Debug Rigid Registration tool cancel

[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 0248a1ec007262561431d49f9ccf4db00de59f93..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}")"
@@ -19,15 +19,20 @@ 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)"
 }
 # -------------------------------------------------
 
 test $# -eq 0 && usage && exit 0
 
-SCRIPTDIR="${HOME}/git/gate-tests/bin"
 RELEASESUFFIX=${3:-"${DEFAULTRELEASESUFFIX}"}
 RELEASEDIR="${HOME}/releases/grid_release${RELEASESUFFIX}"
-JOBFILE="$(dirname $0)/gate_job_cluster.job"
+if test "$(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 ${JOBFILE}"
@@ -42,12 +47,18 @@ MACRODIR=$(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")
+    ssh -i ${HOME}/.ssh/ccin2p3 linux1.dg.creatis.insa-lyon.fr mkdir -p "cc/$(basename ${OUTPUTDIR})"
+else
+    OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+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}"
@@ -74,15 +85,31 @@ 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
 
     if test "${QSUB}" = "noqsub"
-    then 
+    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 &
+        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 "$(dnsdomainname)" = "in2p3.fr"
+    then
+        PROJECTGROUP=creatis 
+        qsub -o "${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},SCRIPTDIR=${SCRIPTDIR},OUTPUTDIR=${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
 
@@ -90,3 +117,7 @@ while test $NJOBS -gt 0; do
 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 ${OUTPUTDIR})" --exclude '.__afs*' --exclude "${OUTPUTDIR}/gatejob.*.o*"
+fi