From 87685dcedbd62e1f1401f25ee8a5ced9953ee875 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 30 May 2022 11:55:43 +0100
Subject: [PATCH] RF: Use an array instead of separate vars for extra arguments
---
eddy/runEddy | 8 +++-----
1 file changed, 3 insertions(+), 5 deletions(-)
diff --git a/eddy/runEddy b/eddy/runEddy
index 222b8f1..fb7a0da 100755
--- a/eddy/runEddy
+++ b/eddy/runEddy
@@ -30,7 +30,7 @@ set -e
# added by this script.
exedir="$1"; shift;
outdir="$1"; shift;
-eddy_args="$@"
+eddy_args=("$@")
# Find all eddy_cuda* executables
cuda_exes=""
@@ -71,15 +71,13 @@ do
if [[ "${exe_name}" == *"cuda"* ]]; then
fsl_sub="fsl_sub -l ${outdir} --coprocessor=cuda"
exe="${exe_name}"
- extra_args=""
-
else
# unpack eddy_cpu_nthr_N
# into eddy_cpu --nthr=N
fsl_sub="fsl_sub -l ${outdir} -q long.q"
exe="${exe_name%_nthr*}"
nthr="${exe_name#eddy_cpu_nthr_}"
- extra_args="--nthr=${nthr}"
+ eddy_args+=("--nthr=${nthr}")
if [ "${nthr}" != "1" ]; then
fsl_sub="${fsl_sub} -s openmp,${nthr}"
fi
@@ -89,7 +87,7 @@ do
# output a job id) if we try to run a
# cuda exe on a non-cuda-capable machine
# or queue. So we allow it to fail.
- jid=$(${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${extra_args} ${eddy_args} || true)
+ jid=$(${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args} || true)
if [ "${jid}" == "" ]; then
echo "Error submitting ${exe_name} - skipping"
continue
--
GitLab