From cc9072c5acc18200fb3e34d22b4c1c2f823d18b1 Mon Sep 17 00:00:00 2001
From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Tue, 11 Dec 2018 09:47:15 +0100
Subject: [PATCH] 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
---
 cluster_tools/gate_job_ccin2p3.job | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

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
-- 
2.47.1