[Swift-devel] Fwd: NumberFormatException
Mihael Hategan
hategan at mcs.anl.gov
Wed Jul 13 18:57:54 CDT 2011
The full log will help here, but the "Reply wait timeout" exception is
not necessarily an indication of a bad path (though I'm not saying it's
not).
In the meantime, can you check that you have GLOBUS_HOSTNAME set
properly and that your client machine is not behind a firewall?
On Wed, 2011-07-13 at 13:00 -0500, Jonathan Monette wrote:
> Mike mentioned that this path is correct and makes sense. I was able
> to use the globus-url-copy from the swift bin directory and make a
> copy from that GSIURI. The error that I am receiving is
>
>
> Caused by: Exception in getFile
> Caused by:
> org.globus.cog.abstraction.impl.file.IrrecoverableResourceException:
> Exception in getFile
> Caused by: org.globus.ftp.exception.ServerException: Reply wait
> timeout. (error code 4)
> at
> org.globus.cog.karajan.workflow.nodes.functions.KException.function(KException.java:29)
> at
> org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:27)
> 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.FlowElementWrapper.event(FlowElementWrapper.java:230)
> 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)
>
>
> I don't know if I mentioned this but this is with the 0.92.1 release.
>
>
> On Jul 13, 2011, at 11:29 AM, Jonathan Monette wrote:
>
> > 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
> > >
> > >
> >
> >
>
> _______________________________________________
> Swift-devel mailing list
> Swift-devel at ci.uchicago.edu
> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-devel
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