job.simulation.sh.tmpl

#!/bin/sh

#job
#PBS -N runSimulation-<TMPL_VAR NAME=conditionSetTimeStamp>-<TMPL_VAR NAME=n>

#user
#PBS -P <TMPL_VAR NAME=linuxRunUser>:<TMPL_VAR NAME=linuxRunUser>

#notification
#PBS -M <TMPL_VAR NAME=emailAddress>
#PBS -m a

#resources
#PBS -l walltime=72:00:00
#PBS -l nodes=1:ppn=1
#PBS -l mem=1300mb
#PBS -l vmem=3gb

#log
#PBS -o <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/out.log
#PBS -e <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/err.log
#PBS -W umask=002

#staging
#PBS -v TMPDIR=<TMPL_VAR NAME=nodeTmpDir>
#PBS -W stagein=<TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID/@<TMPL_VAR NAME=storageServer>:<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/bin/runSimulation/
#PBS -W stagein=<TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID/conditions.xml@<TMPL_VAR NAME=storageServer>:<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/conditions.xml
##PBS -W stageout=<TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID/<TMPL_VAR NAME=conditionSetTimeStamp>@<TMPL_VAR NAME=storageServer>:<TMPL_VAR NAME=outDir>

#set environment
export MATLAB_PREFDIR=/tmp/emptydir
export MCR_CACHE_ROOT=/tmp/mcr_cache_$PBS_JOBID
mkdir -p $MCR_CACHE_ROOT

#setup
cd <TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID
mkdir <TMPL_VAR NAME=conditionSetTimeStamp>
mkdir <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>
mv conditions.xml <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>

#job
./run_runSimulation.sh <TMPL_VAR NAME=pathToRunTime> \
  'outDir' <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n> \
  'logToDisk' true

#set permissions, store data
rm -f <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/conditions.xml
chmod -R 775 <TMPL_VAR NAME=conditionSetTimeStamp>/
cp -R <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n> <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>

#cleanup
rm -rf <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/
rm -rf $MCR_CACHE_ROOT/*

#resources
echo ""
echo "=============="
echo "=== status ==="
echo "=============="
qstat -f $PBS_JOBID

#status
if [[ -f "<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/err.mat" ]]
then
  exit 1
fi
exit 0