[med-svn] [Git][med-team/hyphy][master] 3 commits: Refresh patches
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Jan 30 09:39:00 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / hyphy
Commits:
400d3881 by Michael R. Crusoe at 2021-01-30T10:01:06+01:00
Refresh patches
- - - - -
386e6c64 by Michael R. Crusoe at 2021-01-30T10:02:29+01:00
debian/rules: build avx and sse3 version for amd64
- - - - -
bd2e5ebf by Michael R. Crusoe at 2021-01-30T10:03:12+01:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- + debian/bin/simd-dispatch
- debian/changelog
- debian/patches/rm_arch_specific_flags.patch
- debian/patches/use_debian_sqlite.patch
- debian/rules
Changes:
=====================================
debian/bin/simd-dispatch
=====================================
@@ -0,0 +1,20 @@
+#!/bin/sh
+
+DIR=/usr/lib/hyphy/bin
+EXE=${DIR}/$(basename "$0")
+CMDARGS="$@"
+
+test_and_run () {
+ if lscpu | grep -q "$1" && [ -x "${EXE}-$1" ]; then
+ echo "Using ${EXE}-$1" 1>&2
+ "${EXE}-$1" "${CMDARGS}"
+ exit
+ fi
+}
+
+
+for SIMD in avx sse3 ; do test_and_run ${SIMD} ; done
+
+# fallback to plain option
+echo "Using $EXE without SIMD support"
+"${EXE}" "${CMDARGS}" 1>&2
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+hyphy (2.5.27+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * Refresh patches.
+ * debian/rules: build avx and sse3 version for amd64
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 30 Jan 2021 10:03:12 +0100
+
hyphy (2.5.27+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/patches/rm_arch_specific_flags.patch
=====================================
@@ -7,7 +7,7 @@ Last-Update: 2020-09-28
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- hyphy.orig/CMakeLists.txt
+++ hyphy/CMakeLists.txt
-@@ -154,9 +154,8 @@
+@@ -181,9 +181,8 @@
#set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info")
if(NOAVX)
@@ -18,7 +18,16 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
else(NOSSE3)
PCL_CHECK_FOR_SSE3()
if(${HAVE_SSE3_EXTENSIONS})
-@@ -192,7 +191,7 @@
+@@ -194,7 +193,7 @@
+ else(NOAVX)
+ PCL_CHECK_FOR_AVX()
+ if(${HAVE_AVX_EXTENSIONS})
+- set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")
++ set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mavx")
+ add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
+ PCL_CHECK_FOR_FMA3()
+ if (${HAVE_FMA3})
+@@ -219,7 +218,7 @@
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 ")
if(NOAVX)
if(NOSSE3)
@@ -27,3 +36,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
else(NOSSE3)
PCL_CHECK_FOR_SSE3()
if(${HAVE_SSE3_EXTENSIONS})
+@@ -230,7 +229,7 @@
+ else(NOAVX)
+ PCL_CHECK_FOR_AVX()
+ if(${HAVE_AVX_EXTENSIONS})
+- set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")
++ set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mavx")
+ add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
+ PCL_CHECK_FOR_FMA3()
+ if (${HAVE_FMA3})
=====================================
debian/patches/use_debian_sqlite.patch
=====================================
@@ -4,10 +4,11 @@ Description: Use Debian packaged sqlite3
- in src/lib/setup.py
Reviewed-by: Étienne Mollier <etienne.mollier at mailoo.org>
Last-Update: 2020-09-24
+Forwarded: not-needed
--- hyphy.orig/CMakeLists.txt
+++ hyphy/CMakeLists.txt
-@@ -119,12 +119,11 @@
+@@ -146,12 +146,11 @@
file(GLOB SRC_CONTRIB src/contrib/*.cpp)
set(SRC_LINK src/lib/link/THyPhy.cpp)
@@ -21,7 +22,7 @@ Last-Update: 2020-09-24
set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")
#-------------------------------------------------------------------------------
-@@ -279,6 +278,35 @@
+@@ -313,6 +312,35 @@
add_definitions (-D__HYPHYCURL__)
endif(${CURL_FOUND} AND NOT APPLE)
@@ -57,7 +58,7 @@ Last-Update: 2020-09-24
#-------------------------------------------------------------------------------
-@@ -313,11 +341,6 @@
+@@ -347,11 +375,6 @@
)
set_property(
@@ -69,7 +70,7 @@ Last-Update: 2020-09-24
SOURCE src/core/calcnode2.cpp
APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
)
-@@ -337,7 +360,6 @@
+@@ -371,7 +394,6 @@
src/core/include
src/contrib
src/lib/Link src/new/include
=====================================
debian/rules
=====================================
@@ -18,7 +18,13 @@ override_dh_auto_clean:
dh_auto_clean
override_dh_auto_configure:
+ifeq (amd64,$(DEB_HOST_ARCH))
dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON
+ dh_auto_configure --builddirectory obj_avx -- -DINSTALL_PREFIX=/usr -DNOAVX=OFF -DNOSSE3=OFF
+ dh_auto_configure --builddirectory obj_sse3 -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=OFF
+else
+ dh_auto_configure -- -DINSTALL_PREFIX=/usr -DNOAVX=ON -DNOSSE3=ON
+endif
override_dh_auto_build:
# convert a few ISO-8859-1 files to address national-encoding
@@ -27,9 +33,31 @@ override_dh_auto_build:
; do iconv -f ISO-8859-1 -t UTF-8 < $${file} > "$${file}.new" \
; mv "$${file}.new" "$${file}" \
; done
- # no idea about the purpose of the dynamic library - executables are not simply linked against it
+ifeq (amd64,$(DEB_HOST_ARCH))
+ dh_auto_build -- MP MPI
+ dh_auto_build --builddirectory obj_avx -- MP MPI
+ dh_auto_build --builddirectory obj_sse3 -- MP MPI
+else
dh_auto_build -- MP MPI
- # LIB
+endif
+
+override_dh_install:
+ dh_install
+ifeq (amd64,$(DEB_HOST_ARCH))
+ mkdir -p debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin
+ mkdir -p debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin
+ cp obj_avx/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-avx
+ cp obj_sse3/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/HYPHYMPI-sse3
+ cp obj_avx/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-avx
+ cp obj_sse3/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/hyphy-sse3
+ dh_install -phyphy-common debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/bin
+ mv debian/hyphy-mpi/usr/bin/HYPHYMPI debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin/
+ mv debian/hyphy-pt/usr/bin/hyphy debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin/
+ cd $(CURDIR)/debian/hyphy-mpi/usr/bin && \
+ ln -s ../lib/$(DEB_SOURCE)/bin/simd-dispatch HYPHYMPI
+ cd $(CURDIR)/debian/hyphy-pt/usr/bin && \
+ ln -s ../lib/$(DEB_SOURCE)/bin/simd-dispatch hyphy
+endif
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/335d827edf4ee4f2ae700bd95bd855ac4d44e76c...bd2e5ebf6c8f69c23ca8ff64ff3a87abfa8960de
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