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 11:43:50 -0500
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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
>>>>>
>>>>> _______________________________________________
>>>>> 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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Follow-Ups:
- Re: [ptp-dev] IOException Pipe closed
  - From: Greg Watson

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
  - From: Greg Watson

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