From 4374034ae59e02ada66f585ca1eadc52063fda39 Mon Sep 17 00:00:00 2001
From: David Flitney <dave.flitney@ndcn.ox.ac.uk>
Date: Mon, 17 Aug 2009 15:55:44 +0000
Subject: [PATCH] Try to make the monitor script a little better.
---
bedpostx | 32 +++++++++++++++++++++++++++++---
1 file changed, 29 insertions(+), 3 deletions(-)
diff --git a/bedpostx b/bedpostx
index 9095edd..281453b 100755
--- a/bedpostx
+++ b/bedpostx
@@ -117,7 +117,10 @@ if [ "x$SGE_ROOT" = "x" ]; then
#!/bin/sh
finished=0
logdir=${subjdir}.bedpostX/logs
-while [ \$finished -eq 0 ] ; do
+
+trap "echo Final check; exit_test; exit" SIGUSR1
+
+check() {
nfin=0
slice=0
while [ "\$slice" -le $nslices ];do
@@ -133,7 +136,29 @@ while [ \$finished -eq 0 ] ; do
fi
echo "\$nfin slices processed"
- sleep 600;
+}
+
+exit_test() {
+ check;
+ if [ \$finished -eq 0 ] ; then
+ echo For some reason the bedpostX process DOES NOT appear
+ echo to have successfully completed. Please examine your
+ echo results carefully.
+ else
+ echo All slices processed
+ fi
+}
+
+check
+n=0
+while [ \$finished -eq 0 ] ; do
+ sleep 10;
+ if [ \$n -eq 60 ] ; then
+ check
+ n=0
+ else
+ n=\$((\$n + 1))
+ fi
done
EOM
chmod +x ${subjdir}.bedpostX/monitor
@@ -153,11 +178,12 @@ do
slice=$(($slice + 1))
done
bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
-[ "x$SGE_ROOT" = "x" ] && kill $monitorpid
echo Queuing post processing stage
mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -T 60 -m as -N bpx_postproc -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
+[ "x$SGE_ROOT" = "x" ] && kill -USR1 $monitorpid
+
if [ "x$SGE_ROOT" != "x" ]; then
echo
echo Type ${subjdir}.bedpostX/monitor to show progress.
--
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