Major re-arrangement of eddy tests

so that job submission / monitoring code is shared across all tests in a common runEddy script. Also test both $FSLDIR/bin/eddy_openmp and $FSLDIR/bin/eddy_cpu if either exist. Tests can be executed either on a cluster submission node, or locally

eddy/runEddy

@@ -19,7 +19,7 @@
 
 set -e
 
-# First argument is directory in which to search 
+# First argument is directory in which to search
 # for eddy executables (typically $FSLDIR/bin).
 # All remaining arguments are to be passed to
 # eddy. Don't pass the --out option, as that is
@@ -52,30 +52,32 @@ if [ "${cuda_exes}" == "" ] && [ "${cpu_exes}" == "" ]; then
 fi
 
 # Launch both GPU and CPU versions
+# Store job IDs separately so we
+# can qalter the openmp jobs below
 cuda_jids=""
-for cuda_exe in ${cuda_exes};
+cpu_jids=""
+for exe in ${cuda_exes} ${cpu_exes};
 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
+  variant=`basename ${exe}`
+  variant=`echo ${variant} | sed 's/eddy_//'`
+
+  if [[ "${exe}" == *"cuda"* ]]; then
+    fsl_sub="fsl_sub -l ${outdir} -q cuda.q"
+  else
+    fsl_sub="fsl_sub -l ${outdir} -q long.q -s openmp,6"
   fi
-  cuda_jids="${cuda_jids} ${jid}"
-done
 
-cpu_jids=""
-for cpu_exe in ${cpu_exes};
-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} ${eddy_args}`
+  jid=`${fsl_sub} ${exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
   if [ $? -ne 0 ]; then
-    echo "Error submitting ${cuda_exe} ${cuda_args}"
+    echo "Error submitting ${exe} ${eddy_args}"
     exit 1
-  fi    
-  cpu_jids="${cpu_jids} ${jid}"
+  fi
+
+  if [[ "${exe}" == *"cuda"* ]]; then
+    cuda_jids="${cuda_jids} ${jid}"
+  else
+    cpu_jids="${cpu_jids} ${jid}"
+  fi
 done
 
 # If running on a cluster, wait
@@ -85,7 +87,7 @@ done
 # have blocked until completion.
 if [ ! -z "${SGE_ROOT}" ]; then
 
-  # Ensure that slots are being reserved 
+  # Ensure that slots are being reserved
   # on the queue for CPU jobs
   for jid in ${cpu_jids}; do
     qalter ${jid} -R y
@@ -104,17 +106,17 @@ if [ ! -z "${SGE_ROOT}" ]; then
     if [ $tmp -eq 0 ]; then
       break
     fi
-    sleep 5m
+    sleep 1m
   done
 fi
 
 # Gather output prefixes for each run,
-# and check that the main output file 
+# and check that the main output file
 # was created
 outputs=""
 for exe in ${cuda_exes} ${cpu_exes};
 do
-  tmp=`basename ${cuda_exe}`
+  tmp=`basename ${exe}`
   variant=`echo ${tmp} | sed 's/eddy_//'`
   prefix="${outdir}/eddyOutput_${variant}"
   outputs="${outputs} ${prefix}"