Use ITK-gdcm with clitkImage2DicomDoseGenericFilter

[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 29427bd8cf93b7d937bf01ac68e7e22b6b293dfa..904a0d7162e2f12c664db4cec1e37efd16de5d4c 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
+#! /bin/bash -lx
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -52,7 +52,16 @@ 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=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+    unamestr=`uname`
+    if [[ "$unamestr" == 'Darwin' ]]; then
+        ## On OSX (Darwin), mktemp version is different from Linux version . We
+        ## need the absolute folder here
+        OUTPUTDIR=$(mktemp -d run.XXXX || error "can't create temp dir")
+        OUTPUTDIR=${MACRODIR}/${OUTPUTDIR}
+    else
+        OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
+    fi
+    echo $OUTPUTDIR
 fi
 test -d ${OUTPUTDIR} || error "can't locate output dir"
 RUNID=${OUTPUTDIR##*.}
@@ -102,13 +111,14 @@ 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}" \
+            -l sps=1 \
              -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 "${OUTPUTDIR}" \
+        qsub -N "gatejob.${RUNID}" -o "${OUTPUTDIR}" \
            -v "PARAM=${PARAM},INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \
            "${JOBFILE}" || error "submission error"
     fi
@@ -117,7 +127,3 @@ 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