[med-svn] [Git][med-team/ampliconnoise][master] 5 commits: d/t/Run.sh: remove openmpi specific --use-hwthread-cpu argument.

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Tue Nov 26 21:15:39 GMT 2024



Étienne Mollier pushed to branch master at Debian Med / ampliconnoise


Commits:
11fbeb59 by Étienne Mollier at 2024-11-26T22:07:20+01:00
d/t/Run.sh: remove openmpi specific --use-hwthread-cpu argument.

- - - - -
597874b9 by Étienne Mollier at 2024-11-26T22:09:42+01:00
d/rules: do not enforce openmpi compiler.

- - - - -
3f4b99c6 by Étienne Mollier at 2024-11-26T22:10:17+01:00
d/bin_override/mpicc: remove now unneeded wrapper.

- - - - -
ec80faad by Étienne Mollier at 2024-11-26T22:10:39+01:00
d/{,t}/control: migrate to mpi-default- packages.

This replaces the use of openmpi specifically.

Closes: #1087997

- - - - -
b19ede77 by Étienne Mollier at 2024-11-26T22:15:06+01:00
d/changelog: ready for upload to unstable.

- - - - -


6 changed files:

- − debian/bin_override/mpicc
- debian/changelog
- debian/control
- debian/rules
- debian/tests/Run.sh
- debian/tests/control


Changes:

=====================================
debian/bin_override/mpicc deleted
=====================================
@@ -1,4 +0,0 @@
-#!/bin/sh
-
-#Force use of mpicc without ugly patching of Makefiles
-exec mpicc.openmpi "$@"


=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+ampliconnoise (1.29-15) unstable; urgency=medium
+
+  * d/t/Run.sh: remove openmpi specific --use-hwthread-cpu argument.
+  * d/rules: do not enforce openmpi compiler.
+  * d/bin_override/mpicc: remove now unneeded wrapper.
+  * d/{,t}/control: migrate to mpi-default- packages.
+    This replaces the use of openmpi specifically. (Closes: #1087997)
+    MPICH4 seems to be operating properly with ampliconnoise.
+
+ -- Étienne Mollier <emollier at debian.org>  Tue, 26 Nov 2024 22:12:39 +0100
+
 ampliconnoise (1.29-14) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper-compat (= 13),
                libgsl-dev,
-               libopenmpi-dev
+               mpi-default-dev
 Standards-Version: 4.7.0
 Vcs-Browser: https://salsa.debian.org/med-team/ampliconnoise
 Vcs-Git: https://salsa.debian.org/med-team/ampliconnoise.git
@@ -19,7 +19,7 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          mafft
-Recommends: openmpi-bin
+Recommends: mpi-default-bin
 Description: removal of noise from 454 sequenced PCR amplicons
  AmpliconNoise is a package of applications to clean up high-throughput
  sequence data.  It consists of three main parts:


=====================================
debian/rules
=====================================
@@ -8,10 +8,6 @@ include /usr/share/dpkg/architecture.mk
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
-# Override path as a way to hook mpicc
-PATH := $(CURDIR)/debian/bin_override:${PATH}
-export PATH
-
 # Compensate test result mismatches occurring on i386 only.
 ifeq ($(DEB_HOST_ARCH),i386)
 export DEB_CFLAGS_MAINT_APPEND=-ffloat-store


=====================================
debian/tests/Run.sh
=====================================
@@ -13,7 +13,7 @@ stub=${file%.dat}
 
 echo "Calculating .fdist file"
 
-mpirun $mpiextra --use-hwthread-cpus PyroDist -in $file -out ${stub} > ${stub}.fout
+mpirun $mpiextra PyroDist -in $file -out ${stub} > ${stub}.fout
 
 echo "Clustering .fdist file"
 
@@ -23,24 +23,24 @@ rm ${stub}.fdist
 rm ${stub}_X.otu ${stub}_X.tree
 echo "Running PyroNoise"
 
-mpirun $mpiextra --use-hwthread-cpus PyroNoiseM -din ${file} -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01.pout
+mpirun $mpiextra PyroNoiseM -din ${file} -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01.pout
 
 /usr/share/ampliconnoise/Scripts/Truncate.pl 220 < ${stub}_s60_c01_cd.fa > ${stub}_s60_c01_T220.fa
 
 echo "Running SeqDist"
-mpirun $mpiextra --use-hwthread-cpus SeqDist -in ${stub}_s60_c01_T220.fa > ${stub}_s60_c01_T220.seqdist
+mpirun $mpiextra SeqDist -in ${stub}_s60_c01_T220.fa > ${stub}_s60_c01_T220.seqdist
 
 FCluster -in ${stub}_s60_c01_T220.seqdist -out ${stub}_s60_c01_T220_S > ${stub}_s60_c01_T220.fcout
 
 echo "Running SeqNoise"
-mpirun $mpiextra --use-hwthread-cpus SeqNoise -in ${stub}_s60_c01_T220.fa -din ${stub}_s60_c01_T220.seqdist -lin ${stub}_s60_c01_T220_S.list -out ${stub}_s60_c01_T220_s30_c08 -s 30.0 -c 0.08 -min ${stub}_s60_c01.mapping > ${stub}_s60_c01_T220.snout
+mpirun $mpiextra SeqNoise -in ${stub}_s60_c01_T220.fa -din ${stub}_s60_c01_T220.seqdist -lin ${stub}_s60_c01_T220_S.list -out ${stub}_s60_c01_T220_s30_c08 -s 30.0 -c 0.08 -min ${stub}_s60_c01.mapping > ${stub}_s60_c01_T220.snout
 
 rm ${stub}_s60_c01_T220_S.otu ${stub}_s60_c01_T220_S.tree ${stub}_s60_c01_T220.seqdist
 
 echo "Remove degenerate primers"
 sed 's/^${primer}//' ${stub}_s60_c01_T220_s30_c08_cd.fa > ${stub}_s60_c01_T220_s30_c08_P.fa
 echo "Clustering OTUs"
-mpirun $mpiextra --use-hwthread-cpus NDist -i -in ${stub}_s60_c01_T220_s30_c08_P.fa > ${stub}_s60_c01_T220_s30_c08_P.ndist
+mpirun $mpiextra NDist -i -in ${stub}_s60_c01_T220_s30_c08_P.fa > ${stub}_s60_c01_T220_s30_c08_P.ndist
   
 FCluster -i -in ${stub}_s60_c01_T220_s30_c08_P.ndist -out ${stub}_s60_c01_T220_s30_c08_P > ${stub}_s60_c01_T220_s30_c08_P.fcout
 


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
-Depends: @, openmpi-bin
+Depends: @, mpi-default-bin
 Restrictions: allow-stderr



View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/d9111378102e7353ee72cd4e34cf6c18f9120991...b19ede7761d236bcfe8f3e5fef9d4ac0c907a356

-- 
View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/compare/d9111378102e7353ee72cd4e34cf6c18f9120991...b19ede7761d236bcfe8f3e5fef9d4ac0c907a356
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