From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Tue, 11 Dec 2018 08:47:15 +0000 (+0100)
Subject: Prefer to use link instead of copy for ccIn2p3 data
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=cc9072c5acc18200fb3e34d22b4c1c2f823d18b1;p=clitk.git

Prefer to use link instead of copy for ccIn2p3 data

Before, the job copied data into the temp calculation folder. We prefer to avoid copy of large data, so we use link now
---

diff --git a/cluster_tools/gate_job_ccin2p3.job b/cluster_tools/gate_job_ccin2p3.job
index c7abaac..f07f9c2 100644
--- a/cluster_tools/gate_job_ccin2p3.job
+++ b/cluster_tools/gate_job_ccin2p3.job
@@ -22,6 +22,7 @@ function transferJobData {
     mkdir "${OUTPUTDIR}/output.${JOB_ID%%.*}"
     rsync -av --remove-source-files output/ "${OUTPUTDIR}/output.${JOB_ID%%.*}"
     echo "Cleanup"
+    unlink "${LOCALMACRODIR}"/data
     rm -r ${LOCALMACRODIR}
 }
 
@@ -76,7 +77,9 @@ echo "Copying inputs"
 LOCALMACRODIR=$(mktemp -d)
 trap "wait ; transferJobData ; exit 1" 1 2 3 15
 cd ${LOCALMACRODIR}
-cp -r -L "${MACRODIR}"/{data,mac} .
+cp -r -L "${MACRODIR}"/mac .
+ln -s "${MACRODIR}"/data ./data
+#cp -r -L "${MACRODIR}"/{data,mac} .
 mkdir output
 
 # Enforce one thread