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

@@ -74,11 +74,15 @@ do
     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=${exe_name#eddy_cpu_nthr_}"
+    nthr="${exe_name#eddy_cpu_nthr_}"
+    extra_args="--nthr=${nthr}"
+    if [ "${nthr}" != "1" ]; then
+      fsl_sub="${fsl_sub} -s openmp,${nthr}"
+    fi
   fi
 
   # fsl_sub will return an error (and not