X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=cluster_tools%2Fgate_run_submit_cluster.sh;h=2ae6186bcfc38a27bfc230d4052d6c4f338e16e6;hb=59b095a8458559b550afcb50d7e0bfb3b61848f0;hp=24fdab92e04d4408917ee8e98a9ede280753dc0d;hpb=f3457815210ffe8646f3288be3362d34fcc7c3af;p=clitk.git

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 24fdab9..2ae6186 100755
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/bin/bash -l
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -19,6 +19,7 @@ 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)"
 }
 # -------------------------------------------------
 
@@ -57,7 +58,7 @@ 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}"
@@ -90,6 +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
 
@@ -101,14 +103,14 @@ 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}" \
              "${JOBFILE}" || error "submission error"
     else
-        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
-	    -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
+	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