Bf/set sge

fsl_course/fdt/bedpostx_gpu/feedsRun

 #!/bin/bash
 
-# This test needs to be executed
-# on a CUDA-capable machine
+# This test will attempt to submit to a cuda-capable queue via fsl_sub
 
 set -e
 
-unset SGE_ROOT
-
 outdir=$1
 datadir=$2
 
@@ -14,5 +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