[med-svn] [Git][med-team/ampliconnoise][master] Try --use-hwthread-cpus in openmpi for autopkgtest

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / ampliconnoise


Commits:
bd6bbbed by Pranav Ballaney at 2020-08-08T18:21:24+05:30
Try --use-hwthread-cpus in openmpi for autopkgtest

- - - - -


1 changed file:

- debian/tests/Run.sh


Changes:

=====================================
debian/tests/Run.sh
=====================================
@@ -2,7 +2,7 @@
 
 set -e
 
-nodes=4                              #no. of cluster nodes to use
+nodes=2                              #no. of cluster nodes to use
 
 file=$1; #first argument name of dat file
 defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
@@ -13,7 +13,7 @@ stub=${file%.dat}
 
 echo "Calculating .fdist file"
 
-mpirun $mpiextra -np $nodes PyroDist -in $file -out ${stub} > ${stub}.fout
+mpirun $mpiextra --use-hwthread-cpus 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 -np $nodes PyroNoiseM -din ${file} -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01.pout
+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
 
 /usr/share/ampliconnoise/Scripts/Truncate.pl 220 < ${stub}_s60_c01_cd.fa > ${stub}_s60_c01_T220.fa
 
 echo "Running SeqDist"
-mpirun $mpiextra -np $nodes SeqDist -in ${stub}_s60_c01_T220.fa > ${stub}_s60_c01_T220.seqdist
+mpirun $mpiextra --use-hwthread-cpus 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 -np $nodes 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 --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
 
 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 -np $nodes NDist -i -in ${stub}_s60_c01_T220_s30_c08_P.fa > ${stub}_s60_c01_T220_s30_c08_P.ndist
+mpirun $mpiextra --use-hwthread-cpus 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
 



View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/commit/bd6bbbed3115f8668fca27bfbc7ca9fd19d77f28

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View it on GitLab: https://salsa.debian.org/med-team/ampliconnoise/-/commit/bd6bbbed3115f8668fca27bfbc7ca9fd19d77f28
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