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

[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 ab348d91dd94679e05d2c4e4bd0a750ee9fb64b7..91120500e4ae817ff51e0ef958125c0843a0ba87 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#! /usr/local/bin/bash -lx
 
 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}"
@@ -107,8 +108,8 @@ while test $NJOBS -gt 0; do
              -v "PARAM=\"${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
 
@@ -118,5 +119,5 @@ 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})"
+    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