[Swift-commit] r2546 - in trunk: libexec src/org/griphyn/vdl/karajan

[noreply at svn.ci.uchicago.edu]

Author: benc
Date: 2009-02-15 18:03:58 -0600 (Sun, 15 Feb 2009)
New Revision: 2546

Modified:
   trunk/libexec/seq.sh
   trunk/libexec/vdl-int.k
   trunk/libexec/wrapper.sh
   trunk/src/org/griphyn/vdl/karajan/VDSTaskTransformer.java
Log:
attempt at fixing clusters

Modified: trunk/libexec/seq.sh
===================================================================
--- trunk/libexec/seq.sh	2009-02-16 00:02:52 UTC (rev 2545)
+++ trunk/libexec/seq.sh	2009-02-16 00:03:58 UTC (rev 2546)
@@ -1,5 +1,8 @@
 #!/bin/bash
 
+#WFDIR=$(dirname $(dirname $0))
+#cd $WFDIR
+
 SEQID="$1"
 shift
 
@@ -11,6 +14,7 @@
 WRAPPERLOG=$PWD/$LOGPATH/$SEQID.clusterlog
 
 echo `date +%s` START > $WRAPPERLOG
+echo `date +%s` WORKING DIRECTORY IS $PWD >> $WRAPPERLOG
 
 ls >>$WRAPPERLOG
 

Modified: trunk/libexec/vdl-int.k
===================================================================
--- trunk/libexec/vdl-int.k	2009-02-16 00:02:52 UTC (rev 2545)
+++ trunk/libexec/vdl-int.k	2009-02-16 00:03:58 UTC (rev 2546)
@@ -401,7 +401,7 @@
 				
 						vdl:setprogress("Submitting")
 						vdl:execute("/bin/bash",
-							list("{sharedDir}/wrapper.sh", jobid,
+							list("shared/wrapper.sh", jobid,
 								"-jobdir", jobdir,
 								"-e", vdl:executable(tr, rhost), 
 								"-out", stdout, 

Modified: trunk/libexec/wrapper.sh
===================================================================
--- trunk/libexec/wrapper.sh	2009-02-16 00:02:52 UTC (rev 2545)
+++ trunk/libexec/wrapper.sh	2009-02-16 00:03:58 UTC (rev 2546)
@@ -100,6 +100,10 @@
 WFDIR=$(dirname $(dirname $0))
 
 cd $WFDIR
+
+# make the WFDIR absolute
+WFDIR=$(pwd)
+
 openinfo "wrapper.log"
 ID=$1
 checkEmpty "$ID" "Missing job ID"
@@ -241,12 +245,16 @@
 	fail 254 "The executable $EXEC does not have the executable bit set"
 fi
 if [ "$KICKSTART" == "" ]; then
+log "command line is $EXEC $@"
+log "pwd is $(pwd)"
 	if [ "$STDIN" == "" ]; then
 		"$EXEC" "$@" 1>"$STDOUT" 2>"$STDERR"
 	else
 		"$EXEC" "$@" 1>"$STDOUT" 2>"$STDERR" <"$STDIN"
 	fi
 	checkError $? "Exit code $?"
+find . >& "$INFO" 
+
 else
 	if [ ! -f "$KICKSTART" ]; then
 		log "Kickstart executable ($KICKSTART) not found"
@@ -273,6 +281,7 @@
 
 cd $WFDIR
 
+log "Moving back to workflow directory $WFDIR"
 logstate "EXECUTE_DONE"
 log "Job ran successfully"
 

Modified: trunk/src/org/griphyn/vdl/karajan/VDSTaskTransformer.java
===================================================================
--- trunk/src/org/griphyn/vdl/karajan/VDSTaskTransformer.java	2009-02-16 00:02:52 UTC (rev 2545)
+++ trunk/src/org/griphyn/vdl/karajan/VDSTaskTransformer.java	2009-02-16 00:03:58 UTC (rev 2546)
@@ -122,8 +122,11 @@
 			}
 			List l =   spec.getArgumentsAsList();
 			// perhaps should check for /bin/bash in the executable, or some other way of detecting we need to do a substitution here... or equally could assume that the second parameter always needs to undergo this substitution...
-			if(((String)l.get(0)).endsWith("shared/wrapper.sh")) {
-				String s  = workdir+"/"+l.get(0);
+			String executable = (String)l.get(0);
+			if(executable.endsWith("shared/wrapper.sh") || 
+			   executable.endsWith("shared/seq.sh")) {
+
+				String s  = spec.getDirectory()+"/"+executable;
 				l.set(0,s);
 			}