Debug RTStruct conversion with empty struc

[clitk.git] / cluster_tools / gate_job_cluster.job

diff --git a/cluster_tools/gate_job_cluster.job b/cluster_tools/gate_job_cluster.job
index 86d277ae7892beaad53d4c35c3dda352babf9c55..be749e50f4f46e1627f219dfd3eb4de34425b2e7 100644 (file)
--- a/cluster_tools/gate_job_cluster.job
+++ b/cluster_tools/gate_job_cluster.job
@@ -4,7 +4,6 @@
 # MACROFILE
 # RELEASEDIR
 # OUTPUTDIR
-# SCRIPTDIR
 # INDEX
 # INDEXMAX
 # PARAM
@@ -12,10 +11,7 @@
 #PBS -r n
 #PBS -l walltime=100:00:00
 #PBS -j oe
-
-#env
-#pwd
-#exit 1
+#PBS -l mem=3Gb
 
 
 function error {
@@ -36,66 +32,79 @@ echo "MACRODIR=${MACRODIR:?"unknown MACRODIR"}"
 echo "MACROFILE=${MACROFILE:?"unknown MACROFILE"}"
 echo "RELEASEDIR=${RELEASEDIR:?"unknown RELEASEDIR"}"
 echo "OUTPUTDIR=${OUTPUTDIR:?"unknown OUTPUTDIR"}"
-echo "SCRIPTDIR=${SCRIPTDIR:?"unknown SCRIPTDIR"}"
 echo "PBS_JOBID=${PBS_JOBID}"
 echo "INDEX=${INDEX}"
 echo "INDEXMAX=${INDEX}"
 echo "PARAM=${PARAM}"
-test -d "${RELEASEDIR}" || error "can't find release"
-test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
-md5sum ${RELEASEDIR}/Gate
-test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
 
-echo "Finding libraries"
-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:${RELEASEDIR}/libThread.so:"
-echo "ROOTLIBS=${ROOTLIBS}"
-G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
-echo "G4LIBS=${G4LIBS}"
-CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
-echo "CLHEPLIBS=${CLHEPLIBS}"
-GATELIBS=""
-test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
-echo "GATELIBS=${GATELIBS}"
+if test "$RELEASEDIR" = "NONE"
+then
+       echo Using $(which Gate)
+  unamestr=`uname`
+  if [[ "$unamestr" != 'Darwin' ]]; then
+      ldd $(which Gate)
+  else
+      ## ldd "equivalent" on osx is otool
+      otool -L $(which Gate)
+  fi
+else
+       test -d "${RELEASEDIR}" || error "can't find release"
+       md5sum ${RELEASEDIR}/Gate
+       test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
+
+       echo "Finding libraries"
+       ROOTLIBS="${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:"
+       echo "ROOTLIBS=${ROOTLIBS}"
+       G4LIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libG4*.so'); do echo -n "${library}:"; done)"
+       echo "G4LIBS=${G4LIBS}"
+       CLHEPLIBS="$(for library in $(find "${RELEASEDIR}" -maxdepth 1 -name 'libCLHEP*.so'); do echo -n "${library}:"; done)"
+       echo "CLHEPLIBS=${CLHEPLIBS}"
+       GATELIBS=""
+       test -f ${RELEASEDIR}/libGate.so && GATELIBS="${RELEASEDIR}/libGate.so:"
+       echo "GATELIBS=${GATELIBS}"
+fi
+test -d "${MACRODIR}" && test -d "${MACRODIR}/mac" || error "invalid macro"
 
 
 echo "Copying inputs"
 LOCALMACRODIR=$(mktemp -d)
+trap "mv output ${OUTPUTDIR}/output.${PBS_JOBID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
 cd ${LOCALMACRODIR}
-cp -r -L "${MACRODIR}"/{data,mac} .
+unamestr=`uname`
+if [[ "$unamestr" == 'Darwin' ]]; then
+    ## cp is slightly different on OSX
+    cp -R -L "${MACRODIR}"/{data,mac} .
+else
+    cp -r -L "${MACRODIR}"/{data,mac} .
+fi
 mkdir output
 
-#echo "Search for param generation script"
-#if [ -x "${MACRODIR}/generate_placements.py" -a ! -z "${PARAM}" ]; then
-#    echo "found generate_placements.py and non null param"
-#    cp "${MACRODIR}/generate_placements.py" .
-#    ./generate_placements.py ${PARAM}
-#fi
+# Enforce one thread
+ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
 
 echo "Lauching macro"
 date
-LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
-G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
-G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
-G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
-G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
-G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
-G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
-G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
-G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
-/usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
-${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
-|| error "gate failed"
-
-#echo "Convert to energy"
-#${SCRIPTDIR}/phsptoenergy.py output/phspTarget.root output/energyTarget.mat || warning "convertion failed"
-
-if test $(find output -name '*-detected.root' | wc -l) -ne 0
+if test "$RELEASEDIR" = "NONE"
 then
-    echo "Parsing detected particle"
-    ${SCRIPTDIR}/phspdetected.py output || warning "detection failed"
+    echo Gate ${PARAM} ${MACROFILE}
+         eval Gate ${PARAM} ${MACROFILE} || error "gate failed"
+else
+       LD_PRELOAD="${ROOTLIBS}${G4LIBS}${CLHEPLIBS}${GATELIBS}" \
+       G4LEVELGAMMADATA="${RELEASEDIR}/PhotonEvaporation2.1" \
+       G4RADIOACTIVEDATA="${RELEASEDIR}/RadioactiveDecay3.3" \
+       G4LEDATA="${RELEASEDIR}/G4EMLOW6.19" \
+       G4NEUTRONHPDATA="${RELEASEDIR}/G4NDL3.14" \
+       G4ABLADATA="${RELEASEDIR}/G4ABLA3.0" \
+       G4REALSURFACEDATA="${RELEASEDIR}/RealSurface1.0" \
+       G4NEUTRONXSDATA="${RELEASEDIR}/G4NEUTRONXS1.0" \
+       G4PIIDATA="${RELEASEDIR}/G4PII1.2" \
+       /usr/bin/time --format="real %es\nuser %Us\nsys %Ss\nmaxmem %Mk" \
+       ${RELEASEDIR}/Gate ${PARAM} ${MACROFILE} \
+       || error "gate failed"
 fi
 
 echo "Copying data back"
+pwd
 mv output "${OUTPUTDIR}/output.${PBS_JOBID%%.*}"
 
 echo "Cleanup"