From: Pierre Gueth <gueth@linux6.dg.creatis.insa-lyon.fr>
Date: Mon, 30 Jan 2012 15:06:15 +0000 (+0100)
Subject: bugfix in cluster jobs and submission script
X-Git-Tag: v1.4.0~177^2~31
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=7c6f86cefdc90cfc796c0f3a3d3a4e0b231db58f;p=clitk.git

bugfix in cluster jobs and submission script
---

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 136a567..ab772dd 100755
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash 
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -9,7 +9,7 @@ usage
 exit 1
 }
 
-DEFAULTRELEASESUFFIX="06o"
+DEFAULTRELEASESUFFIX="06w"
 DEFAULTNUMBEROFJOBS="10"
 
 function usage {
@@ -20,9 +20,9 @@ echo "default releasesuffix = ${DEFAULTRELEASESUFFIX}"
 
 test $# -eq 0 && usage && exit 0
 
-SCRIPTDIR=~/gate/gate-tests/bin
-RELEASEDIR="${HOME}/gate/release${3:-"${DEFAULTRELEASESUFFIX}"}"
-JOBFILE=~/gate/gate-tests/job_release.job
+SCRIPTDIR="${HOME}/git/gate-tests/bin"
+RELEASEDIR="${HOME}/releases/grid_release${3:-"${DEFAULTRELEASESUFFIX}"}"
+JOBFILE="${HOME}/git/gate-tests/job_cluster.job"
 
 echo "Checking stuff"
 test -f ${JOBFILE} || error "can't find job file ${JOBFILE}"
@@ -31,7 +31,7 @@ MACRODIR=$(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)
+OUTPUTDIR=$(mktemp --tmpdir=${MACRODIR} -d run.XXXX || error "can't create temp dir")
 test -d ${OUTPUTDIR} || error "can't locate output dir"
 RUNID=${OUTPUTDIR##*.}
 NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
@@ -40,6 +40,7 @@ PARAM="${4:-""}"
 
 echo "Lets roll!!"
 echo "runid is ${RUNID}"
+echo "qsub is $(which qsub)"
 test -z "${PARAM}" && echo "no param" || echo "param is ${PARAM}"
 echo "using release $(basename ${RELEASEDIR})"
 echo "submitting ${NJOBS} jobs"
@@ -47,7 +48,7 @@ echo "submitting ${NJOBS} jobs"
 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}" \
-	${JOBFILE} || error "submission error"
+	"${JOBFILE}" || error "submission error"
 	let NJOBS--
 done