job.reindexing.sh.tmpl

#!/bin/sh

#job
#PBS -N runReindexing-<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=4:00:00
#PBS -l nodes=1:ppn=4
#PBS -l mem=20gb
#PBS -l vmem=20gb

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

#schedule
#PBS -W depend=afterany:<TMPL_VAR NAME=afterany>

#staging
#PBS -v TMPDIR=<TMPL_VAR NAME=nodeTmpDir>
#PBS -W stagein=<TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID/@<TMPL_VAR NAME=storageServer>:<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/bin/runReindexing/
#PBS -W stagein=<TMPL_VAR NAME=nodeTmpDir>/$PBS_JOBID/@<TMPL_VAR NAME=storageServer>:<TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/
##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
rm -f <TMPL_VAR NAME=n>/{*.sh,*.xml,*.log}
mkdir <TMPL_VAR NAME=conditionSetTimeStamp>
mv <TMPL_VAR NAME=n> <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>

#job
if [ -f <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/state-0.mat ];
then
	./run_runReindexing.sh <TMPL_VAR NAME=pathToRunTime> <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>
else
	echo "No data to reindex"
    exit 0;
fi

#set permissions, store data
rm -rf <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/state-[0-9]*.mat
rm -rf <TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=n>/{fittedConstants,metadata,options,parameters,randStreamStates,summary}.mat
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.reindexing.log" ]]
then
  exit 1
fi
exit 0