Re: [ptp-dev] IOException Pipe closed

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Re: [ptp-dev] IOException Pipe closed

From: Matthew Fotzler <incongruous@xxxxxxxxx>
Date: Thu, 16 Jul 2009 15:47:20 -0500
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Greg,

As far as I can tell, there is no corresponding </stdout>.  Also, the
extra stdout tag shows up in a different place each time I run pop.

Matthew

On Thu, Jul 16, 2009 at 1:11 PM, Greg Watson<g.watson@xxxxxxxxxxxx> wrote:
> Matthew,
>
> Is there are corresponding </stdout> somewhere in the output, or has it just
> been lost?
>
> Greg
>
> On Jul 16, 2009, at 12:43 PM, Matthew Fotzler wrote:
>
>> Hi Greg,
>>
>> I added the debugging lines (I'm working from the cvs version of ptp).
>> The output is very large, so this is the beginning, what seems to be
>> the problem, and end.
>>
>> RTS Open_MPI@Local: new job #16777222
>> RTS Open_MPI@Local, job #16777222: jobState=STARTED
>> RTS Open_MPI@Local: new process #16777223
>> RTS Open_MPI@Local: created 1 new processes
>>
>> ...
>>
>> RTS job #16777222:> <stdout rank="0">time_mix_freq =     17</stdout>
>> RTS job #16777222:> <stdout rank="0">Time m<stdout rank="0">ixing
>> option:</stdout>
>> RTS job #16777222:> <stdout rank="0">  avgfit -- time averaging</stdout>
>> RTS job #16777222:> <stdout rank="0">  with timestep chosen to fit
>> exactly into one day or coupling interval</stdout>
>> RTS job #16777222:> <stdout rank="0">Averaging time steps are at step
>> numbers2,17 each day</stdout>
>> RTS job #16777222:> <stdout rank="0"> </stdout>
>>
>> ...
>>
>> RTS job #16777222:> <stdout
>>
>> rank="0">------------------------------------------------------------------------</stdout>
>> RTS job #16777222:> <stdout rank="0"> </stdout>
>> RTS job #16777222:> <stdout rank="0">POP exiting...</stdout>
>> RTS job #16777222:> <stdout rank="0"> Successful completion of POP
>> run</stdout>
>> RTS job #16777222:> <stdout rank="0"> </stdout>
>> RTS job #16777222:> <stdout
>>
>> rank="0">------------------------------------------------------------------------</stdout>
>> RTS Open_MPI@Local, job #16777222: jobState=ERROR
>> RTS Open_MPI@Local, process #16777223: processState=EXITED
>>
>> The last line that PTP prints in the process details window is "avgfit
>> -- time averaging".
>>
>> Thanks,
>> Matthew
>>
>> On Wed, Jul 15, 2009 at 5:26 PM, Greg Watson<g.watson@xxxxxxxxxxxx> wrote:
>>>
>>> Hi Matthew,
>>>
>>> Please make sure there are no plugins from older builds in your eclipse
>>> plugins folder. Also, I'd suggest starting with a clean workspace and
>>> creating a new resource manager.
>>>
>>> If neither of those things work, please create the file
>>> "<install_dir>/eclipse/Eclipse.app/Contents/MacOS/.options" with the
>>> lines:
>>>
>>> org.eclipse.ptp.rm.core/debug=true
>>> org.eclipse.ptp.rm.core/debug/rts=true
>>> org.eclipse.ptp.rm.core/debug/rts/job/output=true
>>>
>>> Then launch Eclipse from the command line with the -debug flag (i.e.
>>> <install_dir>/eclipse/eclipse -debug).
>>>
>>> When you run the application, you should see output from Eclipse on
>>> stdout.
>>> Please send that to me.
>>>
>>> Regards,
>>> Greg
>>>
>>>
>>>
>>> On Jul 15, 2009, at 4:08 PM, Matthew Fotzler wrote:
>>>
>>>> Greg,
>>>>
>>>> I tried the 200907131120 build and experienced the same problem.  Is
>>>> there a different build I should try?
>>>>
>>>> Thanks,
>>>> Matthew
>>>>
>>>> On Wed, Jul 15, 2009 at 2:22 PM, Greg Watson<g.watson@xxxxxxxxxxxx>
>>>> wrote:
>>>>>
>>>>> Matthew,
>>>>>
>>>>> Which build of PTP 3.0 are you using?Please try the latest and let me
>>>>> know
>>>>> if that fixes the problem.
>>>>>
>>>>> Regards,
>>>>> Greg
>>>>>
>>>>> On Jul 15, 2009, at 3:15 PM, Matthew Fotzler <incongruous@xxxxxxxxx>
>>>>> wrote:
>>>>>
>>>>>> Hi Greg,
>>>>>>
>>>>>> Thank you for your help.  I updated to OpenMPI 1.3.3, but I am now
>>>>>> receiving a different error.  Do you have any ideas what might be
>>>>>> causing this?
>>>>>>
>>>>>> org.eclipse.core.runtime.CoreException: Failed to parse output of Open
>>>>>> MPI command. Check output for errors.
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.OpenMPIPlugin.coreErrorException(OpenMPIPlugin.java:86)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIRuntimeSystemJob.doWaitExecution(OpenMPIRuntimeSystemJob.java:591)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.core.rtsystem.AbstractToolRuntimeSystemJob.run(AbstractToolRuntimeSystemJob.java:258)
>>>>>>  at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
>>>>>> Caused by: java.io.IOException: Unknown XML element: stdout
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIProcessMapXml13Parser.parse(OpenMPIProcessMapXml13Parser.java:518)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIRuntimeSystemJob$1.run(OpenMPIRuntimeSystemJob.java:231)
>>>>>>
>>>>>>
>>>>>> java.io.IOException: Pipe closed
>>>>>>  at
>>>>>>
>>>>>> java.io.PipedInputStream.checkStateForReceive(PipedInputStream.java:190)
>>>>>>  at java.io.PipedInputStream.receive(PipedInputStream.java:156)
>>>>>>  at java.io.PipedOutputStream.write(PipedOutputStream.java:129)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamListenerToOutputStream.newBytes(InputStreamListenerToOutputStream.java:35)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamObserver.newBytes(InputStreamObserver.java:127)
>>>>>>  at
>>>>>>
>>>>>>
>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamObserver.run(InputStreamObserver.java:146)
>>>>>>
>>>>>>
>>>>>> Matthew Fotzler
>>>>>>
>>>>>> On Wed, Jul 15, 2009 at 10:31 AM, Greg Watson<g.watson@xxxxxxxxxxxx>
>>>>>> wrote:
>>>>>>>
>>>>>>> Hi Matthew,
>>>>>>>
>>>>>>> Which version of Open MPI 1.3 do you have installed? Older versions
>>>>>>> cause
>>>>>>> a
>>>>>>> problem if the program output contains a "<" or "&" character which
>>>>>>> confuse
>>>>>>> the XML parser. A fix for this is in 1.3.3 and later.
>>>>>>>
>>>>>>> Regards,
>>>>>>> Greg
>>>>>>>
>>>>>>> On Jul 14, 2009, at 12:39 PM, Matthew Fotzler wrote:
>>>>>>>
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I'm trying to run Parallel Ocean Program with PTP HEAD.  I'm
>>>>>>>> receiving
>>>>>>>> an "Internal Error" part way through execution.  I'm getting some
>>>>>>>> console output, but not all of it.  Then the process is terminated
>>>>>>>> abruptly and there are 2 errors logged.
>>>>>>>>
>>>>>>>> org.eclipse.core.runtime.CoreException: Failed to parse output of
>>>>>>>> Open
>>>>>>>> MPI command. Check output for errors.
>>>>>>>>     at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.OpenMPIPlugin.coreErrorException(OpenMPIPlugin.java:86)
>>>>>>>>     at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIRuntimeSystemJob.doWaitExecution(OpenMPIRuntimeSystemJob.java:591)
>>>>>>>>     at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.core.rtsystem.AbstractToolRuntimeSystemJob.run(AbstractToolRuntimeSystemJob.java:258)
>>>>>>>>     at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
>>>>>>>> Caused by: java.io.IOException: The content of elements must consist
>>>>>>>> of well-formed character data or markup.
>>>>>>>>     at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIProcessMapXml13Parser.parse(OpenMPIProcessMapXml13Parser.java:518)
>>>>>>>>     at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.mpi.openmpi.core.rtsystem.OpenMPIRuntimeSystemJob$1.run(OpenMPIRuntimeSystemJob.java:231)
>>>>>>>>
>>>>>>>>
>>>>>>>> java.io.IOException: Pipe closed
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>> java.io.PipedInputStream.checkStateForReceive(PipedInputStream.java:190)
>>>>>>>> at java.io.PipedInputStream.receive(PipedInputStream.java:156)
>>>>>>>> at java.io.PipedOutputStream.write(PipedOutputStream.java:129)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamListenerToOutputStream.newBytes(InputStreamListenerToOutputStream.java:35)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamObserver.newBytes(InputStreamObserver.java:127)
>>>>>>>> at
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> org.eclipse.ptp.rm.core.utils.InputStreamObserver.run(InputStreamObserver.java:146)
>>>>>>>>
>>>>>>>> This is my session data:
>>>>>>>> eclipse.buildId=I20090611-1540
>>>>>>>> java.version=1.5.0_19
>>>>>>>> java.vendor=Apple Inc.
>>>>>>>> BootLoader constants: OS=macosx, ARCH=x86, WS=cocoa, NL=en_US
>>>>>>>> Framework arguments:  -product org.eclipse.sdk.ide
>>>>>>>>
>>>>>>>> Thanks for your help!
>>>>>>>> Matthew Fotzler (UIUC)
>>>>>>>> _______________________________________________
>>>>>>>> ptp-dev mailing list
>>>>>>>> ptp-dev@xxxxxxxxxxx
>>>>>>>> https://dev.eclipse.org/mailman/listinfo/ptp-dev
>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
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>>>>>
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References:
- [ptp-dev] IOException Pipe closed
  - From: Matthew Fotzler
- Re: [ptp-dev] IOException Pipe closed
  - From: Greg Watson
- Re: [ptp-dev] IOException Pipe closed
  - From: Matthew Fotzler
- Re: [ptp-dev] IOException Pipe closed
  - From: Greg Watson
- Re: [ptp-dev] IOException Pipe closed
  - From: Matthew Fotzler
- Re: [ptp-dev] IOException Pipe closed
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- Re: [ptp-dev] IOException Pipe closed
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- Re: [ptp-dev] IOException Pipe closed
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