X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=cluster_tools%2Fgate_run_submit_cluster.sh;h=4df0be78dbad8d0b307f796bd68c5eddadb2047a;hb=d964acf3ee5b9c88194791613a06bee333671200;hp=513e644cea7a4a609d9cb4f8016dc61a0413aeef;hpb=0a492ae26676b176ed0a2b18b7b3a92ecf5596f0;p=clitk.git

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 513e644..4df0be7 100755
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,32 +1,43 @@
-#!/usr/bin/env bash 
+#!/usr/bin/env bash
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
 
+# -------------------------------------------------
 function error {
-echo "ERROR: $1"
-usage
-exit 1
+    echo "ERROR: $1"
+    usage
+    exit 1
 }
+# -------------------------------------------------
 
-DEFAULTRELEASESUFFIX="06w"
+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)"
 }
+# -------------------------------------------------
 
 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${RELEASESUFFIX}"
+JOBFILE="$(dirname $0)/gate_job_cluster.job"
 
 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"}
@@ -40,9 +51,22 @@ 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 +74,28 @@ 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 $NJOBS -gt 0; do
-	qsub -N "gatejob.${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 test "${QSUB}" = "noqsub"
+    then
+        echo "Launching Gate log in ${OUTPUTDIR}/gate_${NJOBS}.log"
+        PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} SCRIPTDIR=${SCRIPTDIR} OUTPUTDIR=${OUTPUTDIR}  RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
+    else
+        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"
+    fi
+
+    let NJOBS--
 done
 
 echo "runid is ${RUNID}"