cluster_tools/gate_job_ccin2p3.job

   1 #! /usr/local/bin/bash -lx
   2 #
   3 # MACRODIR
   4 # MACROFILE
   5 # RELEASEDIR
   6 # OUTPUTDIR
   7 # INDEX
   8 # INDEXMAX
   9 # PARAM
  10 #
  11 #$ -P "P_creatis"
  12 #$ -l vmem=4G
  13 #$ -l fsize=1G
  14 #$ -l ct=30:00:00
  15 #$ -j yes
  16 #$ -r no
  17
  18 function transferJobData {
  19     echo "Copying data back"
  20     pwd
  21     echo ${OUTPUTDIR}
  22     mkdir "${OUTPUTDIR}/output.${JOB_ID%%.*}"
  23     rsync -av --remove-source-files output/ "${OUTPUTDIR}/output.${JOB_ID%%.*}"
  24     echo "Cleanup"
  25     rm -r ${LOCALMACRODIR}
  26 }
  27
  28 function error {
  29     echo "ERROR: $1"
  30     exit 1
  31 }
  32
  33 function warning {
  34     echo "WARNING: $1"
  35 }
  36
  37 date
  38 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  39 set -u
  40
  41 echo "Checking"
  42 uname -a
  43 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  44 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  45 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  46 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  47 echo "JOB_ID=${JOB_ID}"
  48 echo "INDEX=${INDEX}"
  49 echo "INDEXMAX=${INDEX}"
  50 echo "PARAM=${PARAM}"
  51
  52 if test "$RELEASEDIR" = "NONE"
  53 then
  54           echo Using $(which Gate)
  55           ldd $(which Gate)
  56 else
  57           test -d "${RELEASEDIR}" || error "can't find release"
  58           md5sum ${RELEASEDIR}/Gate
  59           test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  60
  61           echo "Finding libraries"
  62           ROOTLIBS="${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:"
  63           echo "ROOTLIBS=${ROOTLIBS}"
  64           G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  65           echo "G4LIBS=${G4LIBS}"
  66           CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  67           echo "CLHEPLIBS=${CLHEPLIBS}"
  68           GATELIBS=""
  69           test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  70           echo "GATELIBS=${GATELIBS}"
  71 fi
  72 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  73
  74
  75 echo "Copying inputs"
  76 LOCALMACRODIR=$(mktemp -d)
  77 trap "wait ; transferJobData ; exit 1" 1 2 3 15
  78 cd ${LOCALMACRODIR}
  79 cp -r -L "${MACRODIR}"/{data,mac} .
  80 mkdir output
  81
  82 # Enforce one thread
  83 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  84
  85 echo "Lauching macro"
  86 date
  87 if test "$RELEASEDIR" = "NONE"
  88 then
  89           Gate ${PARAM} ${MACROFILE} || error "gate failed"
  90 else
  91           LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  92                     G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  93                     G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  94                     G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  95                     G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  96                     G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  97                     G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
  98                     G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
  99                     G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
 100                     /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
 101                     ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
 102               || error "gate failed"
 103 fi
 104
 105 date
 106 transferJobData
 107 date
 108
 109 echo "Success!!!"