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#!/usr/bin/env sh |
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|
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############################################################################## |
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# |
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# Copyright (c) 2003-2016 by The University of Queensland |
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# http://www.uq.edu.au |
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# |
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# Primary Business: Queensland, Australia |
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# Licensed under the Apache License, version 2.0 |
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# http://www.apache.org/licenses/LICENSE-2.0 |
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# |
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# Development until 2012 by Earth Systems Science Computational Center (ESSCC) |
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# Development 2012-2013 by School of Earth Sciences |
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# Development from 2014 by Centre for Geoscience Computing (GeoComp) |
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# |
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############################################################################## |
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|
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# Escript wrapper for python |
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# Sets LD_LIBRARY_PATH and PYTHONPATH and then runs either python or the MPI |
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# launcher. |
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|
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# Extra paths can be configured about a page further down |
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# Search for EXTRA_PATH="" |
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|
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# set to 1 if this is part of a packaged build (.deb) and files will be |
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# installed in standard locations rather than everything in a single directory |
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STDLOCATION=0 |
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|
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# Now we find the location of this script |
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# Note that this location should be absolute but does not need to be unique |
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scriptdir="" |
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CURDIR=$(pwd) |
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|
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# Environment vars which control operations: |
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# ESCRIPT_NUM_NODES, ESCRIPT_NUM_PROCS, ESCRIPT_NUM_THREADS, ESCRIPT_HOSTFILE, ESCRIPT_CREATESTDFILES |
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|
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HOSTFILE=/tmp/escript.$USER.$$ |
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|
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die () { |
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echo "Error: $@" 1>&2 |
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exit 1 |
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} |
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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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#Package building scripts will replace this line |
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ESCRIPT_ROOT=/usr/lib/python-escript |
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else |
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# We don't know the escript root so we need to work it out from the invocation |
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# Need to match if the name contains / |
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if $(echo $0|grep -q /) |
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then |
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# We are not using the PATH to find the script |
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cd "$(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 [ $? -ne 0 ] |
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then |
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die "Unable to determine script directory!" |
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fi |
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scriptdir=$(dirname $tscriptdir) |
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fi |
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|
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cd "$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" |
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|
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fi |
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##### End finding ESCRIPT_ROOT ######## |
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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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|
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if [ $STDLOCATION -eq 1 ] |
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then |
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EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib |
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else |
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EXTRA_LD_LIBRARY_PATH=$ESCRIPT_ROOT/lib |
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fi |
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|
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BUILDINFO_FILE="$ESCRIPT_ROOT/lib/buildvars" |
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if [ ! -r "$BUILDINFO_FILE" ]; then |
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if [ "$1" = "-e" ]; then |
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echo "export LD_LIBRARY_PATH=$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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fi |
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die "Unable to read escript build information!" |
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fi |
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|
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get_buildvar () { |
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echo $(grep "^$1=" "$BUILDINFO_FILE" |cut -d= -f2) |
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} |
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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=$(get_buildvar python) |
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|
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HELP_TEXT=" |
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Usage: run-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 per node |
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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 run in new xterm instance |
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-m tool run with valgrind {tool=m[emcheck]/c[allgrind]/[cac]h[egrind]} |
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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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# Parse the command-line options |
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while getopts 'bn:p:t:f:echim:oVvx' option |
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do |
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case "$option" in |
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"b") DO_BINARY=y |
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;; |
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"m") DO_VALGRIND=$OPTARG |
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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 "$BUILDINFO_FILE" |
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exit 0 |
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;; |
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"V") echo "escript-development(build "$(get_buildvar svn_revision)")" |
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exit 0 |
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;; |
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"h") echo "$HELP_TEXT" |
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exit 0 |
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;; |
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"i") DO_INTERACTIVE=y |
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;; |
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"e") echo "export LD_LIBRARY_PATH=$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:$EXTRA_LD_LIBRARY_PATH:\$DYLD_LIBRARY_PATH" |
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fi |
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exit 0 |
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;; |
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"o") ESCRIPT_CREATESTDFILES=y |
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;; |
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"v") ESCRIPT_VERBOSE=y |
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;; |
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"x") DO_XTERM=y |
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;; |
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?) echo "$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 $(($OPTIND - 1)) |
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|
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vlog () { |
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if [ ! -z $ESCRIPT_VERBOSE ]; then |
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echo "$@" |
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fi |
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} |
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|
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#============================================== |
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# |
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# Read MPI_FLAVOUR and WITH_OPENMP from the buildvars |
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# |
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MPI_FLAVOUR=$(get_buildvar mpi) |
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WITH_OPENMP=$(get_buildvar openmp) |
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|
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vlog "MPI flavour is $MPI_FLAVOUR." |
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if [ "$WITH_OPENMP" = "1" ]; then |
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vlog "OpenMP enabled." |
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else |
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vlog "OpenMP disabled." |
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fi |
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|
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# |
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# Add VisIt paths if required |
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# |
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WITH_VISIT=$(get_buildvar visit) |
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if [ "$WITH_VISIT" = "1" ]; then |
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VISIT_BIN=$(which visit 2>/dev/null) |
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if [ $? -eq 0 ]; then |
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VISIT_PY_PATH=$($VISIT_BIN -env | grep LIBPATH | cut -d= -f2) |
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EXTRA_PYTHONPATH=$EXTRA_PYTHONPATH:$VISIT_PY_PATH |
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EXTRA_LD_LIBRARY_PATH=$EXTRA_LD_LIBRARY_PATH:$VISIT_PY_PATH |
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else |
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vlog "Warning: VisIt module enabled but VisIt not in path!" |
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fi |
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fi |
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|
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# |
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# extend path variables |
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# |
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export PATH=$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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vlog "PATH = $PATH |
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LD_LIBRARY_PATH = $LD_LIBRARY_PATH |
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PYTHONPATH = $PYTHONPATH" |
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if [ ! -z $DYLD_LIBRARY_PATH ]; then |
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vlog "DYLD_LIBRARY_PATH = $DYLD_LIBRARY_PATH" |
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fi |
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|
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#============================================== |
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# |
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# Ensure the variables have sensible values |
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# |
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if [ "$MPI_FLAVOUR" = "none" ] |
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then |
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if [ ! -z "$ESCRIPT_NUM_NODES" ]; then |
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if [ $ESCRIPT_NUM_NODES -gt 1 ]; then |
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echo "Warning: MPI disabled but number of nodes set. Option ignored." |
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fi |
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fi |
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if [ ! -z "$ESCRIPT_NUM_PROCS" ]; then |
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if [ $ESCRIPT_NUM_PROCS -gt 1 ]; then |
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echo "Warning: MPI disabled but number of processors per node set. Option ignored." |
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fi |
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fi |
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if [ ! -z "$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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# use the PBS_NODEFILE if not otherwise specified |
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if [ ! -z "$PBS_NODEFILE" ] && [ -z "$ESCRIPT_HOSTFILE" ] |
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then |
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ESCRIPT_HOSTFILE=$PBS_NODEFILE |
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fi |
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|
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if [ ! -z "$ESCRIPT_HOSTFILE" ] |
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then |
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if [ -f "$ESCRIPT_HOSTFILE" ] |
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then |
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sort -u "${ESCRIPT_HOSTFILE}" > $HOSTFILE |
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HOSTLIST=$(awk 'BEGIN{S=""}{if (S == "") { S = $0 } else {S = S "," $0}}END{print S}' "$HOSTFILE") |
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|
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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 -lt $ESCRIPT_NUM_NODES ] |
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then |
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die "Number of requested nodes must not exceed the number of entries selected in the host file $ESCRIPT_HOSTFILE. You asked for $ESCRIPT_NUM_NODES from $NUM_HOSTS." |
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fi |
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else |
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ESCRIPT_NUM_NODES=$NUM_HOSTS |
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fi |
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else |
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die "Cannot find hostfile $ESCRIPT_HOSTFILE!" |
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fi |
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else |
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echo "localhost" > $HOSTFILE |
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HOSTLIST="localhost" |
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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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vlog "ESCRIPT_NUM_NODES = $ESCRIPT_NUM_NODES\nESCRIPT_NUM_PROCS = $ESCRIPT_NUM_PROCS" |
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fi |
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|
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if [ "$WITH_OPENMP" = "1" ] |
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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 |
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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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vlog "ESCRIPT_NUM_THREADS = $ESCRIPT_NUM_THREADS" |
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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 $ESCRIPT_NUM_THREADS!=1. Option ignored." |
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fi |
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ESCRIPT_NUM_THREADS=1 |
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fi |
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|
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# |
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# Now we compute total number of Processes |
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# |
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TOTPROC=$((ESCRIPT_NUM_NODES * ESCRIPT_NUM_PROCS)) |
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if [ $? -ne 0 ] #Some compute error |
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then #This could happen if the args were not a number |
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die "Expression of total number of processors = $ESCRIPT_NUM_NODES * $ESCRIPT_NUM_PROCS is not numerical!" |
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fi |
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|
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# set up thread binding if unset -- disabled by default because it interfers |
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# with MPI binding |
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#if [ "$OMP_PROC_BIND" = "" ]; then |
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# #Force OpenMP binding for Intel (and GCC, though GCC is on by default) |
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# export OMP_PROC_BIND=true |
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#fi |
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#if [ "$KMP_AFFINITY" = "" ]; then |
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# #Set the style of binding (overrides OMP_PROC_BIND in many cases) |
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# export KMP_AFFINITY=verbose,compact |
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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 $DO_INTERACTIVE ] || [ $# -eq 0 ]) && ([ $TOTPROC -gt 1 ]) |
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then |
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die "Interactive mode cannot be used with more than one process!" |
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fi |
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|
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if [ $TOTPROC -gt 1 ] |
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then |
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if [ "$ESCRIPT_CREATESTDFILES" = "y" ] |
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then |
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PYTHON_MPI=$PYTHON_MPI_REDIRECT |
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else |
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PYTHON_MPI=$PYTHON_MPI_NULL |
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fi |
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else |
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PYTHON_MPI=$PYTHON_MPI_NULL |
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fi |
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#============================================================================== |
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# Must have at least one command-line arg: the python script |
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if [ $# -eq 0 ] |
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then |
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if [ ! -z $DO_BINARY ] |
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then |
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die "No program to run was specified!" |
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else |
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DO_INTERACTIVE=y |
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fi |
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fi |
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|
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#============================================================================== |
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|
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if [ ! -z $DO_XTERM ] |
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then |
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EXEC_CMD="xterm -e" |
| 384 |
else |
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EXEC_CMD="" |
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fi |
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|
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if [ ! -z "$DO_VALGRIND" ] |
| 389 |
then |
| 390 |
VALGRIND_BIN=$(which valgrind 2>/dev/null) |
| 391 |
if [ $? -eq 0 ]; then |
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LOGDIR=$ESCRIPT_ROOT/valgrind_logs |
| 393 |
[ -d $LOGDIR ] || mkdir $LOGDIR |
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VG_TOOL=$(echo $DO_VALGRIND | awk '{ s=substr($0,1,1);print s;}') |
| 395 |
if [ $VG_TOOL = "c" ]; |
| 396 |
then |
| 397 |
# run callgrind |
| 398 |
LOGFILE=${LOGDIR}/callgrind.%p.xml |
| 399 |
VALGRIND="valgrind --tool=callgrind --callgrind-out-file=$LOGFILE" |
| 400 |
EXEC_CMD="$EXEC_CMD $VALGRIND" |
| 401 |
elif [ $VG_TOOL = "h" ]; |
| 402 |
then |
| 403 |
# run cachegrind |
| 404 |
LOGFILE=${LOGDIR}/cachegrind.%p.xml |
| 405 |
VALGRIND="valgrind --tool=cachegrind --cachegrind-out-file=$LOGFILE" |
| 406 |
EXEC_CMD="$EXEC_CMD $VALGRIND" |
| 407 |
else |
| 408 |
# run memcheck by default |
| 409 |
LAST_N=$(ls -1 $LOGDIR|grep "^memcheck"|tail -1|cut -d. -f2) |
| 410 |
NEW_N=$(printf "%04d" $((LAST_N + 1))) |
| 411 |
LOGFILE=${LOGDIR}/memcheck.${NEW_N}.%p.xml |
| 412 |
VALGRIND="valgrind --tool=memcheck --xml=yes --show-reachable=yes --error-limit=no --suppressions=$ESCRIPT_ROOT/scripts/escript.supp --leak-check=full --xml-file=$LOGFILE" |
| 413 |
EXEC_CMD="$EXEC_CMD $VALGRIND" |
| 414 |
fi |
| 415 |
else |
| 416 |
die "Execution with valgrind requested but valgrind not in path!" |
| 417 |
fi |
| 418 |
fi |
| 419 |
|
| 420 |
if [ ! -z $DO_BINARY ] |
| 421 |
then |
| 422 |
EXEC_CMD="$EXEC_CMD $@" |
| 423 |
else |
| 424 |
# Check to see if the python version we were compiled with matches the |
| 425 |
# one of PYTHON_CMD. |
| 426 |
compfull=$(get_buildvar python_version) |
| 427 |
compversion=$(echo $compfull | cut -d. -f1,2) |
| 428 |
compmajor=$(echo $compfull | cut -d. -f1) |
| 429 |
if [ "$PYTHON_CMD" = "python" ] # if people have customised the command they |
| 430 |
then # might not want us changing it |
| 431 |
if [ "$compmajor" = "3" ] |
| 432 |
then |
| 433 |
PYTHON_CMD=python3 |
| 434 |
fi |
| 435 |
fi |
| 436 |
intversion=$($PYTHON_CMD -c 'from __future__ import print_function;import sys;print("%d.%d"%(sys.version_info[0], sys.version_info[1]))') |
| 437 |
if [ "$compversion" != "$intversion" ] |
| 438 |
then |
| 439 |
die "Python versions do not match. Escript was compiled for '$compversion'. |
| 440 |
Current version of Python appears to be '$intversion'." |
| 441 |
fi |
| 442 |
if [ "$MPI_FLAVOUR" = "none" ] |
| 443 |
then |
| 444 |
if [ ! -z $DO_INTERACTIVE ] |
| 445 |
then |
| 446 |
EXEC_CMD="$EXEC_CMD $PYTHON_CMD -i $@" |
| 447 |
else |
| 448 |
EXEC_CMD="$EXEC_CMD $PYTHON_CMD $@" |
| 449 |
fi |
| 450 |
else |
| 451 |
if [ ! -z $DO_INTERACTIVE ] |
| 452 |
then |
| 453 |
EXEC_CMD="$EXEC_CMD $PYTHON_MPI -i $@" |
| 454 |
else |
| 455 |
EXEC_CMD="$EXEC_CMD $PYTHON_MPI $@" |
| 456 |
fi |
| 457 |
fi |
| 458 |
fi |
| 459 |
vlog "Command to be executed is \"$EXEC_CMD\"" |
| 460 |
#============================================================================== |
| 461 |
# |
| 462 |
# now we start to spawn things: |
| 463 |
# |
| 464 |
if [ "$WITH_OPENMP" = "1" ] |
| 465 |
then |
| 466 |
export OMP_NUM_THREADS=$ESCRIPT_NUM_THREADS |
| 467 |
EXPORT_ENV="$EXPORT_ENV,OMP_NUM_THREADS" |
| 468 |
fi |
| 469 |
|
| 470 |
if [ "$MPI_FLAVOUR" = "OPENMPI" ] |
| 471 |
then |
| 472 |
if [ -z `which rsh``which ssh` ] |
| 473 |
then |
| 474 |
AGENTOVERRIDE="--gmca plm_rsh_agent /bin/false" |
| 475 |
fi |
| 476 |
fi |
| 477 |
|
| 478 |
vlog "Pre-launch command: \"@@PRELAUNCH\"" |
| 479 |
@@PRELAUNCH |
| 480 |
vlog "Launch command: \"@@LAUNCH\"" |
| 481 |
@@LAUNCH |
| 482 |
EXIT_CODE=$? |
| 483 |
vlog "Post-launch command: \"@@POSTLAUNCH\"" |
| 484 |
@@POSTLAUNCH |
| 485 |
|
| 486 |
if [ ! -z "$DO_VALGRIND" ]; then |
| 487 |
echo "Valgrind log file written to ${LOGFILE}" |
| 488 |
fi |
| 489 |
|
| 490 |
rm -f $HOSTFILE |
| 491 |
|
| 492 |
exit $EXIT_CODE |
| 493 |
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