[Swift-devel] Fwd: NumberFormatException
Mihael Hategan
hategan at mcs.anl.gov
Tue Jul 12 20:21:31 CDT 2011
gsiftp://host:port/path/somefile.txt means a relative path to
somefile.txt (i.e. typically /home/you/path/somefile.txt).
You probably want an absolute path, in which case you need two slashes
after the host[port]:
gsiftp://host:port//gpfs/...
You can look up the URL/URI RFCs for why that is (well, I'm not sure
they really explain why).
On Tue, 2011-07-12 at 17:14 -0500, Jonathan Monette wrote:
> 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
>
>
> _______________________________________________
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