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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Hi Michael,</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>I used swift version 0.8. I was able to run the same swift script last week, but I don't know why I cannot run it now. Yesterday, I was trying to set up sites.xml and tc.data for NCSA and SDSC clusters, but it didn't run. So I removed those configurations and just used all the original files to see if I can still run swift. That's when I ran into errors. The sites.xml and tc.data were in the /home/yuechen/swift-0.8/etc/. PTMap run by itself seems normal. To test PTMap, I use the following command in PTMap directory at /home/yuechen/PTMap/:</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>$ ./PTMap BSASolution.mzXML fasta172 inputs.txt parameters.txt</FONT></DIV><FONT face=Arial size=2></FONT></DIV>
<P><FONT face=Arial size=2>Thank you very much for help.</FONT></P>
<P><FONT face=Arial size=2>Regards,</FONT></P>
<P><FONT face=Arial size=2>Chen, Yue</FONT><FONT><FONT face=Arial><BR><FONT size=2></FONT></FONT></P></FONT>
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<FONT face=Tahoma size=2><B>From:</B> Michael Wilde [mailto:wilde@mcs.anl.gov]<BR><B>Sent:</B> Thu 3/19/2009 9:22 AM<BR><B>To:</B> swift-devel<BR><B>Cc:</B> Yue, Chen - BMD; Zhao Zhang<BR><B>Subject:</B> User script gets null pointer exception<BR></FONT><BR></DIV>
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<P><FONT size=2>Yue, I should have clarified: this is a Swift bug.<BR><BR>Its perhaps caused by some error in your program, but Swift should never<BR>get a null pointer exception.<BR><BR>Ben, Mihael - The log is in:<BR><BR>/home/yuechen/PTMapZhao/PTMap/PTMap-20090310-1746-zszi94b6.log<BR><BR>The error seems to be related to some boundary condition on the array<BR>"texts" which maps Yue's 375 fasta files, fast01 .. fasta375<BR><BR>This message is in the log:<BR><BR>2009-03-10 17:46:36,188-0500 INFO AbstractDataNode Found data<BR>org.griphyn.vdl.mapping.RootDataNode identifier<BR>tag:benc@ci.uchicago.edu,2008:swift:dataset:20090310-1746-f12dnzdd:720000000382<BR>\<BR>type Inputfile with no value at dataset=parameter (closed).$<BR>2009-03-10 17:46:36,188-0500 INFO New NEW<BR>id=tag:benc@ci.uchicago.edu,2008:swift:dataset:20090310-1746-f12dnzdd:720000000382<BR>2009-03-10 17:46:36,190-0500 DEBUG VDL2ExecutionContext Getting value<BR>for array texts.$[]/375 which is not permitted.<BR>Getting value for array texts.$[]/375 which is not permitted.<BR> vdl:getfieldvalue @ PTMap.kml, line: 124<BR> sys:parallelfor @ PTMap.kml, line: 124<BR> sys:sequential @ PTMap.kml, line: 123<BR> doall @ PTMap.kml, line: 170<BR> sys:sequential @ PTMap.kml, line: 169<BR> vdl:mainp @ PTMap.kml, line: 168<BR> mainp @ vdl.k, line: 165<BR> vdl:mains @ PTMap.kml, line: 166<BR> vdl:mains @ PTMap.kml, line: 166<BR> rlog:restartlog @ PTMap.kml, line: 164<BR> kernel:project @ PTMap.kml, line: 2<BR> PTMap-20090310-1746-zszi94b6<BR>Caused by: java.lang.RuntimeException: Getting value for array<BR>texts.$[]/375 which is not permitted.<BR> at<BR>org.griphyn.vdl.karajan.lib.GetFieldValue.function(GetFieldValue.java:53)<BR> at<BR>org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:67)<BR> at<BR>org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR> at<BR>org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR> at<BR>org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR> at<BR>org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR><BR><BR><BR>-------- Original Message --------<BR>Subject: Re: [Swift-user] swift execution problem<BR>Date: Thu, 19 Mar 2009 08:27:02 -0500<BR>From: Michael Wilde <wilde@mcs.anl.gov><BR>To: Yue, Chen - BMD <yuechen@bsd.uchicago.edu><BR>CC: swift-user@ci.uchicago.edu<BR>References:<BR><AD1FA15416EEBC49A0FE4F8B0C8AD7C5158C28@ADM-EXCHVS04.bsdad.uchicago.edu><BR><BR>Yue, what version of Swift are you using?<BR><BR>Please send the first few lines of your output file, where it says<BR>something like:<BR><BR>Swift svn swift-r2701 cog-r2332<BR><BR>RunID: 20090319-0820-19zttiq9<BR><BR>(in fact please send the whole output file, stdout/err)<BR><BR>Ive tried to run your code in a near-identical test and I cant reproduce<BR>the failure. Ive tried with both swift0.8 and the latest svn rev, and<BR>both seem to work.<BR><BR>Also please can you post the pathname of the directory in which you are<BR>testing (I assume you are running this on a CI machine?) so that I can<BR>look at your logfile? And make it publicly accessible?<BR><BR>Thanks,<BR><BR>- Mike<BR><BR><BR>On 3/18/09 6:32 PM, Yue, Chen - BMD wrote:<BR>> Hi,<BR>> <BR>> I'm new to Swift programming. I was able to run a swift script before,<BR>> but I couldn't run it now. I'm wondering if someone can help me figure<BR>> out why. The swift script, sites.xml, tc.data, and all the error<BR>> messages are copied in this email. Thank you!<BR>> <BR>> Regards,<BR>> <BR>> Chen, Yue<BR>> <BR>> *********************<BR>> Swift script<BR>> *********************<BR>> type Fasta {}<BR>> type PTMapOut {}<BR>> type Solution {}<BR>> type Inputfile {}<BR>> app (PTMapOut ofile) PTMap (Solution sfile, Fasta fastafile, Inputfile<BR>> input, Inputfile parameter)<BR>> {<BR>> PTMap @filename(sfile) @filename(fastafile) @filename(input)<BR>> @filename(parameter) stdout=@filename(ofile<BR>> <<A href="mailto:stdout=@filename(ofile">mailto:stdout=@filename(ofile</A>>);<BR>> }<BR>> Fasta texts[] <filesys_mapper;prefix="fasta">;<BR>><BR>> doall(Fasta texts[])<BR>> {<BR>> Solution sfile <"BSASolution.mzXML">;<BR>> Inputfile input <"inputs.txt">;<BR>> Inputfile parameter <"parameters.txt">;<BR>> foreach p in texts {<BR>> PTMapOut r <regexp_mapper;<BR>> source=@p <<A href="mailto:source=@p">mailto:source=@p</A>>,<BR>> match="fasta(.*)",<BR>> transform="\\1.out <<A href="file://1.out/">file://\\1.out</A>>"<BR>> >;<BR>> r = PTMap(sfile, p, input, parameter);<BR>> }<BR>> }<BR>> // Main<BR>> doall(texts);<BR>> **************<BR>> sites.xml<BR>> **************<BR>> <pool handle="localhost"><BR>> <gridftp url="local://localhost" /><BR>> <execution provider="local" /><BR>> <workdirectory >/var/tmp</workdirectory><BR>> <profile namespace="karajan" key="jobThrottle">0</profile><BR>> </pool><BR>> **************<BR>> tc.data<BR>> **************<BR>> localhost echo /bin/echo INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost cat /bin/cat INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost ls /bin/ls INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost grep /bin/grep INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost sort /bin/sort INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost paste /bin/paste INSTALLED <BR>> INTEL32::LINUX null<BR>> localhost PTMap /home/yuechen/PTMap/PTMap INSTALLED <BR>> INTEL32::LINUX null<BR>> **************<BR>> Error messages<BR>> **************<BR>> [yuechen@communicado PTMap]$ swift PTMap.swift<BR>> Execution failed:<BR>> java.lang.NullPointerException<BR>> at<BR>> org.globus.cog.abstraction.impl.common.task.ServiceImpl.toString(ServiceImpl.java:156)<BR>> at java.lang.String.valueOf(String.java:2577)<BR>> at java.lang.StringBuffer.append(StringBuffer.java:220)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.grid.GridNode.function(GridNode.java:31)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:45)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.ExecuteFile.notificationEvent(ExecuteFile.java:163)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:45)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.user.UserDefinedElement.childCompleted(UserDefinedElement.java:283)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.If.childCompleted(If.java:30)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:33)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:335)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:173)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:299)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:46)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:51)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:27)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.executeChildren(AbstractFunction.java:40)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:240)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:281)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:393)<BR>> at<BR>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:332)<BR>> at<BR>> org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:227)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:125)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventBus.sendHooked(EventBus.java:99)<BR>> at<BR>> org.globus.cog.karajan.workflow.events.EventWorker.run(EventWorker.java:69)<BR>> <BR>> <BR>> <BR>><BR>><BR>> This email is intended only for the use of the individual or entity to<BR>> which it is addressed and may contain information that is privileged and<BR>> confidential. 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