From 7d196a78589a2ef7772280e3d1d926adcb54a1ae Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@jalapeno.cluster.fmrib.ox.ac.uk>
Date: Fri, 18 Mar 2022 11:46:46 +0000
Subject: [PATCH] BF: Works for both queue and local invocation
---
fsl_course/fdt/bedpostx_gpu/feedsRun | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/fsl_course/fdt/bedpostx_gpu/feedsRun b/fsl_course/fdt/bedpostx_gpu/feedsRun
index 7341b6d..11fa495 100755
--- a/fsl_course/fdt/bedpostx_gpu/feedsRun
+++ b/fsl_course/fdt/bedpostx_gpu/feedsRun
@@ -11,5 +11,17 @@ cp -Lr $datadir/fsl_course_data/fdt2/subj1 $outdir/
bedpostx_gpu $outdir/subj1 --nf=2 --fudge=1 --bi=1000 --seed=1234
+# wait for all jobs to finish
+while [ : ]; do
+ jid=`cat $outdir/subj1.bedpostX/logs/postproc_ID`
+ echo "JID $jid"
+ status=`qstat -j ${jid} 2>/dev/null | wc`
+ status=`echo $status | awk '{print $1}'`
+ if [ $status -eq 0 ]; then
+ break
+ fi
+ sleep 60
+done
+
chmod -R u+w $outdir/subj1
rm -r $outdir/subj1
--
GitLab