sort removes duplicates but unfortunately changes precedence too
-# fxm: use uniq instead
-#TMP_LDFLAGS := $(sort ${TMP_LDFLAGS})
+OTHER_CFLAGS := ${NC_CFLAGS} ${MPI_CFLAGS} ${GSL_INC} ${UDUNITS_INC}
+OTHER_LDFLAGS := ${NCO_LDFLAGS} ${NC_LDFLAGS} ${MPI_LDFLAGS} ${GSL_LIB} ${UDUNITS_LIB}
# NB: Do NOT add comment lines, e.g., # This is a comma, to character definitions
null :=
@@ -528,12 +379,9 @@ ifneq (${null},$(findstring AIX,${PVM_ARCH}))
# Visual age compiler headers must occur before g++ headers
CPP_TKN_OS += -I/usr/vacpp/include
endif # AIX
-ifeq (${DAP_NETCDF},Y)
- CPP_TKN_OS += -DENABLE_DAP
-endif # !DAP_NETCDF
-ifeq (${DAP_OPENDAP},Y)
+ifeq (${DAP},Y)
CPP_TKN_OS += -DENABLE_DAP
-endif # !DAP_OPENDAP
+endif # !DAP
ifeq (${MPI},Y)
ifneq (${MPI_FAKE},Y)
CPP_TKN_OS += -DENABLE_MPI
@@ -566,10 +414,10 @@ ifneq (${null},$(findstring xl,${CC}))
CPP_TKN_OS += -I/usr/vacpp/include
endif # xlC compilers
# Add /usr/local/include for libintl.h explicitly until netCDF is moved there
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC} -I/usr/local/include
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS} -I/usr/local/include
FC := xlf95_r
LD := ld
-LDFLAGS += -bh:5 ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += -bh:5 ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -683,13 +531,13 @@ CXX := cxx -std strict_ansi
CC := cc
CFLAGS := ${OMP_FLG}
# OSF1 is for CCM compatibility
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DOSF1 ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DOSF1 ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
FFLAGS := -c ${OMP_FLG} -automatic -fpe3
FIXEDFLAGS := -extend_source
FREEFLAGS := -DHIDE_SHR_MSG -free
LD := ld
-LDFLAGS += ${OMP_FLG} ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OMP_FLG} ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -720,10 +568,10 @@ ifeq (${PVM_ARCH},CRAY)
CXX := g++
CC := cc
CPP := cpp
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
LDFLAGS += -L/lib -lf
LEX := lex
LINT := lint
@@ -752,16 +600,19 @@ ${MY_OBJ_DIR}/%.o : %.f
endif
# endif CRAY
-# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD
-ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSD))
+# Works on LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD and MACOSX
+ifneq (${null},$(findstring ${PVM_ARCH},LINUXALPHALINUXAMD64LINUXARMFREEBSDMACOSX))
CXX := ${LINUX_CXX}
CC := ${LINUX_CC}
CPP := ${CXX}
# HAVE_INLINE is GNU standard to activate inline functions (used by GSL)
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DHAVE_INLINE ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} -DHAVE_INLINE ${CPP_PTH} ${OTHER_CFLAGS}
FC := ${LINUX_FC}
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
+ifeq (${PVM_ARCH},MACOSX)
+ LDFLAGS += -lresolv
+endif # endif MACOSX
LEX := flex
LINT := lint
YACC := bison
@@ -783,8 +634,15 @@ ifeq (${OPTS},X)
endif
CXXFLAGS := ${CFLAGS}
endif # endif Comeau C Compiler
-# GNU Compiler Collection
-ifeq (${CXX},g++)
+# GNU Compiler Collection or LLVM
+# 20140204: gcc and clang should receive identical options
+ifeq (g++,$(firstword ${CXX}))
+ GCC_OR_CLANG := Y
+endif
+ifeq (clang,$(firstword ${CXX}))
+ GCC_OR_CLANG := Y
+endif
+ifeq (${GCC_OR_CLANG},Y)
CPPFLAGS += -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
CFLAGS := -Wall -Wno-unused-variable
# Compilation flags for numerical routines recommended by GSL 1.3 manual, p. 397
@@ -804,7 +662,7 @@ ifeq (${CXX},g++)
# -Wwrite-strings: Apply const-qualifier to string constants, die if overwritten
# -fno-common: Prevent global variables from being simultaneously defined in different files
# -g: Put debugging symbols in executable
-# -O4: Turn on optimization so unitialized variables are flagged
+# -O4: Turn on optimization so uninitialized variables are flagged. Downside: optimizes-out many debugging symbols
# Compilation flags recommended by GSL that I do not like and do not use:
# -ansi: Support only strict ANSI C. Equivalent to -std=c89, conflicts with -std=c99
# --no-alias? -fstrict-aliasing
@@ -816,10 +674,18 @@ ifeq (${CXX},g++)
# -Dinline=: inline is not an ANSI keyword, must undefine inline to work with -ansi
# -fshort-enums: Make enums as short as possible, ususally non-int. Do not ever invoke this! This breaks ABI and causes subtle problems
ifeq (${OMP},Y)
+ifneq (clang,$(firstword ${CXX}))
+# 20140526 clang does not recognize/utilize -fopenmp
OMP_FLG_C := -fopenmp
OMP_FLG_F := -fopenmp
LDFLAGS += -lgomp -lpthread
+endif # endif clang
endif # endif OMP
+ifeq (clang,$(firstword ${CXX}))
+# 20140531 avoid clang error that -O4 is ame as -O3
+ CFLAGS := $(subst -O4,-O3,${CFLAGS})
+ LDFLAGS += -lstdc++
+endif # endif clang
ifeq (${OPTS},O)
CFLAGS += -O -g ${GCC_RCH_ARG}
endif
@@ -840,7 +706,7 @@ ifeq (${ABI},64)
endif # endif ABI
endif # endif LINUXAMD64
CXXFLAGS := ${CFLAGS}
-endif # endif GNU Compiler Collection
+endif # endif GNU Compiler Collection or LLVM
# Intel (Kai) C++ Compiler
ifeq (icpc,$(firstword ${CXX}))
# -cxxlib-gcc: link using C++ run-time libraries provided with GCC (default) (generated code is binary compatible with g++)
@@ -991,17 +857,17 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG_C} ${LDFLAGS}
endif # endif OMP
endif
-# endif LINUX
+# endif LINUX, LINUXALPHA, LINUXAMD64, LINUXARM, and FREEBSD and MACOSX
-ifeq (${PVM_ARCH},MACOSX)
+ifeq (${PVM_ARCH},MACOSXOLD)
CXX := c++
CC := cc
CFLAGS := -Wall
CPP := ${CC}
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lresolv -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lresolv -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1025,7 +891,7 @@ ifeq (${OMP},Y)
LDFLAGS := ${OMP_FLG} ${LDFLAGS}
endif # endif OMP
endif
-# endif MACOSX
+# endif MACOSXOLD
ifeq (${PVM_ARCH},NECSX)
ifeq (${OMP},Y)
@@ -1036,10 +902,10 @@ CXX := c++
CC := cc
CPP := c++ -E
#CPP := /usr/lib/cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${OTHER_CFLAGS}
FC := f90
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
ifeq ($(USE_FORTRAN_ARITHMETIC),Y)
# LDFLAGS += -L/lib -lf
endif
@@ -1070,10 +936,10 @@ ifeq (${PVM_ARCH},RS6K)
CXX := g++
CC := gcc -ansi
CPP := /lib/cpp -P
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${OTHER_CFLAGS}
FC := xlf
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
ifeq ($(USE_FORTRAN_ARITHMETIC),Y)
LDFLAGS += -lxlf90 -lxlf
endif
@@ -1107,10 +973,10 @@ CC := cc -c99
# 20000302: -w suppresses warnings which will swamp linker
#CXX := g++ -w
#CC := gcc
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90 -cpp
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS}
+LDFLAGS += ${OTHER_LDFLAGS}
LEX := flex
LINT := lint
YACC := bison
@@ -1130,7 +996,7 @@ else # ABI=32
endif # endif ABI
endif # endif SGI64, SGIMP64
ifeq (gcc,$(firstword ${CC}))
- LDFLAGS := $(GCC_LDFLAGS_SZ_SPC) ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS := $(GCC_LDFLAGS_SZ_SPC) ${OTHER_LDFLAGS} -lm
CFLAGS := ${GCC_ABI_FLG} -Wall
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1149,7 +1015,7 @@ endif
# endif CC=gcc
ifeq (CC,$(firstword ${CXX}))
# SGI Native C++ headers are in /usr/include/CC
- LDFLAGS := ${SGI_ABI_FLG} ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+ LDFLAGS := ${SGI_ABI_FLG} ${OTHER_LDFLAGS} -lm
CFLAGS := ${SGI_ABI_FLG}
ifeq (${OPTS},O)
CFLAGS += -O2
@@ -1191,12 +1057,12 @@ CXX := g++
CC := gcc
CFLAGS := -Wall
CPP := cpp
-CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS := ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := f90 -DHIDE_SHR_MSG
#FFLAGS := -xs -stackvar -e -Qoption f90comp -r8const
FFLAGS := -xs -stackvar -e
LD := ld
-LDFLAGS := ${TMP_LDFLAGS} ${TMP_LIBS} -lsunmath -lsocket -lnsl
+LDFLAGS := ${OTHER_LDFLAGS} -lsunmath -lsocket -lnsl
#LDFLAGS += -lF77 -lM77 -lresolv
LEX := lex
LINT := lint
@@ -1241,10 +1107,10 @@ CC := gcc -ansi
CPP := cpp
# NB: nameser.h needs -Di386, but gcc sends -Di586 (on pentiums)
CPP_TKN_OS += -Di386 -DNEED_STRCASECMP -DNEED_STRDUP -I/usr/include
-CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} -I${NETCDF_INC}
+CPPFLAGS += ${CPP_TKN} ${CPP_TKN_OS} ${CPP_PTH} ${OTHER_CFLAGS}
FC := g77
LD := ld
-LDFLAGS += ${TMP_LDFLAGS} ${TMP_LIBS} -lm
+LDFLAGS += ${OTHER_LDFLAGS} -lm
LEX := flex
LINT := lint
YACC := bison
@@ -1357,10 +1223,8 @@ dbg:
@printf "CPP_TKN = ${CPP_TKN}\n"
@printf "CXX = ${CXX}\n"
@printf "CXXFLAGS = ${CXXFLAGS}\n"
- @printf "DAP_NETCDF = ${DAP_NETCDF}\n"
- @printf "DAP_NETCDF_ROOT = ${DAP_NETCDF_ROOT}\n"
- @printf "DAP_OPENDAP = ${DAP_OPENDAP}\n"
- @printf "DAP_OPENDAP_ROOT = ${DAP_OPENDAP_ROOT}\n"
+ @printf "DAP = ${DAP}\n"
+ @printf "DAP_ROOT = ${DAP_ROOT}\n"
@printf "DBG = ${DBG}\n"
@printf "FC = ${FC}\n"
@printf "FFLAGS = ${FFLAGS}\n"
diff --git a/src/nco_c++/libnco_c++.hh b/src/nco_c++/libnco_c++.hh
index 1164950..d5080fc 100644
--- a/src/nco_c++/libnco_c++.hh
+++ b/src/nco_c++/libnco_c++.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/libnco_c++.hh,v 1.19 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/libnco_c++.hh,v 1.20 2014/06/15 21:06:25 zender Exp $
// Purpose: Prototypes, typedefs, and global variables for libnco_c++
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
/* libnco_c++.hh headers depend only on system headers
Thus libnco_c++.a may be built independently of any other libraries
diff --git a/src/nco_c++/nco_att.cc b/src/nco_c++/nco_att.cc
index 9052bb9..6ce37ad 100644
--- a/src/nco_c++/nco_att.cc
+++ b/src/nco_c++/nco_att.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_att.cc,v 1.22 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_att.cc,v 1.23 2014/06/15 21:06:25 zender Exp $
// Implementation (declaration) of C++ interface to netCDF attribute routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_att.hh> // C++ interface to netCDF attribute routines
diff --git a/src/nco_c++/nco_att.hh b/src/nco_c++/nco_att.hh
index 8da59dc..ce983d4 100644
--- a/src/nco_c++/nco_att.hh
+++ b/src/nco_c++/nco_att.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_att.hh,v 1.20 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_att.hh,v 1.22 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of C++ interface to netCDF attribute routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_att.hh> // C++ interface to netCDF attribute routines
@@ -363,6 +364,7 @@ nco_get_att // [fnc] Get attribute value
// Purpose: Wrapper for nco_get_att()
typ_ntr att_val; // O [frc] Attribute value
int rcd=nco_get_att(nc_id,var_id,att_nm,att_val);
+ rcd+=0; // 20140531 CEWI to prevent -Wunused-variable
return att_val;
} // end nco_get_att<typ_ntr>()
@@ -390,6 +392,7 @@ nco_get_att // [fnc] Get attribute value
typ_ntr att_val; // O [frc] Attribute value
int rcd=nco_get_att(nc_id,nco_inq_varid(nc_id,var_nm),att_nm,att_val);
+ rcd+=0; // 20140531 CEWI to prevent -Wunused-variable
return att_val;
} // end nco_get_att<typ_ntr>()
diff --git a/src/nco_c++/nco_dmn.cc b/src/nco_c++/nco_dmn.cc
index eb352aa..d527854 100644
--- a/src/nco_c++/nco_dmn.cc
+++ b/src/nco_c++/nco_dmn.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_dmn.cc,v 1.17 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_dmn.cc,v 1.18 2014/06/15 21:06:25 zender Exp $
// Implementation (declaration) of C++ interface to netCDF dimension routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_dmn.hh> // C++ interface to netCDF dimension routines
diff --git a/src/nco_c++/nco_dmn.hh b/src/nco_c++/nco_dmn.hh
index 2a72e7b..55a96ed 100644
--- a/src/nco_c++/nco_dmn.hh
+++ b/src/nco_c++/nco_dmn.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_dmn.hh,v 1.16 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_dmn.hh,v 1.17 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of C++ interface to netCDF dimension routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_dmn.hh> // C++ interface to netCDF dimension routines
diff --git a/src/nco_c++/nco_fl.cc b/src/nco_c++/nco_fl.cc
index 9527fe7..c84e306 100644
--- a/src/nco_c++/nco_fl.cc
+++ b/src/nco_c++/nco_fl.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_fl.cc,v 1.17 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_fl.cc,v 1.18 2014/06/15 21:06:25 zender Exp $
// Purpose: Implementation (declaration) of C++ interface to netCDF file-level routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_fl.hh> // C++ interface to netCDF file-level routines
diff --git a/src/nco_c++/nco_fl.hh b/src/nco_c++/nco_fl.hh
index 24d067f..e71658e 100644
--- a/src/nco_c++/nco_fl.hh
+++ b/src/nco_c++/nco_fl.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_fl.hh,v 1.16 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_fl.hh,v 1.17 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of C++ interface to netCDF file-level routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_fl.hh> // C++ interface to netCDF file-level routines
diff --git a/src/nco_c++/nco_hgh.cc b/src/nco_c++/nco_hgh.cc
index 5d04f2c..6c3d25e 100644
--- a/src/nco_c++/nco_hgh.cc
+++ b/src/nco_c++/nco_hgh.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_hgh.cc,v 1.20 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_hgh.cc,v 1.21 2014/06/15 21:06:25 zender Exp $
// Implementation (declaration) of C++ interface to high-level NCO utilities
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_hgh.hh> // High-level NCO utilities
diff --git a/src/nco_c++/nco_hgh.hh b/src/nco_c++/nco_hgh.hh
index ca1c1e2..5065b76 100644
--- a/src/nco_c++/nco_hgh.hh
+++ b/src/nco_c++/nco_hgh.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_hgh.hh,v 1.16 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_hgh.hh,v 1.17 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of high-level NCO routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_hgh.hh> // High-level NCO routines
diff --git a/src/nco_c++/nco_utl.cc b/src/nco_c++/nco_utl.cc
index a893866..2dd3177 100644
--- a/src/nco_c++/nco_utl.cc
+++ b/src/nco_c++/nco_utl.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_utl.cc,v 1.28 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_utl.cc,v 1.29 2014/06/15 21:06:25 zender Exp $
// Implementation (declaration) of C++ interface utilities for netCDF routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_utl.hh> // C++ interface utilities for netCDF routines
diff --git a/src/nco_c++/nco_utl.hh b/src/nco_c++/nco_utl.hh
index f679400..5f30884 100644
--- a/src/nco_c++/nco_utl.hh
+++ b/src/nco_c++/nco_utl.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_utl.hh,v 1.28 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_utl.hh,v 1.29 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of C++ interface utilities for netCDF routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_utl.hh> // C++ interface utilities for netCDF routines
diff --git a/src/nco_c++/nco_var.cc b/src/nco_c++/nco_var.cc
index 82bf5c1..0cb1513 100644
--- a/src/nco_c++/nco_var.cc
+++ b/src/nco_c++/nco_var.cc
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_var.cc,v 1.36 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_var.cc,v 1.37 2014/06/15 21:06:25 zender Exp $
// Purpose: Implementation (declaration) of C++ interface to netCDF variable routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
#include <nco_var.hh> // C++ interface to netCDF variable routines
diff --git a/src/nco_c++/nco_var.hh b/src/nco_c++/nco_var.hh
index b4035d8..7520dab 100644
--- a/src/nco_c++/nco_var.hh
+++ b/src/nco_c++/nco_var.hh
@@ -1,10 +1,11 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/nco_var.hh,v 1.32 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/nco_var.hh,v 1.33 2014/06/15 21:06:25 zender Exp $
// Purpose: Description (definition) of C++ interface to netCDF variable routines
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
+/* Copyright (C) 1995--2014 Charlie Zender
+ This file is part of NCO, the netCDF Operators. NCO is free software.
+ You can redistribute and/or modify NCO under the terms of the
+ GNU General Public License (GPL) Version 3 with exceptions described in the LICENSE file */
// Usage:
// #include <nco_var.hh> // C++ interface to netCDF variable routines
diff --git a/src/nco_c++/tst.cc b/src/nco_c++/tst.cc
index 65b75f8..336b087 100644
--- a/src/nco_c++/tst.cc
+++ b/src/nco_c++/tst.cc
@@ -1,10 +1,7 @@
-// $Header: /cvsroot/nco/nco/src/nco_c++/tst.cc,v 1.40 2013/12/31 05:14:02 zender Exp $
+// $Header: /cvsroot/nco/nco/src/nco_c++/tst.cc,v 1.41 2014/06/15 21:06:25 zender Exp $
// Purpose: Test for C++ programs using libnco_c++ API
-/* Copyright (C) 2001--2014 Charlie Zender
- License: GNU General Public License (GPL) Version 3
- See http://www.gnu.org/copyleft/gpl.html for full license text */
/* Compilation
make -W tst.cc OPTS=D tst
@@ -58,10 +55,10 @@ int main(int argc,char **argv)
long sz_nbr(1); // [nbr] Number of sizes
register long idx; // [idx] Counting index
- const std::string CVS_Date("$Date: 2013/12/31 05:14:02 $"); // [sng] CVS date string
- const std::string CVS_Header("$Header: /cvsroot/nco/nco/src/nco_c++/tst.cc,v 1.40 2013/12/31 05:14:02 zender Exp $"); // [sng] CVS header string
- const std::string CVS_Id("$Id: tst.cc,v 1.40 2013/12/31 05:14:02 zender Exp $"); // [sng] CVS identification string
- const std::string CVS_Revision("$Revision: 1.40 $"); // [sng] CVS revision string
+ const std::string CVS_Date("$Date: 2014/06/15 21:06:25 $"); // [sng] CVS date string
+ const std::string CVS_Header("$Header: /cvsroot/nco/nco/src/nco_c++/tst.cc,v 1.41 2014/06/15 21:06:25 zender Exp $"); // [sng] CVS header string
+ const std::string CVS_Id("$Id: tst.cc,v 1.41 2014/06/15 21:06:25 zender Exp $"); // [sng] CVS identification string
+ const std::string CVS_Revision("$Revision: 1.41 $"); // [sng] CVS revision string
const std::string date_cvs(CVS_Date.length() > 7 ? CVS_Date.substr(7,19) : static_cast<std::string>("Unknown")); // [sng] Date from CVS
const std::string sbr_nm("main"); // [sng] Subroutine name
const std::string prg_nm("libnco_c++"); // [sng] Program name
--
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