| 1 |
#!/bin/bash |
| 2 |
|
| 3 |
# Escript/Finley wrapper for python |
| 4 |
# Sets LD_LIBRARY_PATH and PYTHONPATH and then runs either python or the MPI launcher |
| 5 |
|
| 6 |
#Extra paths can be configured about a page further down |
| 7 |
#Search for EXTRA_PATH="" |
| 8 |
|
| 9 |
#set to 1 if performing this is a standalone build and ../../pkg contains the relevant tools |
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STANDALONE=0 |
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|
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#set to 1 if this is part of a packaged build (.deb) and files will be installed in standard locations |
| 13 |
#rather than everything in a single directory |
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#Do not use this together with $STANDALONE |
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STDLOCATION=0 |
| 16 |
|
| 17 |
#Now we find the location of this script |
| 18 |
#Note that this location should be absolute but does not need to be unique |
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scriptdir="" |
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CURDIR=`pwd` |
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|
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#Environment vars which control operations: |
| 23 |
# ESCRIPT_NUM_NODES, ESCRIPT_NUM_PROCS, ESCRIPT_NUM_THREADS, ESCRIPT_HOSTFILE, ESCRIPT_CREATESTDFILES |
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|
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HOSTFILE=/tmp/escript.$$ |
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HOSTFILE2=/tmp/escript2.$$ |
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|
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#Begin finding ESCRIPT_ROOT |
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if [ $STDLOCATION -ne 0 ] |
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then |
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ESCRIPT_ROOT=/usr/lib/escript |
| 32 |
else |
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#We don't know the escript root so we need to work it out from the invocation |
| 34 |
#Need to match if the name contains / |
| 35 |
if [[ $0 =~ / ]] |
| 36 |
then |
| 37 |
# We are not using the PATH to find the script |
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cd `dirname $0` |
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scriptdir=`pwd` |
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cd $CURDIR |
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else |
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# name does not contain / therefore we are using |
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tscriptdir=`which $0` |
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if [ $? != 0 ] |
| 45 |
then |
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echo "Error! Unable to determine script directory. Exiting." |
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exit 1 |
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fi |
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scriptdir=`dirname $tscriptdir` |
| 50 |
fi |
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|
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cd $scriptdir/.. |
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ESCRIPT_ROOT=`pwd` |
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cd .. |
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ESCRIPT_PARENT=`pwd` |
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cd $CURDIR |
| 57 |
|
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fi |
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##### End finding ESCRIPT_ROOT ######## |
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|
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if [ ! -r $ESCRIPT_ROOT/lib/buildvars ]; then |
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echo "Error! Unable to read escript build information. Exiting." |
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exit 1 |
| 64 |
fi |
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|
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PYTHON_MPI_NULL="$ESCRIPT_ROOT/lib/pythonMPI" |
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PYTHON_MPI_REDIRECT="$ESCRIPT_ROOT/lib/pythonMPIredirect" |
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PYTHON_CMD=python |
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|
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# if possible please express paths relative to $ESCRIPT_ROOT unless |
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# they are in an unrelated location |
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|
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EXTRA_DYLD_LIBRARY_PATH="" |
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EXTRA_PATH=$ESCRIPT_ROOT/bin |
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EXTRA_PYTHONPATH=$ESCRIPT_ROOT |
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EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib |
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|
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if [ $STANDALONE -eq 1 ] |
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then |
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EXTRA_PATH=$ESCRIPT_PARENT/pkg/python/bin:$EXTRA_PATH |
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EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/boost/lib:$ESCRIPT_PARENT/pkg/netcdf/lib/:$EXTRA_LD_LIBRARY_PATH |
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EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH |
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EXTRA_LD_LIBRARY_PATH=$ESCRIPT_PARENT/pkg/python/lib:$EXTRA_LD_LIBRARY_PATH |
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EXTRA_PYTHONPATH=$ESCRIPT_PARENT/pkg/numpy/lib/python2.6/site-packages:$ESCRIPT_PARENT/pkg/matplotlib/lib/python2.6/site-packages:$EXTRA_PYTHONPATH |
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fi |
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|
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|
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|
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HELP_TEXT=" |
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Usage: escript [options] script.py [arguments...] |
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-n nn number of nodes to use |
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-p np number of MPI processes to spawn |
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-t nt number of OpenMP threads to use |
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-f file name of MPI hostfile |
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-c print compile information for escript and exit |
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-V print escript version and exit |
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-i interactive mode |
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-b do not invoke python (run non-python programs) |
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-e print export statements for environment and exit |
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-o redirect output from MPI to files |
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-v print diagnostics |
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-x ..reserved for future use .. |
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script.py Your python script |
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arguments... The optional command-line arguments to your script |
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" |
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|
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if [ "$1" = "--help" ]; then |
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echo "$HELP_TEXT" |
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exit 0 |
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fi |
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#======================================================================================= |
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|
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# Avoid bug in hybrid runs with MPT MPI |
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|
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|
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# Parse the command-line options |
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# option e should not be followed by a : |
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while getopts 'bn:p:t:f:h:ecVviox' option |
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do |
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case "$option" in |
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"b") DOBINARY=yes |
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;; |
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"n") ESCRIPT_NUM_NODES=$OPTARG |
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;; |
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"p") ESCRIPT_NUM_PROCS=$OPTARG |
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;; |
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"t") ESCRIPT_NUM_THREADS=$OPTARG |
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;; |
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"f") ESCRIPT_HOSTFILE=$OPTARG |
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;; |
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"c") cat $ESCRIPT_ROOT/lib/buildvars |
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exit 0 |
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;; |
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"V") echo "escript-development(build "`grep svn_revision $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2`")" |
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exit 0 |
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;; |
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"h") echo "$HELPTEXT" |
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exit 0 |
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;; |
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"i") DOINTERACTIVE=yes |
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;; |
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"e") echo "export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:\$LD_LIBRARY_PATH" |
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echo "export PYTHONPATH=$EXTRA_PYTHONPATH:\$PYTHONPATH" |
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echo "export PATH=$EXTRA_PATH:\$PATH" |
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if [ "`uname`" = "Darwin" ] |
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then |
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echo "export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH" |
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fi |
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exit 0 |
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;; |
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"o") ESCRIPT_CREATESTDFILES="yes" |
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;; |
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"v") ESCRIPT_VERBOSE="yes" |
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;; |
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"x") echo "-x not implemented yet" |
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exit 1 |
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;; |
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?) echo "$HELP_TEXT" |
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exit 1 |
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;; |
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esac |
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done |
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shift `expr $OPTIND - 1` |
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#============================================== |
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# |
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# Read the MPI_FLAVOUR from the buildvars |
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# |
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MPI_FLAVOUR=`grep mpi_flavour $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2` |
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WITH_OPENMP=`grep useopenmp $ESCRIPT_ROOT/lib/buildvars |cut -d= -f2` |
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|
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if [ ! -z $ESCRIPT_VERBOSE ]; then |
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echo "MPI flavour is $MPI_FLAVOUR." |
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if [ "$WITH_OPENMP" = "y" ]; then echo "OpenMP enabled."; fi |
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fi |
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|
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# |
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# extend path variables |
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# |
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export PATH=$EXTRA_PATH:$PATH |
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export LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$LD_LIBRARY_PATH |
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export PYTHONPATH=$EXTRA_PYTHONPATH:$PYTHONPATH |
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EXPORT_ENV="PATH,LD_LIBRARY_PATH,PYTHONPATH" |
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if [ "`uname`" = "Darwin" ] |
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then |
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export DYLD_LIBRARY_PATH=$EXTRA_DYLD_LIBRARY_PATH:$EXTRA_LD_LIBRARY_PATH:$DYLD_LIBRARY_PATH |
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EXPORT_ENV="$EXPORT_ENV,DYLD_LIBRARY_PATH" |
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fi |
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if [ ! -z $ESCRIPT_VERBOSE ] |
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then |
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echo "PATH = $PATH " |
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echo "LD_LIBRARY_PATH = $LD_LIBRARY_PATH " |
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echo "PYTHONPATH = $PYTHONPATH " |
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if [ ! -z $DYLD_LIBRARY_PATH ]; then echo "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH "; fi |
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fi |
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#============================================== |
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# |
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# Ensure the variables have sensible values |
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# |
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if [ "$MPI_FLAVOUR" = "none" ] |
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then |
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if [ ! -z $ESCRIPT_NUM_NODES ] |
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then |
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echo "Warning: MPI disabled but number of nodes set. Option ignored." |
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fi |
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if [ ! -z $ESCRIPT_NUM_PROCS ] |
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then |
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echo "Warning: MPI disabled but number of processors per node set. Option ignored." |
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fi |
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if [ ! -z $ESCRIPT_HOSTFILE ] |
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then |
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echo "Warning: MPI disabled but host file is given. Option ignored." |
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fi |
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ESCRIPT_NUM_NODES=1 |
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ESCRIPT_NUM_PROCS=1 |
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else |
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if [ ! -z $ESCRIPT_HOSTFILE ] |
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then |
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if [ -f $ESCRIPT_HOSTFILE ] |
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then |
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cat $ESCRIPT_HOSTFILE | sort -u > $HOSTFILE |
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NUM_HOSTS=`cat $HOSTFILE | wc -l` |
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if [ ! -z $ESCRIPT_NUM_NODES ] |
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then |
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if [ $NUM_HOSTS -ne $ESCRIPT_NUM_NODES ] |
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then |
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echo "number of hosts selected in the host file $ESCRIPT_HOSTFILE needs to match the requested number of nodes $ESCRIPT_NUM_NODES." |
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exit 1 |
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fi |
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else |
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ESCRIPT_NUM_NODES=$NUM_HOSTS |
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fi |
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else |
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echo "cannot find hostfile $ESCRIPT_HOSTFILE." |
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exit 1 |
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fi |
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else |
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HOSTFILE='' |
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fi |
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|
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if [ -z $ESCRIPT_NUM_NODES ] |
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then |
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ESCRIPT_NUM_NODES=1 |
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fi |
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|
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if [ -z $ESCRIPT_NUM_PROCS ] |
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then |
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ESCRIPT_NUM_PROCS=1 |
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fi |
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|
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if [ ! -z $ESCRIPT_VERBOSE ] |
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then |
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echo "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES " |
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echo "ESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS " |
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fi |
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fi |
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|
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if [ "$WITH_OPENMP" = "y" ] |
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then |
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if [ -z $ESCRIPT_NUM_THREADS ] |
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then |
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ESCRIPT_NUM_THREADS=$OMP_NUM_THREADS |
| 262 |
if [ -z $ESCRIPT_NUM_THREADS ] |
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then |
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ESCRIPT_NUM_THREADS=1 |
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fi |
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fi |
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if [ ! -z $ESCRIPT_VERBOSE ] |
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then |
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echo "ESCRIPT_NUM_THREADS is $ESCRIPT_NUM_THREADS." |
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fi |
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else |
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if [[ ( ! -z $ESCRIPT_NUM_THREADS ) && ( $ESCRIPT_NUM_THREADS != 1 ) ]] |
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then |
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echo "Warning: OpenMP is disabled but number of threads requested is $ESCRIPT_NUM_THREADS!=1. Running without threads." |
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fi |
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ESCRIPT_NUM_THREADS=1 |
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fi |
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# |
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# Now we compute total number of Processes |
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# |
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(( TOTPROC=$ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS)) |
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if [ $? -ne 0 ] #Some compute error |
| 283 |
then #This could happen if the args were not a number |
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echo "expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical." |
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exit 1 |
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fi |
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|
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# |
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# Test to ensure people aren't trying to combine interactive and multi-process |
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# |
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if [[ ( ( ! -z $DOINTERACTIVE ) || ( $# -eq 0 ) ) && ( $TOTPROC -gt 1) ]] |
| 292 |
then |
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echo "Interactive mode cannot be used with more than one process" |
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exit 1 |
| 295 |
fi |
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|
| 297 |
if [ $TOTPROC -gt 1 ] |
| 298 |
then |
| 299 |
if [ "$ESCRIPT_CREATESTDFILES" = "yes" ] |
| 300 |
then |
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PYTHON_MPI=$PYTHON_MPI_REDIRECT |
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else |
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PYTHON_MPI=$PYTHON_MPI_NULL |
| 304 |
fi |
| 305 |
else |
| 306 |
PYTHON_MPI=$PYTHON_MPI_NULL |
| 307 |
fi |
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#========================================================================================================= |
| 309 |
# Must have at least one command-line arg: the python script |
| 310 |
if [ $# -eq 0 ] |
| 311 |
then |
| 312 |
if [ ! -z $DOBINARY ] |
| 313 |
then |
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echo "No program to run was specified. Exiting." |
| 315 |
exit 1 |
| 316 |
fi |
| 317 |
fi |
| 318 |
if [ -z $@ ] |
| 319 |
then |
| 320 |
if [ ! -z $DOBINARY ] |
| 321 |
then |
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echo "Program must be given." |
| 323 |
exit 1 |
| 324 |
else |
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DOINTERACTIVE="yes" |
| 326 |
fi |
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fi |
| 328 |
|
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#========================================================================================================= |
| 330 |
if [ ! -z $DOBINARY ] |
| 331 |
then |
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EXEC_CMD="$@" |
| 333 |
else |
| 334 |
if [ "$MPI_FLAVOUR" = "none" ] |
| 335 |
then |
| 336 |
# Check to see if the python version we were compiled with matches the one of EXEC_CMD |
| 337 |
# We should only do this check if they are running a python script |
| 338 |
if [ -f $ESCRIPT_ROOT/lib/pyversion ] |
| 339 |
then |
| 340 |
compversion=`cat $ESCRIPT_ROOT/lib/pyversion` |
| 341 |
intversion=`$PYTHON_CMD -V 2>&1` |
| 342 |
if [ "$compversion" != "$intversion" ] |
| 343 |
then |
| 344 |
echo "Python versions do not match. Escript was compiled for "$compversion"." |
| 345 |
echo "Current version of Python appears to be "$intversion"." |
| 346 |
exit 1 |
| 347 |
fi |
| 348 |
fi |
| 349 |
if [ ! -z $DOINTERACTIVE ] |
| 350 |
then |
| 351 |
EXEC_CMD="$PYTHON_CMD -i $@" |
| 352 |
else |
| 353 |
EXEC_CMD="$PYTHON_CMD $@" |
| 354 |
fi |
| 355 |
else |
| 356 |
if [ ! -z $DOINTERACTIVE ] |
| 357 |
then |
| 358 |
EXEC_CMD="$PYTHON_MPI -i $@" |
| 359 |
else |
| 360 |
EXEC_CMD="$PYTHON_MPI $@" |
| 361 |
fi |
| 362 |
fi |
| 363 |
fi |
| 364 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "Command to be executed is \"$EXEC_CMD\"."; fi |
| 365 |
#=============================================================================================== |
| 366 |
# |
| 367 |
# now we start to spwan things: |
| 368 |
# |
| 369 |
if [ "$WITH_OPENMP" = "y" ] |
| 370 |
then |
| 371 |
export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS |
| 372 |
EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS" |
| 373 |
fi |
| 374 |
EXIT_CODE=1 |
| 375 |
#=============== no MPI =================================== |
| 376 |
if [ "$MPI_FLAVOUR" = "none" ] |
| 377 |
then |
| 378 |
$EXEC_CMD |
| 379 |
EXIT_CODE=$? |
| 380 |
#=============== OpenMPI =================================== |
| 381 |
elif [ "$MPI_FLAVOUR" = "OPENMPI" ] |
| 382 |
then |
| 383 |
if [ ! -z $HOSTFILE ] |
| 384 |
then |
| 385 |
HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE` |
| 386 |
CMD="mpirun --gmca mpi_warn_on_fork 0 -x ${EXPORT_ENV//,/ -x } --bynode -np $TOTPROC --host $HOST_LIST $EXEC_CMD" |
| 387 |
else |
| 388 |
CMD="mpirun --gmca mpi_warn_on_fork 0 -x ${EXPORT_ENV//,/ -x } -np $TOTPROC $EXEC_CMD" |
| 389 |
fi |
| 390 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi |
| 391 |
$CMD |
| 392 |
EXIT_CODE=$? |
| 393 |
|
| 394 |
#=============== Intel MPI =================================== |
| 395 |
elif [ "$MPI_FLAVOUR" = "INTELMPI" ] |
| 396 |
then |
| 397 |
|
| 398 |
if [ "$WITH_OPENMP" = "y" ] |
| 399 |
then |
| 400 |
export I_MPI_PIN_DOMAIN=omp |
| 401 |
EXPORT_ENV="$EXPORT_ENV, I_MPI_PIN_DOMAIN" |
| 402 |
fi |
| 403 |
|
| 404 |
if [ ! -z $HOSTFILE ] |
| 405 |
then |
| 406 |
mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE |
| 407 |
if [ $? -ne 0 ] |
| 408 |
then |
| 409 |
echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed." |
| 410 |
exit 1 |
| 411 |
else |
| 412 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi |
| 413 |
fi |
| 414 |
else |
| 415 |
mpdboot -n 1 -r ssh |
| 416 |
if [ $? -ne 0 ] |
| 417 |
then |
| 418 |
echo "mpdboot failed." |
| 419 |
exit 1 |
| 420 |
else |
| 421 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started."; fi |
| 422 |
fi |
| 423 |
fi |
| 424 |
CMD="mpiexec -perhost $ESCRIPT_NUM_PROCS -envall -n $TOTPROC $EXEC_CMD" |
| 425 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi |
| 426 |
$CMD |
| 427 |
EXIT_CODE=$? |
| 428 |
mpdallexit |
| 429 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi |
| 430 |
#=============== SGI's MPIMPT =================================== |
| 431 |
elif [ "$MPI_FLAVOUR" = "MPT" ] |
| 432 |
then |
| 433 |
export MPI_NUM_MEMORY_REGIONS=0 |
| 434 |
EXPORT_ENV="$EXPORT_ENV,MPI_NUM_MEMORY_REGIONS" |
| 435 |
if [ ! -z $HOSTFILE ] |
| 436 |
then |
| 437 |
HOST_LIST=`awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' $HOSTFILE` |
| 438 |
CMD="mpirun $HOST_LIST -np $ESCRIPT_NUM_PROCS $EXEC_CMD" |
| 439 |
else |
| 440 |
CMD="mpirun -np $TOTPROC $EXEC_CMD" |
| 441 |
fi |
| 442 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi |
| 443 |
$CMD |
| 444 |
EXIT_CODE=$? |
| 445 |
#=============== MPICH =================================== |
| 446 |
elif [ "$MPI_FLAVOUR" = "MPICH" ] |
| 447 |
then |
| 448 |
if [ ! -z $HOSTFILE ] |
| 449 |
then |
| 450 |
touch $HOSTFILE2 |
| 451 |
for (( i=1;i<=$ESCRIPT_NUM_PROCS;i+=1 )) ; do cat $HOSTFILE >> $HOSTFILE2 ; done |
| 452 |
CMD="mpirun -machinefile $HOSTFILE2 -np $TOTPROC $EXEC_CMD" |
| 453 |
else |
| 454 |
CMD="mpirun -np $TOTPROC $EXEC_CMD" |
| 455 |
fi |
| 456 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi |
| 457 |
$CMD |
| 458 |
EXIT_CODE=$? |
| 459 |
#=============== MPICH2 =================================== |
| 460 |
elif [ "$MPI_FLAVOUR" = "MPICH2" ] |
| 461 |
then |
| 462 |
if [ ! -z $HOSTFILE ] |
| 463 |
then |
| 464 |
mpdboot -n $ESCRIPT_NUM_NODES -r ssh -f $HOSTFILE |
| 465 |
if [ $? -ne 0 ] |
| 466 |
then |
| 467 |
echo "mpdboot with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes failed." |
| 468 |
exit 1 |
| 469 |
else |
| 470 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started with host file $ESCRIPT_HOSTFILE for $ESCRIPT_NUM_NODES nodes."; fi |
| 471 |
fi |
| 472 |
else |
| 473 |
mpdboot -n 1 -r ssh |
| 474 |
if [ $? -ne 0 ] |
| 475 |
then |
| 476 |
echo "mpdboot failed." |
| 477 |
exit 1 |
| 478 |
else |
| 479 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdboot was started."; fi |
| 480 |
fi |
| 481 |
fi |
| 482 |
CMD="mpiexec -genvlist $EXPORT_ENV -np $TOTPROC $EXEC_CMD" |
| 483 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "MPI command is \"$CMD\"."; fi |
| 484 |
$CMD |
| 485 |
EXIT_CODE=$? |
| 486 |
mpdallexit |
| 487 |
if [ ! -z $ESCRIPT_VERBOSE ]; then echo "mpdallexit executed."; fi |
| 488 |
else |
| 489 |
echo "unknown MPI flavour '$MPI_FLAVOUR'." |
| 490 |
fi |
| 491 |
exit $EXIT_CODE |
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