Debug RTStruct conversion with empty struc

[clitk.git] / cluster_tools / gate_run_submit_cluster.sh

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 07463eb3bd48713c1a79bdece233cc38ab8b5e44..7f1568dcfd801ff1b5deeea8672c699090a9084c 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,48 +1,91 @@
-#!/usr/bin/env bash 
+#! /bin/bash -lx
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
 
+# -------------------------------------------------
 function error {
-echo "ERROR: $1"
-usage
-exit 1
+    echo "ERROR: $1"
+    usage
+    exit 1
 }
+# -------------------------------------------------
 
-DEFAULTRELEASESUFFIX="06z"
+DEFAULTRELEASESUFFIX="NONE"
 DEFAULTNUMBEROFJOBS="10"
 
+# -------------------------------------------------
 function usage {
-echo "${SCRIPTNAME} mac/main.mac njobs releasesuffix paramtogate"
-echo "default njobs = ${DEFAULTNUMBEROFJOBS}"
-echo "default releasesuffix = ${DEFAULTRELEASESUFFIX}"
+    echo "${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
 
-SCRIPTDIR="${HOME}/git/gate-tests/bin"
-RELEASEDIR="${HOME}/releases/grid_release${3:-"${DEFAULTRELEASESUFFIX}"}"
-JOBFILE="${HOME}/git/gate-tests/job_cluster.job"
+RELEASESUFFIX=${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}"
-test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
+if test "${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"
-OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+if test "$(dnsdomainname)" = "in2p3.fr"
+then
+    OUTPUTDIR=$(mktemp -d -p "${MACRODIR}" run.XXXX || error "can't create temp dir")
+else
+    unamestr=`uname`
+    if [[ "$unamestr" == 'Darwin' ]]; then
+        ## On OSX (Darwin), mktemp version is different from Linux version . We
+        ## need the absolute folder here
+        OUTPUTDIR=$(mktemp -d run.XXXX || error "can't create temp dir")
+        OUTPUTDIR=${MACRODIR}/${OUTPUTDIR}
+    else
+        OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+    fi
+    echo $OUTPUTDIR
+fi
 test -d ${OUTPUTDIR} || error "can't locate output dir"
 RUNID=${OUTPUTDIR##*.}
 NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
 NJOBSMAX=${NJOBS}
-PARAM="${4:-""}"
+PARAM="${4:-\"\"}"
 
 echo "Lets roll!!"
 echo "runid is ${RUNID}"
-echo "qsub is $(which qsub)"
+
+QSUB=$(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}"
-echo "using release $(basename ${RELEASEDIR})"
+if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX"
+then
+    echo "Gate is $(which Gate)"
+else
+    echo "Gate release is $(basename ${RELEASEDIR})"
+fi
 echo "submitting ${NJOBS} jobs"
 
 PARAMFILE="${OUTPUTDIR}/params.txt"
@@ -50,11 +93,45 @@ 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
+cp mac/* ${OUTPUTDIR}/mac/
+files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
+for i in $files
+do
+    cp $i ${OUTPUTDIR}/mac
+done
+
 while test $NJOBS -gt 0; do
-       qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
-       -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
-       "${JOBFILE}" || error "submission error"
-       let NJOBS--
+
+    if [ "$PARAM" = "\"\"" ]
+    then
+        JPARAM="-a [JOB_ID,${NJOBS}]"
+    else
+        JPARAM="${PARAM} [JOB_ID,${NJOBS}]"
+    fi
+
+    if test "${QSUB}" = "noqsub"
+    then
+        echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+        PARAM=\"${JPARAM}\" INDEX=${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}" \
+             -e "${OUTPUTDIR}" \
+             -l sps=1 \
+             -N "gate.${RUNID}" \
+             -v "PARAM=\"${JPARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+             "${JOBFILE}" || error "submission error"
+    else
+        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
+      -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}"