Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

diff --git a/cluster_tools/gate_job_ccin2p3.job b/cluster_tools/gate_job_ccin2p3.job
index e4437808c250c5ca32aa46849860bda8416a4460..016b2368de00972fc3348668de2b7d56489b048d 100644 (file)
--- a/cluster_tools/gate_job_ccin2p3.job
+++ b/cluster_tools/gate_job_ccin2p3.job
@@ -9,22 +9,34 @@
 # PARAM
 #
 #$ -P "P_creatis"
-#$ -l vmem=2G
+#$ -l vmem=4G
 #$ -l fsize=1G
 #$ -l ct=30:00:00
 #$ -j yes
 #$ -r no
 
+function transferJobData {
+    echo "Copying data back"
+    #ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
+    #rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
+    pwd
+    echo ${OUTPUTDIR}
+    mkdir "${OUTPUTDIR}/output.${JOB_ID%%.*}"
+    rsync -av --remove-source-files output/ "${OUTPUTDIR}/output.${JOB_ID%%.*}"
+    echo "Cleanup"
+    rm -r ${LOCALMACRODIR}
+}
 
 function error {
-echo "ERROR: $1"
-exit 1
+    echo "ERROR: $1"
+    exit 1
 }
 
 function warning {
-echo "WARNING: $1"
+    echo "WARNING: $1"
 }
 
+date
 test -f ${HOME}/.bashrc && echo "Sourcing bashrc" && source ${HOME}/.bashrc
 set -u
 
@@ -41,30 +53,30 @@ echo "PARAM=${PARAM}"
 
 if test "$RELEASEDIR" = "NONE"
 then
-       echo Using $(which Gate)
-       ldd $(which Gate)
+         echo Using $(which Gate)
+         ldd $(which Gate)
 else
-       test -d "${RELEASEDIR}" || error "can't find release"
-       md5sum ${RELEASEDIR}/Gate
-       test -f ${RELEASEDIR}/libGate.so && md5sum ${RELEASEDIR}/libGate.so
+         test -d "${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=${GATELIBS}"
+         echo "Finding libraries"
+         ROOTLIBS="${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 ${OUTPUTDIR}/output.${JOB_ID%%.*} ; rm -r ${LOCALMACRODIR} ; exit 1" 1 2 3 15
+trap "wait ; transferJobData ; exit 1" 137 138 152 153
 cd ${LOCALMACRODIR}
 cp -r -L "${MACRODIR}"/{data,mac} .
 mkdir output
@@ -76,29 +88,24 @@ echo "Lauching macro"
 date
 if test "$RELEASEDIR" = "NONE"
 then
-       Gate ${PARAM} ${MACROFILE} || error "gate failed"
+         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} ${MACROFILE} \
-       || error "gate failed"
+         LD_PRELOAD="${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
 
 date
-echo "Copying data back"
-ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr "mkdir cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
-rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" output/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})/output.${JOB_ID%%.*}"
-
-echo "Cleanup"
-rm -r ${LOCALMACRODIR}
+transferJobData
 date
 
 echo "Success!!!"

diff --git a/cluster_tools/gate_power_merge.sh b/cluster_tools/gate_power_merge.sh
index aaf063b18d4f8cc85be856ef0f19df1087c1570d..fa2904a5a33855557dff6e68c221858a3152173c 100755 (executable)
--- a/cluster_tools/gate_power_merge.sh
+++ b/cluster_tools/gate_power_merge.sh
@@ -51,9 +51,9 @@ END { print xsize * ysize * zsize * byte_per_pixel; }' "${input_interfile}")
 
 function write_mhd_header {
     local input_interfile="${1:?"provide input interfile"}"
-    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").mhd"
+    local output_mhd="$(dirname "${input_interfile}")/$(basename "${input_interfile}" ".hdr").hdr.mhd"
 
-    check_interfile "${input_interfile}" || error "${input_interfile} isn't an interfile image"
+    check_interfile "${input_interfile}" || warning "${input_interfile} isn't an interfile image (or unknown format)"
 
     local header_start='ObjectType = Image
 NDims = 3
@@ -334,8 +334,8 @@ function merge_dispatcher {
         echo "${indent}this is a interfile image"
         echo "${indent}creating mhd headers"
         for partialoutputfile in $partialoutputfiles; do write_mhd_header "${partialoutputfile}"; done
-        local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.mhd"; done)"
-        local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").mhd"
+        local mhd_partialoutputfiles="$(for partialoutputfile in $partialoutputfiles; do echo "${partialoutputfile%.*}.hdr.mhd"; done)"
+        local mhd_mergedfile="${outputdir}/$(basename "${firstpartialoutputfile}" ".hdr").hdr.mhd"
         merge_mhd_image "${mhd_mergedfile}" ${mhd_partialoutputfiles} || error "error while merging"
         echo "${indent}cleaning mhd headers"
         for mhd_partialoutputfile in $mhd_partialoutputfiles; do rm "${mhd_partialoutputfile}"; done

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 91120500e4ae817ff51e0ef958125c0843a0ba87..2ae6186bcfc38a27bfc230d4052d6c4f338e16e6 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#! /usr/local/bin/bash -lx
+#!/bin/bash -l
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -91,6 +91,7 @@ cp ${MACROFILE} ${OUTPUTDIR}/mac
 files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
 for i in $files
 do
+    echo $i
     cp $i ${OUTPUTDIR}/mac
 done
 
@@ -102,7 +103,7 @@ while test $NJOBS -gt 0; do
         PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR}  RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
     elif test "$(dnsdomainname)" = "in2p3.fr"
     then
-        PROJECTGROUP=creatis 
+        PROJECTGROUP=creatis
         qsub -o "${OUTPUTDIR}" \
              -N "gate.${RUNID}" \
              -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \

diff --git a/cluster_tools/gate_run_submit_cluster_sps.sh b/cluster_tools/gate_run_submit_cluster_sps.sh
new file mode 100755 (executable)
index 0000000..ddc48ca
--- /dev/null
+++ b/cluster_tools/gate_run_submit_cluster_sps.sh
@@ -0,0 +1,125 @@
+#! /usr/local/bin/bash -lx
+
+set -u
+SCRIPTNAME="$(basename "${0}")"
+
+# -------------------------------------------------
+function error {
+    echo "ERROR: $1"
+    usage
+    exit 1
+}
+# -------------------------------------------------
+
+DEFAULTRELEASESUFFIX="NONE"
+DEFAULTNUMBEROFJOBS="10"
+
+# -------------------------------------------------
+function usage {
+    echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
+    echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
+    echo "default releasesuffix = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
+    echo "default paramtogate = \"\" (use \"\" around params and \\ in front of commas)"
+}
+# -------------------------------------------------
+
+test $# -eq 0 && usage && exit 0
+
+RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
+RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+    JOBFILE="$(dirname $0)/gate_job_ccin2p3.job"
+else
+    JOBFILE="$(dirname $0)/gate_job_cluster.job"
+fi
+
+echo "Checking stuff"
+test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
+if test "${RELEASESUFFIX}" = "${DEFAULTRELEASESUFFIX}"
+then
+    RELEASEDIR="NONE"
+    which Gate 2>&1 >/dev/null || error "there is no Gate in the PATH"
+else
+    test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
+fi
+MACRODIR=$(pwd)
+test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path"
+MACROFILE=${1:?"provide relative macro path"}
+test -f ${MACRODIR}/${MACROFILE} || error "invalid macro"
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+    OUTPUTDIR=$(mktemp -d -p "${MACRODIR}" run.XXXX || error "can't create temp dir")
+    ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr mkdir -p "cc/$(basename ${OUTPUTDIR})"
+else
+    OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+fi
+test -d ${OUTPUTDIR} || error "can't locate output dir"
+RUNID=${OUTPUTDIR##*.}
+NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
+NJOBSMAX=${NJOBS}
+PARAM="${4:-""}"
+
+echo "Lets roll!!"
+echo "runid is ${RUNID}"
+
+QSUB=$(which qsub 2> /dev/null)
+# echo "qsub is $(which qsub)"
+test -z "${QSUB}" && QSUB="noqsub"
+if test "${QSUB}" = "noqsub"
+then
+    echo "qsub is not found. Simply run Gate on multiple cores."
+fi
+
+test -z "${PARAM}" && echo "no param" || echo "param is ${PARAM}"
+if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX"
+then
+    echo "Gate is $(which Gate)"
+else
+    echo "Gate release is $(basename ${RELEASEDIR})"
+fi
+echo "submitting ${NJOBS} jobs"
+
+PARAMFILE="${OUTPUTDIR}/params.txt"
+echo "njobs = ${NJOBS}" >> "${PARAMFILE}"
+echo "macro = ${MACROFILE}" >> "${PARAMFILE}"
+test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}"
+
+# Copy macros files (for log)
+mkdir ${OUTPUTDIR}/mac
+cp ${MACROFILE} ${OUTPUTDIR}/mac
+files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
+for i in $files
+do
+    cp $i ${OUTPUTDIR}/mac
+done
+
+while test $NJOBS -gt 0; do
+
+    if test "${QSUB}" = "noqsub"
+    then
+        echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+        PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR}  RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+    elif test "$(dnsdomainname)" = "in2p3.fr"
+    then
+        PROJECTGROUP=creatis 
+        qsub -o "${OUTPUTDIR}" \
+            -l sps=1 \
+             -N "gate.${RUNID}" \
+             -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+             "${JOBFILE}" || error "submission error"
+    else
+        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+             -l sps=1 \
+           -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+           "${JOBFILE}" || error "submission error"
+    fi
+
+    let NJOBS--
+done
+
+echo "runid is ${RUNID}"
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+    rsync -av --remove-source-files -e "ssh -i ${HOME}/.ssh/ccin2p3" ${OUTPUTDIR}/ "linux1.dg.creatis.insa-lyon.fr:./cc/$(basename ${OUTPUTDIR})" --exclude '.__afs*' --exclude "${OUTPUTDIR}/gatejob.*.o*"
+fi