[Swift-devel] Fwd: NumberFormatException

Wed Jul 13 11:29:58 CDT 2011

I am starting to believe that this maybe a bug.  I have this line in the log.

2011-07-13 16:17:50,835+0000 DEBUG vdl:dostageinfile FILE_STAGE_IN_START file=data.txt srchost=gridftp.pads.ci.uchicago.edu:2811 srcdir=/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test srcname=data.txt desthost=localhost destdir=script-20110713-1617-lzk6sxj3/shared/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test provider=gsiftp policy=DEFAULT

The desthost is localhost.  That is correct.  But why does the destdir have /gpfs in it?  My localhost is VM.  It does not have access to gpfs.

The files for this run are in ~jonmon/run.0002 on the ci machines.

On Jul 13, 2011, at 9:13 AM, Michael Wilde wrote:

> I was going to suggest that same as Sarah pointed out, suspecting that the short-form of single_file_mapper is not correctly parsing the GSIFTP URI.  If thats the case, please file it as a bug, Jon.
> 
> Can you try both forms of the mapper syntax with a known-good URI?
> 
> Thanks,
> 
> - Mike
> 
> 
> Thanks.  I just verified that something maybe wrong with the path.  I could not globus-url-copy that URI so I will continue to investigate
> 
> On Jul 12, 2011, at 4:59 PM, Sarah Kenny wrote:
> 
> i've used this successfully in the past:
> 
> file mybrain<single_file_mapper; file="gsiftp://calero.bsd.uchicago.edu/gpfs/pads/projects/stroke_recovery/dude.mgz")>;
> 
> it's been a while though...haven't tested with the latest swift...
> 
> On Tue, Jul 12, 2011 at 1:59 PM, Jonathan Monette <jonmon at utexas.edu> wrote:
> How does this syntax look when mapping with the GSIURI?  How does it work?  I am still getting errors when trying to map a file with a GSIURI.  It says file not found.  Maybe I have a different understanding on how it works.
> 
> The files and the logs are in ~jonmon/run.0001 on the ci machines.
> 
> On Jul 12, 2011, at 2:16 AM, Mihael Hategan wrote:
> 
> > You have a colon after the host name but no port. Either remove the
> > colon or put a number after it.
> >
> > On Mon, 2011-07-11 at 22:45 -0500, Jonathan Monette wrote:
> >> I actually meant to send this to swift-devel.
> >>
> >>
> >> Here is the background to the problem.  I have data on PADS, I am
> >> executing Swift on a VM, and I want to use OSG to compute with the
> >> data.  Before Mike left for vacation he said that you can map data in
> >> Swift using the GSIURI scheme but he did not tell me how.  What I did
> >> below is
> >>
> >>
> >> file
> >> data<"gsiftp://stor01.pads.ci.uchicago.edu:/gpfs/pads/projects/CI-CCR000013/jonmon/Swift/tests/cat_test/data.txt">;
> >>
> >>
> >> This does not seem to work in release 0.92.1 as the error below
> >> shows.  How do you map data in Swift using the GSIURI scheme?
> >>
> >> Begin forwarded message:
> >>
> >>> From: Jonathan Monette <jonmon at utexas.edu>
> >>>
> >>> Date: July 11, 2011 2:30:34 PM CDT
> >>>
> >>> To: swift-devel Devel <swift-devel at ci.uchicago.edu>
> >>>
> >>> Cc: Mihael Hategan Hategan <hategan at mcs.anl.gov>
> >>>
> >>> Subject: NumberFormatException
> >>>
> >>>
> >>> Mihael,
> >>>  I am getting this error using release 0.92.1.
> >>>
> >>> 2011-07-11 19:24:44,395+0000 INFO  unknown RUNID
> >>> id=run:20110711-1924-c944yl9c
> >>> 2011-07-11 19:24:44,508+0000 DEBUG VDL2ExecutionContext vdl:new @
> >>> script.kml, line: 69: java.lang.RuntimeException:
> >>> java.lang.NumberFormatException: For input string: ""
> >>> java.lang.RuntimeException: java.lang.NumberFormatException: For
> >>> input string: ""
> >>> Caused by: java.lang.RuntimeException:
> >>> java.lang.NumberFormatException: For input string: ""
> >>> at org.griphyn.vdl.mapping.AbsFile.exists(AbsFile.java:109)
> >>> at
> >>> org.griphyn.vdl.mapping.file.SingleFileMapper.existing(SingleFileMapper.java:24)
> >>> at
> >>> org.griphyn.vdl.mapping.RootDataNode.checkInputs(RootDataNode.java:97)
> >>> at
> >>> org.griphyn.vdl.mapping.RootDataNode.checkInputs(RootDataNode.java:75)
> >>> at
> >>> org.griphyn.vdl.mapping.RootDataNode.innerInit(RootDataNode.java:61)
> >>> at org.griphyn.vdl.mapping.RootDataNode.init(RootDataNode.java:37)
> >>> at org.griphyn.vdl.karajan.lib.New.function(New.java:126)
> >>> at org.griphyn.vdl.karajan.lib.VDLFunction.post(VDLFunction.java:68)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
> >>> 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:290)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.user.SequentialImplicitExecutionUDE.childCompleted(SequentialImplicitExecutionUDE.java:85)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.functions.Argument.post(Argument.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:32)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.functions.Map_Map.post(Map_Map.java:55)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.childCompleted(Sequential.java:44)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> >>> at org.globus.cog.karajan.workflow.nodes.Each.post(Each.java:31)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402)
> >>> at
> >>> org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173)
> >>> at
> >>> org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44)
> >>> at edu.emory.mathcs.backport.java.util.concurrent.Executors
> >>> $RunnableAdapter.call(Executors.java:431)
> >>> at
> >>> edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166)
> >>> at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor
> >>> $Worker.runTask(ThreadPoolExecutor.java:643)
> >>> at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor
> >>> $Worker.run(ThreadPoolExecutor.java:668)
> >>> at java.lang.Thread.run(Thread.java:636)
> >>> Caused by: java.lang.NumberFormatException: For input string: ""
> >>> at
> >>> java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
> >>> at java.lang.Integer.parseInt(Integer.java:493)
> >>> at java.lang.Integer.parseInt(Integer.java:514)
> >>> at
> >>> org.globus.cog.abstraction.impl.common.task.ServiceContactImpl.parse(ServiceContactImpl.java:90)
> >>> at
> >>> org.globus.cog.abstraction.impl.common.task.ServiceContactImpl.<init>(ServiceContactImpl.java:27)
> >>> at org.griphyn.vdl.mapping.AbsFile.getFileResource(AbsFile.java:84)
> >>> at org.griphyn.vdl.mapping.AbsFile.exists(AbsFile.java:99)
> >>> ... 63 more
> >>>
> >>> The files needed for this run are located in ~jonmon/run.0000 on the
> >>> ci machines.
> >>
> >>
> >
> >
> > _______________________________________________
> > Swift-devel mailing list
> > Swift-devel at ci.uchicago.edu
> > https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> 
> 
> 
> -- 
> Sarah Kenny
> Programmer
> University of Chicago, Computation Institute
> University of California Irvine, Dept. of Neurology
> 773-818-8300
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> 
> 
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
> 
> 
> 
> -- 
> Michael Wilde
> Computation Institute, University of Chicago
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 

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