[med-svn] [examl] 02/02: Wrapper differentiates between examl and examl-OMP

[Andreas Tille]

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tille pushed a commit to branch master
in repository examl.

commit 79c6c58baac0323eacabd9efb7ca273b27077f14
Author: Andreas Tille <tille at debian.org>
Date:   Fri Feb 17 14:37:21 2017 +0100

    Wrapper differentiates between examl and examl-OMP
---
 debian/bin/examl           | 37 +++++++++++++++++++++++--------------
 debian/control             |  3 ++-
 debian/examl.1             |  6 +++++-
 debian/links               |  2 +-
 debian/tests/run-unit-test |  4 +++-
 5 files changed, 34 insertions(+), 18 deletions(-)

diff --git a/debian/bin/examl b/debian/bin/examl
index ce6b820..947d219 100755
--- a/debian/bin/examl
+++ b/debian/bin/examl
@@ -1,22 +1,31 @@
 #!/bin/sh
 
 EXAMLDIR=/usr/lib/examl/bin
+if echo $0 | grep -qi omp ; then
+  EXE=examl-OMP
+else
+  EXE=examl
+fi
+
 NPROC=`nproc`
 
+if echo "$@" | grep -q -- -np ; then
+  NP=`echo "$@" | sed 's/^.* *-np *\([0-9]\+\) *.*/\1/'`
+  echo "Run MPI on $NP processors as requested"
+  CMDARGS=`echo "$@" | sed 's/\(^.* \)-np *[0-9]\+\( .*\)/\1\2/'`
+else
+  NP=$((NPROC/2)) # leave 50% processors for other jobs - if you want to force more just use -np option
+  if [ $NP -eq 1 ] ; then
+    NP=$NPROC
+  fi
+  echo "Run MPI on $NP of $NPROC available processors"
+  CMDARGS="$@"
+fi
+
 if grep -q avx /proc/cpuinfo; then
-    if [ $NPROC -gt 1 ] ; then
-        echo "Use examl with OMP and AVX support"
-        ${EXAMLDIR}/examl-OMP-AVX "$@"
-    else
-        echo "Use examl with AVX support without OMP"
-        ${EXAMLDIR}/examl-AVX "$@"
-    fi
+    echo "Use $EXE with AVX support and $NP processors"
+    mpirun -np $NP ${EXAMLDIR}/${EXE}-AVX "CMDARGS"
 else
-    if [ $NPROC -gt 1 ] ; then
-        echo "Use examl with AVX support with overriden number of threads"
-        ${EXAMLDIR}/examl-OMP "$@"
-    else
-       echo "Use plain examl without AVX and OMP"
-       ${EXAMLDIR}/examl "$@"
-    fi
+    echo "Use $EXE without AVX support and $NP processors"
+    mpirun -np $NP ${EXAMLDIR}/${EXE} "CMDARGS"
 fi
diff --git a/debian/control b/debian/control
index aba9955..37b5003 100644
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,8 @@ Homepage: https://github.com/stamatak/ExaML
 Package: examl
 Architecture: any
 Depends: ${shlibs:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         openmpi-bin
 Description: Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
  Exascale Maximum Likelihood (ExaML) is a code for phylogenetic inference
  using MPI. This code implements the popular RAxML search algorithm for
diff --git a/debian/examl.1 b/debian/examl.1
index e6b33da..c4c212d 100644
--- a/debian/examl.1
+++ b/debian/examl.1
@@ -1,4 +1,3 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
 .TH EXAML "1" "February 2017" "examl 3.0.18" "User Commands"
 .SH NAME
 examl \- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
@@ -11,6 +10,7 @@ examl-OMP-AVX \- Exascale Maximum Likelihood (ExaML) code for phylogenetic infer
 \fB\-n\fR outputFileNames
 \fB\-m\fR rateHeterogeneityModel
 \fB\-t\fR userStartingTree|\-R binaryCheckpointFile|\-g constraintTree \fB\-p\fR randomNumberSeed
+[\-np NP]
 [\-a]
 [\-B numberOfMLtreesToSave]
 [\-c numberOfCategories]
@@ -29,6 +29,10 @@ examl-OMP-AVX \- Exascale Maximum Likelihood (ExaML) code for phylogenetic infer
 [\-\-auto\-prot=ml|bic|aic|aicc]
 .SH OPTIONS
 .TP
+\fB\-np NP\fR
+NP is the number of processors to use for MPI.  If not specified some hopefully sensible
+guess is made.  \fBThis is a specific option of the Debian wrapper in /usr/bin.\fR
+.TP
 \fB\-a\fR
 use the median for the discrete approximation of the GAMMA model of rate heterogeneity
 .IP
diff --git a/debian/links b/debian/links
index 479a682..545a0b4 100644
--- a/debian/links
+++ b/debian/links
@@ -1,5 +1,5 @@
 usr/lib/examl/bin/examl-AVX	usr/bin/examl-AVX
-usr/lib/examl/bin/examl-OMP	usr/bin/examl-OMP
+usr/bin/examl			usr/bin/examl-OMP
 usr/lib/examl/bin/examl-OMP-AVX	usr/bin/examl-OMP-AVX
 usr/share/man/man1/examl.1.gz	usr/share/man/man1/examl-AVX.1.gz
 usr/share/man/man1/examl.1.gz	usr/share/man/man1/examl-OMP.1.gz
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index c1438f5..194a3f4 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -5,12 +5,14 @@ pkg="examl"
 
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+#  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
 fi
 
 cp -a /usr/share/doc/${pkg}/testData $ADTTMP
 
 cd $ADTTMP
 
-gunzip -r *.gz
+gunzip -r *
 
 parse-examl -s testData/49 -m DNA -n 49.unpartitioned
+parse-examl -s testData/49 -q testData/49.model -m DNA -n 49.partitioned

-- 
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