job.dataexport.sh.tmpl

#!/bin/sh

#job
#PBS -N runDataExport-<TMPL_VAR NAME=iSim>

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

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

#resources
#PBS -l walltime=48:00:00
#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=iSim>/json/out.dataexport.log
#PBS -e <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=iSim>/json/err.dataexport.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>

#delete any existing data
rm -rf <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=iSim>/json/*

#data export
./run.sh runDataExport \
  <TMPL_VAR NAME=pathToRunTime> \
  <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=iSim>/json/matlab.dataexport.log \
  <TMPL_VAR NAME=conditionSetTimeStamp> <TMPL_VAR NAME=iSim>
  
#create FtsZ ring data
python2.7 /home/projects/WholeCellViz/data/ftszring_draw.py <TMPL_VAR NAME=outDir> <TMPL_VAR NAME=conditionSetTimeStamp> <TMPL_VAR NAME=iSim>
  
#set permissions
sudo chown -R <TMPL_VAR NAME=linuxUser>:<TMPL_VAR NAME=linuxUser> <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=iSim>/json
chmod -R 775 <TMPL_VAR NAME=outDir>/<TMPL_VAR NAME=conditionSetTimeStamp>/<TMPL_VAR NAME=iSim>/json

#cleanup
rm -rf $MCR_CACHE_ROOT/*

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

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