From 00ff6fddbef56d312f2b45f9900ba6d3383eb51c Mon Sep 17 00:00:00 2001
From: Moises Fernandez <moisesf@fmrib.ox.ac.uk>
Date: Thu, 28 Feb 2013 16:13:43 +0000
Subject: [PATCH] Change to don't repeat all slices in case of fail in one
---
CUDA/bedpostx_multigpu_LSF | 35 ++++++++++++++++++++---------------
1 file changed, 20 insertions(+), 15 deletions(-)
diff --git a/CUDA/bedpostx_multigpu_LSF b/CUDA/bedpostx_multigpu_LSF
index 34d17f8..5ec32c8 100755
--- a/CUDA/bedpostx_multigpu_LSF
+++ b/CUDA/bedpostx_multigpu_LSF
@@ -205,7 +205,6 @@ echo "Compilation Time: $diff seconds" >> ${subjdir}.bedpostX/times
echo "CUDA CODE compiled successfully"
-mailto=`whoami`@fmrib.ox.ac.uk
before=`date +%s`
echo Preprocessing stages
${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir} ${gflag}
@@ -224,21 +223,27 @@ post_string="bsub -o ${subjdir}'.bedpostX/logs/output.log -e ${subjdir}.bedpostX
post_string=$post_string" -w "
echo Submitting slices to GPUs
+first_job=1
while [ $slice -lt $nslices ];do
-
- string=$(bsub -o ${subjdir}'.bedpostX/logs/output.log' -e ${subjdir}'.bedpostX/logs/error.log' -W 0:15 -n 1 ${FSLDIR}'/bin/splitter_multigpu' $subjdir $gflag $nfibres $slice $opts)
- array=(`echo $string | tr "<" ' '`)
- aux=${array[1]}
- array=(`echo $aux | tr ">" ' '`)
- job=${array[0]}
- #echo $job
-
-if [ $slice -eq $(($nslices-1)) ];then
- post_string=$post_string"done("${job}")"
-else
- post_string=$post_string"done("${job}")&&"
-fi
- slice=$(($slice + 1))
+ slicezp=`$FSLDIR/bin/zeropad $slice 4`
+ if [ `$FSLDIR/bin/imtest ${subjdir}.bedpostX/diff_slices/data_slice_$slicezp/dyads1` -eq 1 ];then
+ echo "Slice $slice has already been processed"
+ else
+ string=$(bsub -o ${subjdir}'.bedpostX/logs/output.log' -e ${subjdir}'.bedpostX/logs/error.log' -W 0:30 -n 1 ${FSLDIR}'/bin/splitter_multigpu' $subjdir $gflag $nfibres $slice $opts)
+ array=(`echo $string | tr "<" ' '`)
+ aux=${array[1]}
+ array=(`echo $aux | tr ">" ' '`)
+ job=${array[0]}
+ #echo $job
+
+ if [ $first_job -eq 1 ];then
+ post_string=$post_string"done("${job}")"
+ first_job=0
+ else
+ post_string=$post_string"&&done("${job}")"
+ fi
+ fi
+ slice=$(($slice + 1))
done
post_string=$post_string" ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir"
--
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