From f8cda2a34f505cba258d14d254775577f0aa5c2d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Nov 2021 15:17:24 +0000
Subject: [PATCH] RF: Allow eddy tests to run if eddy_openmp(/eddy_cpu) is not
installed.
---
eddy/EddyHigh_b_Test/feedsRun | 65 ++++++++++++++++++--------------
eddy/EddyLSRTest/feedsRun | 69 +++++++++++++++++++---------------
eddy/EddyMBSTest/feedsRun | 66 +++++++++++++++++++--------------
eddy/EddyS2VTest/feedsRun | 67 +++++++++++++++++++--------------
eddy/EddyTest/feedsRun | 70 +++++++++++++++++++++--------------
5 files changed, 197 insertions(+), 140 deletions(-)
diff --git a/eddy/EddyHigh_b_Test/feedsRun b/eddy/EddyHigh_b_Test/feedsRun
index ec81bcd..83cb34f 100755
--- a/eddy/EddyHigh_b_Test/feedsRun
+++ b/eddy/EddyHigh_b_Test/feedsRun
@@ -30,7 +30,7 @@ fi
# Find all eddy_cuda* executables
cuda_exes=""
-openmp_exe=""
+cpu_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
if [ -x "${cuda_exe}" ]; then
@@ -38,12 +38,12 @@ do
fi
done
-# Find the eddy_openmp executable
+# Find the eddy_cpu executable
if [ -x "${exedir}/eddy_openmp" ]; then
- openmp_exe="${exedir}/eddy_openmp"
+ cpu_exe="${exedir}/eddy_openmp"
fi
-if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exe}" == "" ]; then
echo "Cannot find any eddy executables in ${exedir}!"
exit 1
fi
@@ -67,31 +67,37 @@ do
cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyHigh_b_TestData/eddyData/testData --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --out=${odir}/eddyCudaOutput${version} --very_verbose`"
done
-omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyHigh_b_TestData/eddyData/testData --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --out=${odir}/eddyOmpOutput --very_verbose`
+if [ "${cpu_exe}" != "" ]; then
+ cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${indir}/EddyHigh_b_TestData/eddyData/testData --mask=${indir}/EddyHigh_b_TestData/eddyData/testMask --bvals=${indir}/EddyHigh_b_TestData/eddyData/testBvals --bvecs=${indir}/EddyHigh_b_TestData/eddyData/testBvecs --index=${indir}/EddyHigh_b_TestData/eddyData/testIndex --acqp=${indir}/EddyHigh_b_TestData/eddyData/testAcqparams --topup=${indir}/EddyHigh_b_TestData/eddyData/testTopup --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --out=${odir}/eddyCpuOutput --very_verbose`
+fi
# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
- qalter ${omp_jid} -R y
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
+ if [ "${cpu_exe}" != "" ]; then
+ qalter ${cpu_jid} -R y
+ fi
+ while [ : ]; do
+ for jid in ${cuda_jid};
+ do
+ tmp=`qstat -j ${jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
+ if [ $tmp -ne 0 ]; then
+ break
+ fi
+ done
+ if [ "${cpu_exe}" != "" ]; then
+ if [ $tmp -eq 0 ]; then
+ tmp=`qstat -j ${cpu_jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${omp_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
+ break
fi
- sleep 5m
- done
+ fi
+ fi
+ sleep 5m
+ done
fi
# Check that eddy output exists
@@ -104,8 +110,11 @@ do
exit 1
fi
done
-if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
+if [ "${cpu_exe}" != "" ]; then
+ if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
+ echo "eddyCpuOutput missing"
exit 1
+ fi
fi
# Define some constants
@@ -124,11 +133,13 @@ do
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./EddyHigh_b_Feeds.py ${odir} Omp `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
-
-omp_exit_status=$?
+cpu_exit_status=0
+if [ "${cpu_exe}" != "" ]; then
+ ./EddyHigh_b_Feeds.py ${odir} Cpu `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyHigh_b_TestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
+ cpu_exit_status=$?
+fi
-if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
+if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
echo "Test failed"
exit 1
else
diff --git a/eddy/EddyLSRTest/feedsRun b/eddy/EddyLSRTest/feedsRun
index c70abee..4a5dad8 100755
--- a/eddy/EddyLSRTest/feedsRun
+++ b/eddy/EddyLSRTest/feedsRun
@@ -27,7 +27,7 @@ fi
# Find all eddy_cuda* executables
cuda_exes=""
-openmp_exe=""
+cpu_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
if [ -x "${cuda_exe}" ]; then
@@ -35,12 +35,12 @@ do
fi
done
-# Find the eddy_openmp executable
+# Find the eddy_cpu executable
if [ -x "${exedir}/eddy_openmp" ]; then
- openmp_exe="${exedir}/eddy_openmp"
+ cpu_exe="${exedir}/eddy_openmp"
fi
-if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exe}" == "" ]; then
echo "Cannot find any eddy executables in ${exedir}!"
exit 1
fi
@@ -64,32 +64,38 @@ do
cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyLSRTestData/eddyData/testData --mask=${indir}/EddyLSRTestData/eddyData/testMask --bvals=${indir}/EddyLSRTestData/eddyData/testBvals --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs --index=${indir}/EddyLSRTestData/eddyData/testIndex --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams --topup=${indir}/EddyLSRTestData/eddyData/testTopup --out=${odir}/eddyCudaOutput${version} --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`"
done
-omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyLSRTestData/eddyData/testData --mask=${indir}/EddyLSRTestData/eddyData/testMask --bvals=${indir}/EddyLSRTestData/eddyData/testBvals --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs --index=${indir}/EddyLSRTestData/eddyData/testIndex --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams --topup=${indir}/EddyLSRTestData/eddyData/testTopup --out=${odir}/eddyOmpOutput --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`
+if [ "${cpu_exe}" != "" ]; then
+ cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${indir}/EddyLSRTestData/eddyData/testData --mask=${indir}/EddyLSRTestData/eddyData/testMask --bvals=${indir}/EddyLSRTestData/eddyData/testBvals --bvecs=${indir}/EddyLSRTestData/eddyData/testBvecs --index=${indir}/EddyLSRTestData/eddyData/testIndex --acqp=${indir}/EddyLSRTestData/eddyData/testAcqparams --topup=${indir}/EddyLSRTestData/eddyData/testTopup --out=${odir}/eddyCpuOutput --resamp=lsr --fep --nvoxhp=5000 --repol --fwhm=10,0,0,0,0 --dont_peas --very_verbose`
+fi
# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
- qalter ${omp_jid} -R y
-
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
+ if [ "${cpu_exe}" != "" ]; then
+ qalter ${cpu_jid} -R y
+ fi
+
+ while [ : ]; do
+ for jid in ${cuda_jid};
+ do
+ tmp=`qstat -j ${jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
+ if [ $tmp -ne 0 ]; then
+ break
+ fi
+ done
+ if [ "${cpu_exe}" != "" ]; then
+ if [ $tmp -eq 0 ]; then
+ tmp=`qstat -j ${cpu_jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${omp_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
+ break
fi
- sleep 5m
- done
+ fi
+ fi
+ sleep 5m
+ done
fi
# Check that eddy output exists
@@ -102,8 +108,11 @@ do
exit 1
fi
done
-if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
- exit 1
+if [ "${cpu_exe}" != "" ]; then
+ if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
+ echo "eddyCpuOutput missing"
+ exit 1
+ fi
fi
# Define some constants
@@ -122,11 +131,13 @@ do
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./EddyLSRFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
-
-omp_exit_status=$?
+cpu_exit_status=0
+if [ "${cpu_exe}" != "" ]; then
+ ./EddyLSRFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyLSRTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyLSRTestData/eddyData/Precomputed/eddy_openmp_output` $max_mean_ima_diff $max_max_ima_diff
+ cpu_exit_status=$?
+fi
-if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
+if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
echo "Test failed"
exit 1
else
diff --git a/eddy/EddyMBSTest/feedsRun b/eddy/EddyMBSTest/feedsRun
index 00fca93..9be5681 100755
--- a/eddy/EddyMBSTest/feedsRun
+++ b/eddy/EddyMBSTest/feedsRun
@@ -32,7 +32,7 @@ fi
# Find all eddy_cuda* executables
cuda_exes=""
-openmp_exe=""
+cpu_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
if [ -x "${cuda_exe}" ]; then
@@ -40,12 +40,12 @@ do
fi
done
-# Find the eddy_openmp executable
+# Find the eddy_cpu executable
if [ -x "${exedir}/eddy_openmp" ]; then
- openmp_exe="${exedir}/eddy_openmp"
+ cpu_exe="${exedir}/eddy_openmp"
fi
-if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exe}" == "" ]; then
echo "Cannot find any eddy executables in ${exedir}!"
exit 1
fi
@@ -76,31 +76,37 @@ do
cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyMBSTestData/eddyData/testData --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams --mask=${indir}/EddyMBSTestData/eddyData/testMask --index=${indir}/EddyMBSTestData/eddyData/testIndex --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs --bvals=${indir}/EddyMBSTestData/eddyData/testBvals --topup=${indir}/EddyMBSTestData/eddyData/testTopup --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 --flm=quadratic --dont_peas --estimate_move_by_susceptibility --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --out=${odir}/eddyCudaOutput${version} --very_verbose`"
done
-omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyMBSTestData/eddyData/testData --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams --mask=${indir}/EddyMBSTestData/eddyData/testMask --index=${indir}/EddyMBSTestData/eddyData/testIndex --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs --bvals=${indir}/EddyMBSTestData/eddyData/testBvals --topup=${indir}/EddyMBSTestData/eddyData/testTopup --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 --flm=quadratic --dont_peas --estimate_move_by_susceptibility --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --out=${odir}/eddyOmpOutput --very_verbose`
+if [ "${cpu_exe}" != "" ]; then
+ cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${indir}/EddyMBSTestData/eddyData/testData --acqp=${indir}/EddyMBSTestData/eddyData/testAcqparams --mask=${indir}/EddyMBSTestData/eddyData/testMask --index=${indir}/EddyMBSTestData/eddyData/testIndex --bvecs=${indir}/EddyMBSTestData/eddyData/testBvecs --bvals=${indir}/EddyMBSTestData/eddyData/testBvals --topup=${indir}/EddyMBSTestData/eddyData/testTopup --fwhm=10,5,2,0,0,0,0,0 --niter=8 --nvoxhp=2000 --flm=quadratic --dont_peas --estimate_move_by_susceptibility --mbs_niter=20 --mbs_lambda=10 --mbs_ksp=10 --out=${odir}/eddyCpuOutput --very_verbose`
+fi
# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
- qalter ${omp_jid} -R y
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
+ if [ "${cpu_exe}" != "" ]; then
+ qalter ${cpu_jid} -R y
+ fi
+ while [ : ]; do
+ for jid in ${cuda_jid};
+ do
+ tmp=`qstat -j ${jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
+ if [ $tmp -ne 0 ]; then
+ break
+ fi
+ done
+ if [ "${cpu_exe}" != "" ]; then
+ if [ $tmp -eq 0 ]; then
+ tmp=`qstat -j ${cpu_jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${omp_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
+ break
fi
- sleep 5m
- done
+ fi
+ fi
+ sleep 5m
+ done
fi
# Check that eddy output exists
@@ -113,8 +119,10 @@ do
exit 1
fi
done
-if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
- exit 1
+if [ "${cpu_exe}" != "" ]; then
+ if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
+ exit 1
+ fi
fi
# Check the results against precomputed results
@@ -128,11 +136,13 @@ do
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./MoveBySuscFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyOmpOutput.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
-
-omp_exit_status=$?
+cpu_exit_status=0
+if [ "${cpu_exe}" != "" ]; then
+ ./MoveBySuscFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/BrainMaskForComparison` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults` `imglob -extension ${odir}/eddyCpuOutput.eddy_mbs_first_order_fields` `imglob -extension ${indir}/EddyMBSTestData/eddyData/Precomputed/PrecomputedResults.eddy_mbs_first_order_fields` ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff}
+ cpu_exit_status=$?
+fi
-if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
+if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
echo "Test failed"
exit 1
else
diff --git a/eddy/EddyS2VTest/feedsRun b/eddy/EddyS2VTest/feedsRun
index f1dc7b7..37f6a1e 100755
--- a/eddy/EddyS2VTest/feedsRun
+++ b/eddy/EddyS2VTest/feedsRun
@@ -28,7 +28,7 @@ fi
# Find all eddy_cuda* executables
cuda_exes=""
-openmp_exe=""
+cpu_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
if [ -x "${cuda_exe}" ]; then
@@ -36,12 +36,12 @@ do
fi
done
-# Find the eddy_openmp executable
+# Find the eddy_cpu executable
if [ -x "${exedir}/eddy_openmp" ]; then
- openmp_exe="${exedir}/eddy_openmp"
+ cpu_exe="${exedir}/eddy_openmp"
fi
-if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exe}" == "" ]; then
echo "Cannot find any eddy executables in ${exedir}!"
exit 1
fi
@@ -65,31 +65,37 @@ do
cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --ol_nvox=500 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCudaOutput${version} --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`"
done
-omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyOmpOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+if [ "${cpu_exe}" != "" ]; then
+ cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${indir}/EddyS2VTestData/eddyData/testData --mask=${indir}/EddyS2VTestData/eddyData/testMask --bvals=${indir}/EddyS2VTestData/eddyData/testBvals --bvecs=${indir}/EddyS2VTestData/eddyData/testBvecs --index=${indir}/EddyS2VTestData/eddyData/testIndex --acqp=${indir}/EddyS2VTestData/eddyData/testAcqparams --repol --ol_type=slice --ol_nstd=6 --niter=8 --fwhm=10,6,4,2,0,0,0,0 --out=${odir}/eddyCpuOutput --nvoxhp=5000 --mporder=16 --s2v_niter=10 --s2v_interp=trilinear --s2v_lambda=1 --slspec=${indir}/EddyS2VTestData/eddyData/testSlspec --very_verbose`
+fi
# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
- qalter ${omp_jid} -R y
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
+ if [ "${cpu_exe}" != "" ]; then
+ qalter ${cpu_jid} -R y
+ fi
+ while [ : ]; do
+ for jid in ${cuda_jid};
+ do
+ tmp=`qstat -j ${jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
+ if [ $tmp -ne 0 ]; then
+ break
+ fi
+ done
+ if [ "${cpu_exe}" != "" ]; then
+ if [ $tmp -eq 0 ]; then
+ tmp=`qstat -j ${cpu_jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${omp_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
+ break
fi
- sleep 5m
- done
+ fi
+ fi
+ sleep 5m
+ done
fi
# Check that eddy output exists
@@ -103,9 +109,11 @@ do
exit 1
fi
done
-if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
- echo "Omp output eddyOmpOutput missing"
+if [ "${cpu_exe}" != "" ]; then
+ if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
+ echo "eddyCpuOutput missing"
exit 1
+ fi
fi
# Define some constants
@@ -133,12 +141,15 @@ utput${version}.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/
cuda_exit_status=$(($cuda_exit_status + $?))
done
-omp_exit_status=0
-./S2VFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyOmpOutput.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyOmpOutput.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}
-omp_exit_status=$?
+cpu_exit_status=0
+
+if [ "${cpu_exe}" != "" ]; then
+ ./S2VFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyS2VTestData/eddyData/testMask` ${indir}/EddyS2VTestData/eddyData/testBvals `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyS2VTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCpuOutput.eddy_movement_over_time ${indir}/EddyS2VTestData/eddyData/MovementTruth/ground_truth.eddy_movement_over_time ${odir}/eddyCpuOutput.eddy_outlier_map ${indir}/EddyS2VTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_ima_diff} ${max_false_pos} ${max_false_neg} ${max_trans_diff} ${max_rot_diff}
+ cpu_exit_status=$?
+fi
-if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
+if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
echo "Test failed"
exit 1
else
diff --git a/eddy/EddyTest/feedsRun b/eddy/EddyTest/feedsRun
index af955ae..cf3f1ac 100755
--- a/eddy/EddyTest/feedsRun
+++ b/eddy/EddyTest/feedsRun
@@ -26,7 +26,7 @@ fi
# Find all eddy_cuda* executables
cuda_exes=""
-openmp_exe=""
+cpu_exe=""
for cuda_exe in ${exedir}/eddy_cuda*;
do
if [ -x "${cuda_exe}" ]; then
@@ -34,12 +34,12 @@ do
fi
done
-# Find the eddy_openmp executable
+# Find the eddy_cpu executable
if [ -x "${exedir}/eddy_openmp" ]; then
- openmp_exe="${exedir}/eddy_openmp"
+ cpu_exe="${exedir}/eddy_openmp"
fi
-if [ "${cuda_exes}" == "" ] && [ "${openmp_exe}" == "" ]; then
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exe}" == "" ]; then
echo "Cannot find any eddy executables in ${exedir}!"
exit 1
fi
@@ -72,32 +72,38 @@ do
cuda_jid="$cuda_jid `fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --imain=${indir}/EddyTestData/eddyData/testData --mask=${indir}/EddyTestData/eddyData/testMask --bvals=${indir}/EddyTestData/eddyData/testBvals --bvecs=${indir}/EddyTestData/eddyData/testBvecs --index=${indir}/EddyTestData/eddyData/testIndex --acqp=${indir}/EddyTestData/eddyData/testAcqparams --repol --fwhm=10,0,0,0,0 --out=${odir}/eddyCudaOutput${version} --dfields -v`"
done
-omp_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${exedir}/eddy_openmp --imain=${indir}/EddyTestData/eddyData/testData --mask=${indir}/EddyTestData/eddyData/testMask --bvals=${indir}/EddyTestData/eddyData/testBvals --bvecs=${indir}/EddyTestData/eddyData/testBvecs --index=${indir}/EddyTestData/eddyData/testIndex --acqp=${indir}/EddyTestData/eddyData/testAcqparams --repol --fwhm=10,0,0,0,0 --out=${odir}/eddyOmpOutput --dfields -v`
+if [ "${cpu_exe}" != "" ]; then
+ cpu_jid=`fsl_sub -l ${odir} -q long.q -s openmp,6 ${cpu_exe} --imain=${indir}/EddyTestData/eddyData/testData --mask=${indir}/EddyTestData/eddyData/testMask --bvals=${indir}/EddyTestData/eddyData/testBvals --bvecs=${indir}/EddyTestData/eddyData/testBvecs --index=${indir}/EddyTestData/eddyData/testIndex --acqp=${indir}/EddyTestData/eddyData/testAcqparams --repol --fwhm=10,0,0,0,0 --out=${odir}/eddyCpuOutput --dfields -v`
+fi
# If running on a cluster, ensure that
# slots are being reserved on the queue,
# and wait until all jobs have finished
if [ ! -z "${SGE_ROOT}" ]; then
- qalter ${omp_jid} -R y
-
- while [ : ]; do
- for jid in ${cuda_jid};
- do
- tmp=`qstat -j ${jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -ne 0 ]; then
- break
- fi
- done
+ if [ "${cpu_exe}" != "" ]; then
+ qalter ${cpu_jid} -R y
+ fi
+
+ while [ : ]; do
+ for jid in ${cuda_jid};
+ do
+ tmp=`qstat -j ${jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
+ if [ $tmp -ne 0 ]; then
+ break
+ fi
+ done
+ if [ "${cpu_exe}" != "" ]; then
+ if [ $tmp -eq 0 ]; then
+ tmp=`qstat -j ${cpu_jid} | wc`
+ tmp=`echo $tmp | awk '{print $1}'`
if [ $tmp -eq 0 ]; then
- tmp=`qstat -j ${omp_jid} | wc`
- tmp=`echo $tmp | awk '{print $1}'`
- if [ $tmp -eq 0 ]; then
- break
- fi
+ break
fi
- sleep 5m
- done
+ fi
+ fi
+ sleep 5m
+ done
fi
# Check that eddy output exists
@@ -110,8 +116,12 @@ do
exit 1
fi
done
-if [ ! -f ${odir}/eddyOmpOutput.nii* ]; then
- exit 1
+
+if [ "${cpu_exe}" != "" ]; then
+ if [ ! -f ${odir}/eddyCpuOutput.nii* ]; then
+ echo "eddyCpuOutput missing"
+ exit 1
+ fi
fi
# Check the results against ground truth
@@ -125,10 +135,14 @@ do
cuda_exit_status=$(($cuda_exit_status + $?))
done
-./EddyFeeds.py ${odir} Omp `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyOmpOutput` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyOmpOutput.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyOmpOutput.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
-omp_exit_status=$?
+cpu_exit_status=0
+
+if [ "${cpu_exe}" != "" ]; then
+ ./EddyFeeds.py ${odir} Cpu `imglob -extension ${indir}/EddyTestData/eddyData/testMask` `imglob -extension ${odir}/eddyCpuOutput` `imglob -extension ${indir}/EddyTestData/eddyData/GroundTruth/ground_truth` ${odir}/eddyCpuOutput.eddy_displacement_fields ${indir}/EddyTestData/eddyData/DisplacementFields/DisplacementField ${odir}/eddyCpuOutput.eddy_outlier_map ${indir}/EddyTestData/eddyData/OutlierTruth/dropoutLog_1.txt ${max_mean_ima_diff} ${max_max_ima_diff} ${max_mean_dfield_diff} ${max_max_dfield_diff} ${allowed_false_positives} ${allowed_false_negatives}
+ cpu_exit_status=$?
+fi
-if [ $cuda_exit_status -gt 0 ] || [ $omp_exit_status -gt 0 ]; then
+if [ $cuda_exit_status -gt 0 ] || [ $cpu_exit_status -gt 0 ]; then
echo "Test failed"
exit 1
else
--
GitLab