[Swift-devel] User script gets null pointer exception
Michael Wilde
wilde at mcs.anl.gov
Thu Mar 19 09:22:35 CDT 2009
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)
>
>
>
>
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