cluster_tools/gate_job_cluster_nomove.job

   1 #!/bin/bash
   2 #
   3 # MACRODIR
   4 # MACROFILE
   5 # RELEASEDIR
   6 # OUTPUTDIR
   7 # INDEX
   8 # INDEXMAX
   9 # PARAM
  10 #
  11 #PBS -r n
  12 #PBS -l walltime=5:00:00
  13 #PBS -j oe
  14 #PBS -l mem=5Gb
  15
  16
  17 function error {
  18 echo "ERROR: $1"
  19 exit 1
  20 }
  21
  22 function warning {
  23 echo "WARNING: $1"
  24 }
  25
  26 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  27 set -u
  28
  29 echo "Checking"
  30 uname -a
  31 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  32 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  33 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  34 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  35 echo "PBS_JOBID=${PBS_JOBID}"
  36 echo "INDEX=${INDEX}"
  37 echo "INDEXMAX=${INDEX}"
  38 echo "PARAM=${PARAM}"
  39
  40 if test "$RELEASEDIR" = "NONE"
  41 then
  42         echo Using $(which Gate)
  43         ldd $(which Gate)
  44 else
  45         test -d "${RELEASEDIR}" || error "can't find release"
  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=${GATELIBS}"
  59 fi
  60 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  61
  62
  63 echo "Copying/linking inputs"
  64 LOCALMACRODIR=$(mktemp -d)
  65 trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -rf ${LOCALMACRODIR} ; exit 1" 1 2 3 15
  66 cd ${LOCALMACRODIR}
  67 ## below line seems not to be trapped correctly
  68 cp -r -L "${MACRODIR}"/mac .
  69 ln -s "${MACRODIR}"/data ./data
  70 mkdir output
  71
  72 # Enforce one thread
  73 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  74
  75 echo "Lauching macro"
  76 date
  77 if test "$RELEASEDIR" = "NONE"
  78 then
  79         Gate ${PARAM} ${MACROFILE} || error "gate failed"
  80 else
  81         LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  82         G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  83         G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  84         G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  85         G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  86         G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  87         G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
  88         G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
  89         G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
  90         /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
  91         ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
  92         || error "gate failed"
  93 fi
  94
  95 echo "Copying data back"
  96 mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
  97
  98 echo "Cleanup"
  99 unlink "${LOCALMACRODIR}"/data
 100 rm -rf "${LOCALMACRODIR}"
 101
 102 echo "Success!!!"