cluster_tools/gate_job_cluster.job

   1 #!/bin/bash
   2 #
   3 # MACRODIR
   4 # MACROFILE
   5 # RELEASEDIR
   6 # OUTPUTDIR
   7 # SCRIPTDIR
   8 # INDEX
   9 # INDEXMAX
  10 # PARAM
  11 #
  12 #PBS -r n
  13 #PBS -l walltime=100:00:00
  14 #PBS -j oe
  15
  16 #env
  17 #pwd
  18 #exit 1
  19
  20
  21 function error {
  22 echo "ERROR: $1"
  23 exit 1
  24 }
  25
  26 function warning {
  27 echo "WARNING: $1"
  28 }
  29
  30 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  31 set -u
  32
  33 echo "Checking"
  34 uname -a
  35 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  36 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  37 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  38 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  39 echo "SCRIPTDIR=${SCRIPTDIR:?"unknown SCRIPTDIR"}"
  40 echo "PBS_JOBID=${PBS_JOBID}"
  41 echo "INDEX=${INDEX}"
  42 echo "INDEXMAX=${INDEX}"
  43 echo "PARAM=${PARAM}"
  44 test -d "${RELEASEDIR}" || error "can't find release"
  45 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  46 md5sum ${RELEASEDIR}/Gate
  47 test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  48
  49 echo "Finding libraries"
  50 ROOTLIBS="${RELEASEDIR}/libCore.so:${RELEASEDIR}/libCint.so:${RELEASEDIR}/libRIO.so:${RELEASEDIR}/libNet.so:${RELEASEDIR}/libHist.so:${RELEASEDIR}/libGraf.so:${RELEASEDIR}/libGraf3d.so:${RELEASEDIR}/libGpad.so:${RELEASEDIR}/libTree.so:${RELEASEDIR}/libRint.so:${RELEASEDIR}/libPostscript.so:${RELEASEDIR}/libMatrix.so:${RELEASEDIR}/libPhysics.so:${RELEASEDIR}/libMathCore.so:${RELEASEDIR}/libThread.so:"
  51 echo "ROOTLIBS=${ROOTLIBS}"
  52 G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  53 echo "G4LIBS=${G4LIBS}"
  54 CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  55 echo "CLHEPLIBS=${CLHEPLIBS}"
  56 GATELIBS=""
  57 test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  58 echo "GATELIBS=${GATELIBS}"
  59
  60
  61 echo "Copying inputs"
  62 LOCALMACRODIR=$(mktemp -d)
  63 cd ${LOCALMACRODIR}
  64 cp -r -L "${MACRODIR}"/{data,mac} .
  65 mkdir output
  66
  67 #echo "Search for param generation script"
  68 #if [ -x "${MACRODIR}/generate_placements.py" -a ! -z "${PARAM}" ]; then
  69 #    echo "found generate_placements.py and non null param"
  70 #    cp "${MACRODIR}/generate_placements.py" .
  71 #    ./generate_placements.py ${PARAM}
  72 #fi
  73
  74 echo "Lauching macro"
  75 date
  76 LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  77 G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  78 G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  79 G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  80 G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  81 G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  82 G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
  83 G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
  84 G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
  85 /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
  86 ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
  87 || error "gate failed"
  88
  89 #echo "Convert to energy"
  90 #${SCRIPTDIR}/phsptoenergy.py output/phspTarget.root output/energyTarget.mat || warning "convertion failed"
  91
  92 if test $(find output -name '*-detected.root' | wc -l) -ne 0
  93 then
  94     echo "Parsing detected particle"
  95     ${SCRIPTDIR}/phspdetected.py output || warning "detection failed"
  96 fi
  97
  98 echo "Copying data back"
  99 mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
 100
 101 echo "Cleanup"
 102 rm -r ${LOCALMACRODIR}
 103
 104 echo "Success!!!"