[Bug 1048] New: Null pointer exception in 0.94 from MS-String runs
https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1048 Summary: Null pointer exception in 0.94 from MS-String runs Product: Swift Version: 0.94 Platform: PC OS/Version: Mac OS Status: ASSIGNED Severity: major Priority: P1 Component: Runtime AssignedTo: [email protected] ReportedBy: [email protected] The CMTS MD app MS-String is getting occasional random NPEs on midway under Java 1.7. The messages appear at the start of a run, and then Swift hangs. We dont have a log yet from the user, and will try to get a jstack as well. --- mid$ module load swift mid$ swift -version Swift 0.94 swift-r6492 cog-r3658 mid$ java -version java version "1.7.0_17" Java(TM) SE Runtime Environment (build 1.7.0_17-b02) Java HotSpot(TM) 64-Bit Server VM (build 23.7-b01, mixed mode) makena002$ more runtask.68.out Swift 0.94 swift-r6492 cog-r3658 RunID: 20130719-0925-jv69o387 Progress: time: Fri, 19 Jul 2013 09:25:53 +0000 Another uncaught exception while handling an uncaught exception. java.lang.NullPointerException at org.globus.cog.karajan.workflow.FlowElementWrapper.hasProperty(FlowElementWrapper.java:146) at org.globus.cog.karajan.workflow.FlowElementWrapper.toString(FlowElementWrapper.java:319) at java.lang.String.valueOf(String.java:2854) at java.lang.StringBuilder.append(StringBuilder.java:128) at org.globus.cog.karajan.workflow.events.EventBus.start(EventBus.java:120) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:40) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722) The initial exception was java.lang.NullPointerException at org.globus.cog.karajan.workflow.nodes.FlowNode.setProperties(FlowNode.java:398) at org.globus.cog.karajan.workflow.FlowElementWrapper.populate(FlowElementWrapper.java:308) at org.globus.cog.karajan.workflow.FlowElementWrapper.bind(FlowElementWrapper.java:275) at org.globus.cog.karajan.workflow.FlowElementWrapper.start(FlowElementWrapper.java:224) at org.globus.cog.karajan.workflow.events.EventBus.start(EventBus.java:103) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:40) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722) Another uncaught exception while handling an uncaught exception. java.lang.NullPointerException at org.globus.cog.karajan.workflow.FlowElementWrapper.hasProperty(FlowElementWrapper.java:146) at org.globus.cog.karajan.workflow.FlowElementWrapper.toString(FlowElementWrapper.java:319) at java.lang.String.valueOf(String.java:2854) at java.lang.StringBuilder.append(StringBuilder.java:128) at org.globus.cog.karajan.workflow.events.EventBus.start(EventBus.java:120) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:40) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:722) The initial exception was java.lang.NullPointerException at org.globus.cog.karajan.workflow.nodes.FlowNode.setProperties(FlowNode.java:398) at org.globus.cog.karajan.workflow.FlowElementWrapper.populate(FlowElementWrapper.java:308) at org.globus.cog.karajan.workflow.FlowElementWrapper.bind(FlowElementWrapper.java:275) at org.globus.cog.karajan.workflow.FlowElementWrapper.start(FlowElementWrapper.java:224) at org.globus.cog.karajan.workflow.events.EventBus.start(EventBus.java:103) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:40) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) makena002$ ls -lt runtask.68.out -rw-rw-r-- 1 mvolche mvolche 7 -- Michael Wilde Computation Institute, University of Chicago Mathematics and Computer Science Division Argonne National Laboratory -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.
https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1048 Michael Wilde <[email protected]> changed: What |Removed |Added ---------------------------------------------------------------------------- CC| |[email protected] Target Milestone|--- |v0.94 --- Comment #1 from Michael Wilde <[email protected]> 2013-07-22 11:48:46 --- The Swift script and config files that were used are below. Yadu will try to replicate this problem initially using repeated Swift invocations on localhost. My initial suspicion is a race involving some of the conditional ("if") logic in the script. Mihael, does the java traceback from the one incident reported in this ticket give you a clue as to where the problem lies (so that we can focus the attempt to reproduce the problem)? --- swift$ more *.swift *.tx *.cf *tc :::::::::::::: cp2k.swift :::::::::::::: type file; app (file o, file e, file fcoll, file tgz, file ccoll, file cxyz, file abc ) runcp2k (file cp2k, int iter, int i, file xyz, int ff, int first, file temp, file ref, int node) { sh "-c" @strcat("tar xvzf ref.tgz; chmod 744 iterate.cp2k.sh ; ./iterate.cp2k.sh ", i, " ", ff, " ", first, " ", node, " ", iter) stdout=@o stderr=@e; } int iter = @toInt(@arg("iteration")); int ng = @toInt(@arg("ng")); int ff = @toInt(@arg("ff")); int first = @toInt(@arg("first")); int aimage = @toInt(@arg("a")); int zimage = @toInt(@arg("z")); foreach i in [aimage:zimage] { file o<single_file_mapper; file=@strcat("runtask.", iter, ".", i)>; file e<single_file_mapper; file=@strcat("cp2k.", iter, ".", i, ".err")>; # input files file ref <"ref.tgz">; file temp <"temp.init">; file cp2k <single_file_mapper; file=@strcat("iterate.cp2k.sh")>; # output files file fcoll <single_file_mapper; file=@strcat("path.", i, ".free.coll")>; file ccoll <single_file_mapper; file=@strcat("path.", i, ".constr.coll")>; file cxyz <single_file_mapper; file=@strcat("path.", i, ".constr.xyz")>; file tgz <single_file_mapper; file=@strcat("save.", iter, ".", i, ".tgz")>; file abc <single_file_mapper; file=@strcat("new.image.", i, ".xyz")>; if (iter==0) { if (i==1) { file xyz <"image.1.xyz">; (o,e,fcoll,tgz,ccoll,cxyz,abc)=runcp2k(cp2k,iter,1,xyz,ff,first,temp,ref,ng); } else { file xyz <single_file_mapper; file=@strcat("image.", i-1, ".xyz")>; (o,e,fcoll,tgz,ccoll,cxyz,abc)=runcp2k(cp2k,iter,i,xyz,ff,first,temp,ref,ng); } } else { file xyz <single_file_mapper; file=@strcat("image.", i, ".xyz")>; (o,e,fcoll,tgz,ccoll,cxyz,abc)=runcp2k(cp2k,iter,i,xyz,ff,first,temp,ref,ng); } } *.tx: No such file or directory :::::::::::::: cp2k.cf :::::::::::::: status.mode=provider use.provider.staging=false use.wrapper.staging=false wrapperlog.always.transfer=true execution.retries=0 lazy.errors=false provider.staging.pin.swiftfiles=false sitedir.keep=true file.gc.enabled=false :::::::::::::: cp2k.tc :::::::::::::: makena sh /bin/sh swift$ -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.
https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1048 Mihael Hategan <[email protected]> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|ASSIGNED |WAITING FOR USER INPUT --- Comment #2 from Mihael Hategan <[email protected]> 2013-08-10 18:21:03 --- Any updates on this? I remember committing a fix, but I haven't heard back if that worked (or rather said if it didn't work). -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.
https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1048 Michael Wilde <[email protected]> changed: What |Removed |Added ---------------------------------------------------------------------------- Status|WAITING FOR USER INPUT |RESOLVED Resolution| |FIXED --- Comment #3 from Michael Wilde <[email protected]> 2013-08-19 11:03:31 --- The users have been running regularly with this fix in place, and the NPE failure has not recurred. Im marking this as resolved. -- Configure bugmail: https://bugzilla.mcs.anl.gov/swift/userprefs.cgi?tab=email ------- You are receiving this mail because: ------- You are watching all bug changes.
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