RF: Allow eddy tests to run if eddy_openmp(/eddy_cpu) is not installed.

Also rename variables / outputs that refer to openmp to cpu

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