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 #PBS -l mem=3Gb
  15
  16
  17 function error {
  18 echo "ERROR: $1"
  19 exit 1
  20 }
  21
  22 function warning {
  23 echo "WARNING: $1"
  24 }
  25
  26 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
  27 set -u
  28
  29 echo "Checking"
  30 uname -a
  31 echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
  32 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
  33 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
  34 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
  35 echo "PBS_JOBID=${PBS_JOBID}"
  36 echo "INDEX=${INDEX}"
  37 echo "INDEXMAX=${INDEX}"
  38 echo "PARAM=${PARAM}"
  39
  40 if test "$RELEASEDIR" = "NONE"
  41 then
  42         echo Using $(which Gate)
  43   unamestr=`uname`
  44   if [[ "$unamestr" != 'Darwin' ]]; then
  45       ldd $(which Gate)
  46   else
  47       ## ldd "equivalent" on osx is otool
  48       otool -L $(which Gate)
  49   fi
  50 else
  51         test -d "${RELEASEDIR}" || error "can't find release"
  52         md5sum ${RELEASEDIR}/Gate
  53         test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
  54
  55         echo "Finding libraries"
  56         ROOTLIBS="${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:"
  57         echo "ROOTLIBS=${ROOTLIBS}"
  58         G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
  59         echo "G4LIBS=${G4LIBS}"
  60         CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
  61         echo "CLHEPLIBS=${CLHEPLIBS}"
  62         GATELIBS=""
  63         test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
  64         echo "GATELIBS=${GATELIBS}"
  65 fi
  66 test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
  67
  68
  69 echo "Copying inputs"
  70 LOCALMACRODIR=$(mktemp -d)
  71 trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
  72 cd ${LOCALMACRODIR}
  73 unamestr=`uname`
  74 if [[ "$unamestr" == 'Darwin' ]]; then
  75     ## cp is slightly different on OSX
  76     cp -R -L "${MACRODIR}"/{data,mac} .
  77 else
  78     cp -r -L "${MACRODIR}"/{data,mac} .
  79 fi
  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     echo Gate ${PARAM} ${MACROFILE}
  90           eval Gate ${PARAM} ${MACROFILE} || error "gate failed"
  91 else
  92         LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
  93         G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
  94         G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
  95         G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
  96         G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
  97         G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
  98         G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
  99         G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
 100         G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
 101         /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
 102         ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
 103         || error "gate failed"
 104 fi
 105
 106 echo "Copying data back"
 107 pwd
 108 mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
 109
 110 echo "Cleanup"
 111 rm -r ${LOCALMACRODIR}
 112
 113 echo "Success!!!"