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     #ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
  21     #rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
  22     pwd
  23     echo ${OUTPUTDIR}
  24     mkdir "${OUTPUTDIR}/output.${JOB_ID%%.*}"
  25     rsync -av --remove-source-files output/ "${OUTPUTDIR}/output.${JOB_ID%%.*}"
  26     echo "Cleanup"
  27     rm -r ${LOCALMACRODIR}
  28 }
  29
  30 function error {
  31     echo "ERROR: $1"
  32     exit 1
  33 }
  34
  35 function warning {
  36     echo "WARNING: $1"
  37 }
  38
  39 date
  40 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  41 set -u
  42
  43 echo "Checking"
  44 uname -a
  45 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  46 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  47 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  48 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  49 echo "JOB_ID=${JOB_ID}"
  50 echo "INDEX=${INDEX}"
  51 echo "INDEXMAX=${INDEX}"
  52 echo "PARAM=${PARAM}"
  53
  54 if test "$RELEASEDIR" = "NONE"
  55 then
  56           echo Using $(which Gate)
  57           ldd $(which Gate)
  58 else
  59           test -d "${RELEASEDIR}" || error "can't find release"
  60           md5sum ${RELEASEDIR}/Gate
  61           test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  62
  63           echo "Finding libraries"
  64           ROOTLIBS="${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:"
  65           echo "ROOTLIBS=${ROOTLIBS}"
  66           G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  67           echo "G4LIBS=${G4LIBS}"
  68           CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  69           echo "CLHEPLIBS=${CLHEPLIBS}"
  70           GATELIBS=""
  71           test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  72           echo "GATELIBS=${GATELIBS}"
  73 fi
  74 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  75
  76
  77 echo "Copying inputs"
  78 LOCALMACRODIR=$(mktemp -d)
  79 trap "wait ; transferJobData ; exit 1" 137 138 152 153
  80 cd ${LOCALMACRODIR}
  81 cp -r -L "${MACRODIR}"/{data,mac} .
  82 mkdir output
  83
  84 # Enforce one thread
  85 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  86
  87 echo "Lauching macro"
  88 date
  89 if test "$RELEASEDIR" = "NONE"
  90 then
  91           Gate ${PARAM} ${MACROFILE} || error "gate failed"
  92 else
  93           LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  94                     G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  95                     G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  96                     G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  97                     G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  98                     G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  99                     G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
 100                     G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
 101                     G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
 102                     /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
 103                     ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
 104               || error "gate failed"
 105 fi
 106
 107 date
 108 transferJobData
 109 date
 110
 111 echo "Success!!!"