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=2G
  13 #$ -l fsize=1G
  14 #$ -l ct=30:00:00
  15 #$ -j yes
  16 #$ -r no
  17
  18
  19 function error {
  20 echo "ERROR: $1"
  21 exit 1
  22 }
  23
  24 function warning {
  25 echo "WARNING: $1"
  26 }
  27
  28 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  29 set -u
  30
  31 echo "Checking"
  32 uname -a
  33 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  34 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  35 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  36 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  37 echo "JOB_ID=${JOB_ID}"
  38 echo "INDEX=${INDEX}"
  39 echo "INDEXMAX=${INDEX}"
  40 echo "PARAM=${PARAM}"
  41
  42 if test "$RELEASEDIR" = "NONE"
  43 then
  44         echo Using $(which Gate)
  45         ldd $(which Gate)
  46 else
  47         test -d "${RELEASEDIR}" || error "can't find release"
  48         md5sum ${RELEASEDIR}/Gate
  49         test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  50
  51         echo "Finding libraries"
  52         ROOTLIBS="${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:"
  53         echo "ROOTLIBS=${ROOTLIBS}"
  54         G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  55         echo "G4LIBS=${G4LIBS}"
  56         CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  57         echo "CLHEPLIBS=${CLHEPLIBS}"
  58         GATELIBS=""
  59         test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  60         echo "GATELIBS=${GATELIBS}"
  61 fi
  62 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  63
  64
  65 echo "Copying inputs"
  66 LOCALMACRODIR=$(mktemp -d)
  67 trap "mv output ${OUTPUTDIR}/output.${JOB_ID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
  68 cd ${LOCALMACRODIR}
  69 cp -r -L "${MACRODIR}"/{data,mac} .
  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 date
  96 echo "Copying data back"
  97 ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
  98 rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
  99
 100 echo "Cleanup"
 101 rm -r ${LOCALMACRODIR}
 102 date
 103
 104 echo "Success!!!"