job.displacementCalculation.sh.tmpl

#!/bin/sh

#job
#PBS -N runDisplacmentCalculation-<TMPL_VAR NAME=iJob>

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

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

#resources
#PBS -l walltime=20:00:00
#PBS -l nodes=1:ppn=1
#PBS -l mem=1300mb
#PBS -l vmem=5gb

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

#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=baseDir>

#job
./run.sh runDisplacementCalculation \
  <TMPL_VAR NAME=pathToRunTime> \
  <TMPL_VAR NAME=outDir>/matlab.displacmentCalculation.<TMPL_VAR NAME=conditionSetTimeStamp>.<TMPL_VAR NAME=iJob>.log \
  <TMPL_VAR NAME=conditionSetTimeStamp> <TMPL_VAR NAME=iJob> <TMPL_VAR NAME=outDir>

#cleanup
rm -rf $MCR_CACHE_ROOT/*

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

#status
if [[ -f "<TMPL_VAR NAME=outDir>/err.displacmentCalculation-<TMPL_VAR NAME=conditionSetTimeStamp>-<TMPL_VAR NAME=iJob>.log" ]]
then
  exit 1
fi
exit 0