[Swift-user] swift execution problem
Michael Wilde
wilde at mcs.anl.gov
Thu Mar 19 08:27:02 CDT 2009
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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