[Swift-user] swift execution problem
Michael Wilde
wilde at mcs.anl.gov
Thu Mar 19 09:17:43 CDT 2009
Yue, I found the log for the failing run in your working dir.
I'll post it to the swift-devel list for the developers to look at.
The problem seems related to your specific data (your 375 fasta files)
but even when I copy your data I cant repro the problem, at least not
using "echo" instead of "ptmap".
- Mike
On 3/19/09 8:27 AM, Michael Wilde wrote:
> 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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