[Swift-devel] User script gets null pointer exception
Ben Clifford
benc at hawaga.org.uk
Thu Mar 19 10:12:51 CDT 2009
Note that this is a different error to the original message which
Yue posted (and which I just answered) on swift-user.
The log that you show below is 9 days old and is not a log for the error
that Yue reported.
On Thu, 19 Mar 2009, Michael Wilde wrote:
> Yue, I should have clarified: this is a Swift bug.
>
> Its perhaps caused by some error in your program, but Swift should never get a
> null pointer exception.
>
> Ben, Mihael - The log is in:
>
> /home/yuechen/PTMapZhao/PTMap/PTMap-20090310-1746-zszi94b6.log
>
> The error seems to be related to some boundary condition on the array "texts"
> which maps Yue's 375 fasta files, fast01 .. fasta375
>
> This message is in the log:
>
> 2009-03-10 17:46:36,188-0500 INFO AbstractDataNode Found data
> org.griphyn.vdl.mapping.RootDataNode identifier
> tag:benc at ci.uchicago.edu,2008:swift:dataset:20090310-1746-f12dnzdd:720000000382
> \
> type Inputfile with no value at dataset=parameter (closed).$
> 2009-03-10 17:46:36,188-0500 INFO New NEW
> id=tag:benc at ci.uchicago.edu,2008:swift:dataset:20090310-1746-f12dnzdd:720000000382
> 2009-03-10 17:46:36,190-0500 DEBUG VDL2ExecutionContext Getting value for
> array texts.$[]/375 which is not permitted.
> Getting value for array texts.$[]/375 which is not permitted.
> vdl:getfieldvalue @ PTMap.kml, line: 124
> sys:parallelfor @ PTMap.kml, line: 124
> sys:sequential @ PTMap.kml, line: 123
> doall @ PTMap.kml, line: 170
> sys:sequential @ PTMap.kml, line: 169
> vdl:mainp @ PTMap.kml, line: 168
> mainp @ vdl.k, line: 165
> vdl:mains @ PTMap.kml, line: 166
> vdl:mains @ PTMap.kml, line: 166
> rlog:restartlog @ PTMap.kml, line: 164
> kernel:project @ PTMap.kml, line: 2
> PTMap-20090310-1746-zszi94b6
> Caused by: java.lang.RuntimeException: Getting value for array texts.$[]/375
> which is not permitted.
> at
> org.griphyn.vdl.karajan.lib.GetFieldValue.function(GetFieldValue.java:53)
> at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)
> at
> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> at
> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> at
> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> at
> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
>
>
>
> -------- Original Message --------
> Subject: Re: [Swift-user] swift execution problem
> Date: Thu, 19 Mar 2009 08:27:02 -0500
> From: Michael Wilde <wilde at mcs.anl.gov>
> To: Yue, Chen - BMD <yuechen at bsd.uchicago.edu>
> CC: swift-user at ci.uchicago.edu
> References:
> <AD1FA15416EEBC49A0FE4F8B0C8AD7C5158C28 at ADM-EXCHVS04.bsdad.uchicago.edu>
>
> Yue, what version of Swift are you using?
>
> Please send the first few lines of your output file, where it says
> something like:
>
> Swift svn swift-r2701 cog-r2332
>
> RunID: 20090319-0820-19zttiq9
>
> (in fact please send the whole output file, stdout/err)
>
> Ive tried to run your code in a near-identical test and I cant reproduce
> the failure. Ive tried with both swift0.8 and the latest svn rev, and
> both seem to work.
>
> Also please can you post the pathname of the directory in which you are
> testing (I assume you are running this on a CI machine?) so that I can
> look at your logfile? And make it publicly accessible?
>
> Thanks,
>
> - Mike
>
>
> On 3/18/09 6:32 PM, Yue, Chen - BMD wrote:
> > Hi,
> > I'm new to Swift programming. I was able to run a swift script before, but
> > I couldn't run it now. I'm wondering if someone can help me figure out why.
> > The swift script, sites.xml, tc.data, and all the error messages are copied
> > in this email. Thank you!
> > Regards,
> > Chen, Yue
> > *********************
> > Swift script
> > *********************
> > type Fasta {}
> > type PTMapOut {}
> > type Solution {}
> > type Inputfile {}
> > app (PTMapOut ofile) PTMap (Solution sfile, Fasta fastafile, Inputfile
> > input, Inputfile parameter)
> > {
> > PTMap @filename(sfile) @filename(fastafile) @filename(input)
> > @filename(parameter) stdout=@filename(ofile
> > <mailto:stdout=@filename(ofile>);
> > }
> > Fasta texts[] <filesys_mapper;prefix="fasta">;
> >
> > doall(Fasta texts[])
> > {
> > Solution sfile <"BSASolution.mzXML">;
> > Inputfile input <"inputs.txt">;
> > Inputfile parameter <"parameters.txt">;
> > foreach p in texts {
> > PTMapOut r <regexp_mapper;
> > source=@p <mailto:source=@p>,
> > match="fasta(.*)",
> > transform="\\1.out <file://\\1.out>"
> > >;
> > r = PTMap(sfile, p, input, parameter);
> > }
> > }
> > // Main
> > doall(texts);
> > **************
> > sites.xml
> > **************
> > <pool handle="localhost">
> > <gridftp url="local://localhost" />
> > <execution provider="local" />
> > <workdirectory >/var/tmp</workdirectory>
> > <profile namespace="karajan" key="jobThrottle">0</profile>
> > </pool>
> > **************
> > tc.data
> > **************
> > localhost echo /bin/echo INSTALLED
> > INTEL32::LINUX null
> > localhost cat /bin/cat INSTALLED
> > INTEL32::LINUX null
> > localhost ls /bin/ls INSTALLED
> > INTEL32::LINUX null
> > localhost grep /bin/grep INSTALLED
> > INTEL32::LINUX null
> > localhost sort /bin/sort INSTALLED
> > INTEL32::LINUX null
> > localhost paste /bin/paste INSTALLED
> > INTEL32::LINUX null
> > localhost PTMap /home/yuechen/PTMap/PTMap INSTALLED
> > INTEL32::LINUX null
> > **************
> > Error messages
> > **************
> > [yuechen at communicado PTMap]$ swift PTMap.swift
> > Execution failed:
> > java.lang.NullPointerException
> > at
> > org.globus.cog.abstraction.impl.common.task.ServiceImpl.toString(ServiceImpl.java:156)
> > at java.lang.String.valueOf(String.java:2577)
> > at java.lang.StringBuffer.append(StringBuffer.java:220)
> > at
> > org.globus.cog.karajan.workflow.nodes.grid.GridNode.function(GridNode.java:31)
> > at
> > org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:45)
> > at
> > org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.ExecuteFile.notificationEvent(ExecuteFile.java:163)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:45)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> > at
> > org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> > at
> > org.globus.cog.karajan.workflow.nodes.user.UserDefinedElement.childCompleted(UserDefinedElement.java:283)
> > at
> > org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.If.childCompleted(If.java:30)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> > at
> > org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
> > at
> > org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> > at
> > org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)
> > at
> > org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)
> > at
> > org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren(AbstractFunction.java:40)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:240)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:281)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)
> > at
> > org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)
> > at
> > org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)
> > at
> > org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)
> > at
> > org.globus.cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)
> >
> >
> > This email is intended only for the use of the individual or entity to which
> > it is addressed and may contain information that is privileged and
> > confidential. If the reader of this email message is not the intended
> > recipient, you are hereby notified that any dissemination, distribution, or
> > copying of this communication is prohibited. If you have received this email
> > in error, please notify the sender and destroy/delete all copies of the
> > transmittal. Thank you.
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Swift-user mailing list
> > Swift-user at ci.uchicago.edu
> > http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
> _______________________________________________
> Swift-user mailing list
> Swift-user at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-user
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> http://mail.ci.uchicago.edu/mailman/listinfo/swift-devel
>
>
More information about the Swift-devel
mailing list