cluster_tools/gate_job_cluster.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=100:00:00
  13 #PBS -j oe
  14
  15 #env
  16 #pwd
  17 #exit 1
  18
  19
  20 function error {
  21 echo "ERROR: $1"
  22 exit 1
  23 }
  24
  25 function warning {
  26 echo "WARNING: $1"
  27 }
  28
  29 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  30 set -u
  31
  32 echo "Checking"
  33 uname -a
  34 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  35 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  36 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  37 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  38 echo "PBS_JOBID=${PBS_JOBID}"
  39 echo "INDEX=${INDEX}"
  40 echo "INDEXMAX=${INDEX}"
  41 echo "PARAM=${PARAM}"
  42
  43 if test "$RELEASEDIR" = "NONE"
  44 then
  45         echo Using $(which Gate)
  46         ldd $(which Gate)
  47 else
  48         test -d "${RELEASEDIR}" || error "can't find release"
  49         md5sum ${RELEASEDIR}/Gate
  50         test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  51
  52         echo "Finding libraries"
  53         ROOTLIBS="${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:"
  54         echo "ROOTLIBS=${ROOTLIBS}"
  55         G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  56         echo "G4LIBS=${G4LIBS}"
  57         CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  58         echo "CLHEPLIBS=${CLHEPLIBS}"
  59         GATELIBS=""
  60         test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  61         echo "GATELIBS=${GATELIBS}"
  62 fi
  63 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  64
  65
  66 echo "Copying inputs"
  67 LOCALMACRODIR=$(mktemp -d)
  68 trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
  69 cd ${LOCALMACRODIR}
  70 cp -r -L "${MACRODIR}"/{data,mac} .
  71 mkdir output
  72
  73 # Enforce one thread
  74 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  75
  76 echo "Lauching macro"
  77 date
  78 if test "$RELEASEDIR" = "NONE"
  79 then
  80         Gate ${PARAM} ${MACROFILE} || error "gate failed"
  81 else
  82         LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  83         G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  84         G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  85         G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  86         G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  87         G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  88         G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
  89         G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
  90         G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
  91         /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
  92         ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
  93         || error "gate failed"
  94 fi
  95
  96 echo "Copying data back"
  97 mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
  98
  99 echo "Cleanup"
 100 rm -r ${LOCALMACRODIR}
 101
 102 echo "Success!!!"