RF: Add feedsInputs/runEddy, should have been in last commit

eddy/feedsInputs

+EddyTestData/eddyData
+EddyLSRTestData/eddyData
+EddyMBSTestData/eddyData
+EddyS2VTestData/eddyData
+EddyHigh_b_TestData/eddyData

eddy/runEddy

+#!/usr/bin/env bash
+#
+# This script is shared by all of the feedsRun.<eddytest>
+# scripts. It runs eddy with a set of arguments, either
+# directly, or by submitting to a cluster with fsl_sub,
+# and then waits for eddy to finish. All eddy executables
+# that are installed in $FSLDIR/bin/ are executed, and
+# the outputs for each are directed to a different output
+# prefix. All output prefixes are printed to standard
+# output as the final line of output. Thne script returns
+# an exit code of non-0 if something goes wrong.
+#
+# Outputs of each eddy_<variant> executable is saved with
+# prefix ${outdir}/eddyOutput_<variant>. For example, the
+# output of eddy_cuda9.2 will be saved with prefix
+# ${outdir}/eddyOutput_cuda9.2, and the output of
+# eddy_openmp will be saved with prefix
+# ${outdir}/eddyOutput_openmp.
+
+set -e
+
+# 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
+# added by this script.
+exedir="$1"; shift;
+outdir="$2"; shift;
+eddy_args="$@"
+
+# Find all eddy_cuda* executables
+cuda_exes=""
+for cuda_exe in ${exedir}/eddy_cuda*;
+do
+  if [ -x "${cuda_exe}" ]; then
+    cuda_exes="${cuda_exes} ${cuda_exe}"
+  fi
+done
+
+# Find all eddy_cpu/eddy_openmp executables
+cpu_exes=""
+if [ -x "${exedir}/eddy_openmp" ]; then
+  cpu_exes="${exedir}/eddy_openmp"
+fi
+if [ -x "${exedir}/eddy_cpu" ]; then
+  cpu_exes="${cpu_exes} ${exedir}/eddy_cpu"
+fi
+
+if [ "${cuda_exes}" == "" ] && [ "${cpu_exes}" == "" ]; then
+  echo "Cannot find any eddy executables in ${exedir}!"
+  exit 1
+fi
+
+# Launch both GPU and CPU versions
+cuda_jids=""
+for cuda_exe in ${cuda_exes};
+do
+  tmp=`basename ${cuda_exe}`
+  variant=`echo ${tmp} | sed 's/eddy_//'`
+  jid=`fsl_sub -l ${odir} -q cuda.q ${cuda_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+  cuda_jids="${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 ${odir} -q long.q -s openmp,6 ${cpu_exe} --out=${outdir}/eddyOutput_${variant} ${eddy_args}`
+  cpu_jids="${cpu_jids} ${jid}"
+done
+
+# If running on a cluster, wait
+# until all jobs have finished.
+# If not running on a cluster,
+# the above fsl_sub calls will
+# have blocked until completion.
+if [ ! -z "${SGE_ROOT}" ]; then
+
+  # Ensure that slots are being reserved 
+  # on the queue for CPU jobs
+  for jid in ${cpu_jids}; do
+    qalter ${jid} -R y
+  fi
+
+  # wait for all jobs to finish
+  while [ : ]; do
+    for jid in ${cuda_jids} ${cpu_jids};
+    do
+      tmp=`qstat -j ${jid} | wc`
+      tmp=`echo $tmp | awk '{print $1}'`
+      if [ $tmp -ne 0 ]; then
+    	break
+      fi
+    done
+    if [ $tmp -eq 0 ]; then
+      break
+    fi
+    sleep 5m
+  done
+fi
+
+# Gather output prefixes for each run,
+# and check that the main output file 
+# was created
+outputs=""
+for exe in ${cuda_exes} ${cpu_exes};
+do
+  tmp=`basename ${cuda_exe}`
+  variant=`echo ${tmp} | sed 's/eddy_//'`
+  prefix="${odir}/eddyOutput_${variant}"
+  outputs="${outputs} ${prefix}"
+  if [ ! -f ${prefix}.nii* ]; then
+    echo "${prefix} is missing"
+	exit 1
+  fi
+done
+
+echo ${outputs}
+exit 0