Update runEddy script to work with new multi-threaded version.

The eddy_cpu command is called twice - once with --nthr=1, and again with --nthr=8

Note that these changes will not work with the openmp eddy build, so do not merge / use this MR until threddy has been released.

eddy/runEddy

@@ -10,8 +10,10 @@
 # output as the final line of output. Thne script returns
 # an exit code of non-0 if something goes wrong.
 #
-# The eddy_cpu executable is executed twice - once with
-# --nthr=1, and again with --nthr=8.
+# If called from pyfeeds, the eddy_cpu executable is
+# executed twice - once with --nthr=1, and again with
+# --nthr=6. If not called from pyfeeds, the eddy_cpu
+# executable is executed only once, with --nthr=6.
 #
 # Outputs of each eddy_<variant> executable is saved with
 # prefix ${outdir}/eddyOutput_<variant>. For example, the
@@ -30,7 +32,7 @@ set -e
 # added by this script.
 exedir="$1"; shift;
 outdir="$1"; shift;
-eddy_args="$@"
+eddy_args=("$@")
 
 # Find all eddy_cuda* executables
 cuda_exes=""
@@ -46,10 +48,19 @@ done
 # "eddy_cpu_nthr_X" to the list of
 # executables to run. The name is unpacked
 # in the loop below.
+#
+# We're using 6 threads here for the multi-
+# threaded test, as it is the best option on
+# the FMRIB cluster
 cpu_exes=""
 if [ -x "${exedir}/eddy_cpu" ]; then
-  cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_1"
-  cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_8"
+
+  # Only run single-threaded when running
+  # through pyfeeds
+  if [ "$PYFEEDS_TESTING" = "1" ]; then
+    cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_1"
+  fi
+  cpu_exes="${cpu_exes} ${exedir}/eddy_cpu_nthr_6"
 fi
 
 if [ "${cuda_exes}" == "" ] && [ "${cpu_exes}" == "" ]; then
@@ -71,21 +82,23 @@ do
   if [[ "${exe_name}" == *"cuda"* ]]; then
     fsl_sub="fsl_sub -l ${outdir} --coprocessor=cuda"
     exe="${exe_name}"
-    extra_args=""
-
   else
-    fsl_sub="fsl_sub -l ${outdir} -q long.q -s openmp,6"
     # unpack eddy_cpu_nthr_N
     # into eddy_cpu --nthr=N
+    fsl_sub="fsl_sub -l ${outdir} -q long.q"
     exe="${exe_name%_nthr*}"
-    extra_ars="--nthr=${exe_name#eddy_cpu_nthr_}"
+    nthr="${variant#cpu_nthr_}"
+    eddy_args+=("--nthr=${nthr}")
+    if [ "${nthr}" != "1" ]; then
+      fsl_sub="${fsl_sub} -s openmp,${nthr}"
+    fi
   fi
 
   # fsl_sub will return an error (and not
   # 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