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.${JOB_ID%%.*}"
  24     echo "Cleanup"
  25     unlink "${LOCALMACRODIR}"/data
  26     rm -r ${LOCALMACRODIR}
  27 }
  28
  29 function error {
  30     echo "ERROR: $1"
  31     exit 1
  32 }
  33
  34 function warning {
  35     echo "WARNING: $1"
  36 }
  37
  38 date
  39 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  40 set -u
  41
  42 echo "Checking"
  43 uname -a
  44 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  45 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  46 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  47 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  48 echo "JOB_ID=${JOB_ID}"
  49 echo "INDEX=${INDEX}"
  50 echo "INDEXMAX=${INDEX}"
  51 echo "PARAM=${PARAM}"
  52
  53 if test "$RELEASEDIR" = "NONE"
  54 then
  55           echo Using $(which Gate)
  56           ldd $(which Gate)
  57 else
  58           test -d "${RELEASEDIR}" || error "can't find release"
  59           md5sum ${RELEASEDIR}/Gate
  60           test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  61
  62           echo "Finding libraries"
  63           ROOTLIBS="${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:"
  64           echo "ROOTLIBS=${ROOTLIBS}"
  65           G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  66           echo "G4LIBS=${G4LIBS}"
  67           CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  68           echo "CLHEPLIBS=${CLHEPLIBS}"
  69           GATELIBS=""
  70           test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  71           echo "GATELIBS=${GATELIBS}"
  72 fi
  73 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  74
  75
  76 echo "Copying inputs"
  77 LOCALMACRODIR=$(mktemp -d)
  78 trap "wait ; transferJobData ; exit 1" 1 2 3 15
  79 cd ${LOCALMACRODIR}
  80 cp -r -L "${MACRODIR}"/mac .
  81 ln -s "${MACRODIR}"/data ./data
  82 #cp -r -L "${MACRODIR}"/{data,mac} .
  83 mkdir output
  84
  85 # Enforce one thread
  86 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  87
  88 echo "Lauching macro"
  89 date
  90 if test "$RELEASEDIR" = "NONE"
  91 then
  92           Gate ${PARAM} ${MACROFILE} || error "gate failed"
  93 else
  94           LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  95                     G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  96                     G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  97                     G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  98                     G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  99                     G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
 100                     G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
 101                     G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
 102                     G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
 103                     /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
 104                     ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
 105               || error "gate failed"
 106 fi
 107
 108 date
 109 transferJobData
 110 date
 111
 112 echo "Success!!!"