MNT: Run GPU jobs via fsl_sub, so they can be run locally or on the cluster

gpu_test/btest/feedsRun

@@ -8,4 +8,9 @@ indir=$(pwd)
 pushd $outdir
 cp -r $indir/bedpost .
 
-bedpostx_gpu bedpost
+job_id=$(fsl_sub --coprocessor=cuda bedpostx_gpu bedpost)
+touch ${outdir}/wait
+fsl_sub --jobhold ${job_id} rm wait
+while [ -e ${outdir}/wait ]; do
+  sleep 1m
+done

gpu_test/etest/feedsRun

@@ -29,11 +29,18 @@ echo $indx > $dti_txt2
 fslroi $dti $dti_b0 0 1
 bet $dti_b0 $dti_b -f 0.2 -R -n -m
 
-eddy \
-  --imain=$dti                  \
-  --mask=$dti_b --acqp=$dti_txt \
-  --index=$dti_txt2             \
-  --bvecs=$dti_bvec             \
-  --bvals=$dti_bval             \
-  --repol                       \
-  --out=$dti_u
+job_id=$(fsl_sub --coprocessor=cuda eddy \
+                 --imain=$dti            \
+                 --mask=$dti_b           \
+                 --acqp=$dti_txt         \
+                 --index=$dti_txt2       \
+                 --bvecs=$dti_bvec       \
+                 --bvals=$dti_bval       \
+                 --repol                 \
+                 --out=$dti_u)
+
+touch ${outdir}/wait
+fsl_sub --jobhold ${job_id} rm wait
+while [ -e ${outdir}/wait ]; do
+  sleep 1m
+done

gpu_test/ptest/feedsRun

@@ -8,9 +8,15 @@ indir=$(pwd)
 pushd $outdir
 
 for i in {1..172}; do
-   probtrackx2_gpu -x $indir/masks/$i.nii.gz       \
-     --dir=$indir/probtrackx/$i --forcedir  -P 200 \
-     -s $indir/bedpost.bedpostX/merged             \
-     -m $indir/bedpost.bedpostX/nodif_brain_mask   \
-     --opd --pd -l -c 0.2 --distthresh=0
+  job_id=$(fsl_sub --coprocessor=cuda probtrackx2_gpu            \
+                   -x $indir/masks/$i.nii.gz                     \
+                   --dir=$indir/probtrackx/$i --forcedir  -P 200 \
+                   -s $indir/bedpost.bedpostX/merged             \
+                   -m $indir/bedpost.bedpostX/nodif_brain_mask   \
+                   --opd --pd -l -c 0.2 --distthresh=0)
+  touch ${outdir}/wait
+  fsl_sub --jobhold ${job_id} rm wait
+  while [ -e ${outdir}/wait ]; do
+    sleep 1m
+  done
 done

mmorf/feedsRun

@@ -27,7 +27,17 @@ echo "-------------"
 echo "Running mmorf"
 echo "-------------"
 echo ""
-mmorf --version --config ${MMORF_CONFIG}
+
+# Use fsl_sub in case we are running on the
+# cluster.  This will just run normally if running
+# locally (but fsl_sub will still return a job id
+# that can be used in the subsequent hold call).
+job_id=$(fsl_sub --coprocessor=cuda mmorf --version --config ${MMORF_CONFIG})
+touch ${outdir}/wait
+fsl_sub --jobhold ${job_id} rm wait
+while [ -e ${outdir}/wait ]; do
+  sleep 1m
+done
 
 # Combine warps
 echo ""