[Swift-devel] Fwd: NumberFormatException

Jonathan Monette jonmon at utexas.edu
Wed Jul 13 13:00:24 CDT 2011 

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
>> 
> 

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