From efd72eb3a66346ffcba9a7ee11935586ba0855fc Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 24 Nov 2021 12:46:02 +0000
Subject: [PATCH] BF: Couple of typos. Check fsl_sub exit code
---
eddy/runEddy | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/eddy/runEddy b/eddy/runEddy
index 28f5c37..f62eb94 100755
--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -25,7 +25,7 @@ set -e
# eddy. Don't pass the --out option, as that is
# added by this script.
exedir="$1"; shift;
-outdir="$2"; shift;
+outdir="$1"; shift;
eddy_args="$@"
# Find all eddy_cuda* executables
@@ -58,6 +58,10 @@ do
tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'`
jid=`fsl_sub -l ${outdir} -q cuda.q ${cuda_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+ if [ $? -ne 0 ]; then
+ echo "Error submitting ${cuda_exe} ${cuda_args}"
+ exit 1
+ fi
cuda_jids="${cuda_jids} ${jid}"
done
@@ -67,6 +71,10 @@ do
tmp=`basename ${cuda_exe}`
variant=`echo ${tmp} | sed 's/eddy_//'`
jid=`fsl_sub -l ${outdir} -q long.q -s openmp,6 ${cpu_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+ if [ $? -ne 0 ]; then
+ echo "Error submitting ${cuda_exe} ${cuda_args}"
+ exit 1
+ fi
cpu_jids="${cpu_jids} ${jid}"
done
@@ -81,7 +89,7 @@ if [ ! -z "${SGE_ROOT}" ]; then
# on the queue for CPU jobs
for jid in ${cpu_jids}; do
qalter ${jid} -R y
- fi
+ done
# wait for all jobs to finish
while [ : ]; do
--
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