From 25964a70b332af11b254f1bf6e1bf9c8d816d7f7 Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Thu, 18 Jul 2013 11:15:11 +0200
Subject: [PATCH] First version to submit jobs on a single multithread machine
 (if no qsub command exist)

---
 cluster_tools/gate_run_submit_cluster.sh | 52 ++++++++++++++++--------
 1 file changed, 36 insertions(+), 16 deletions(-)

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index f47ed6d..0248a1e 100755
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -3,20 +3,24 @@
 set -u
 SCRIPTNAME="$(basename "${0}")"
 
+# -------------------------------------------------
 function error {
-echo "ERROR: $1"
-usage
-exit 1
+    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 = ${DEFAULTRELEASESUFFIX} (NONE means use Gate in PATH)"
+    echo "${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
 
@@ -29,10 +33,10 @@ 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"
+    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}"
+    test -d ${RELEASEDIR} || error "invalid release dir ${RELEASEDIR}"
 fi
 MACRODIR=$(pwd)
 test -d ${MACRODIR}/mac && test -d ${MACRODIR}/data || error "invalid path"
@@ -47,13 +51,21 @@ PARAM="${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 ${PARAM}"
 if test "$RELEASESUFFIX" = "$DEFAULTRELEASESUFFIX"
 then
-	echo "using $(which Gate)"
+    echo "Gate is $(which Gate)"
 else
-	echo "using release $(basename ${RELEASEDIR})"
+    echo "Gate release is $(basename ${RELEASEDIR})"
 fi
 echo "submitting ${NJOBS} jobs"
 
@@ -63,10 +75,18 @@ echo "macro = ${MACROFILE}" >> "${PARAMFILE}"
 test -z "${PARAM}" || echo "param = ${PARAM}" >> "${PARAMFILE}"
 
 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}"
-- 
2.47.1