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Re: [ptp-user] Failed to parse output of OpenMPI command
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Greg,
I'm using one of my computers at home as the remote machine. Is it
okay if I e-mail you directly about access?
Matthew
On Wed, Aug 19, 2009 at 1:44 PM, Greg Watson<g.watson@xxxxxxxxxxxx> wrote:
> Matthew,
>
> What machine are you on? It might be easier if I log on and take a look.
>
> Greg
>
> On Aug 19, 2009, at 2:32 PM, Matthew Fotzler wrote:
>
>> Greg,
>>
>> Yes, ompi_info reports 1.4a1r21838.
>>
>> I tried recreating the resource manager (the only thing I changed was
>> provider to RSE and location to my RSE connection) and recompiling my
>> workspace, but I'm still running into the same problem. Is there
>> anything else that might be going wrong on this end?
>>
>> Matthew
>>
>> On Wed, Aug 19, 2009 at 1:19 PM, Greg Watson<g.watson@xxxxxxxxxxxx> wrote:
>>>
>>> Matthew,
>>>
>>> Does that mean you're using Open MPI 1.4?
>>>
>>> Have you modified any configuration settings in the resource manager? Try
>>> removing and creating a new resource manager.
>>>
>>> Recompiling your code might also be worth a shot.
>>>
>>> Greg
>>>
>>> On Aug 19, 2009, at 1:24 PM, Matthew Fotzler wrote:
>>>
>>>> Greg,
>>>>
>>>> Thank you for looking into this for me. Unfortunately, I am still
>>>> having problems.
>>>>
>>>> I updated PTP first and tried running my project. I didn't run into
>>>> any parsing errors, but there was no output to the console or the job
>>>> windows in the runtime perspective (I had the combine to console
>>>> output option checked). The debug console output was correct; it just
>>>> wasn't showing up in eclipse.
>>>>
>>>> After that, I updated to the newest svn revision of OpenMPI in case
>>>> Ralph's changes were necessary too. Now I'm getting the following
>>>> error:
>>>>
>>>> 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:563)
>>>> 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:226)
>>>>
>>>> Matthew
>>>>
>>>> On Wed, Aug 19, 2009 at 9:47 AM, Greg Watson<g.watson@xxxxxxxxxxxx>
>>>> wrote:
>>>>>
>>>>> Matthew,
>>>>>
>>>>> After spending way too long on this, I've come to the conclusion that
>>>>> it
>>>>> is
>>>>> not possible to reliably parse the output from Open MPI 1.3.3 and
>>>>> below.
>>>>> I've implemented a work around, but unfortunately it means that the
>>>>> output
>>>>> you get from the program is wrapped in XML tags, but at least you
>>>>> shouldn't
>>>>> be seeing the parser errors any more. The good news is that Ralph has
>>>>> fixed
>>>>> the problems in Open MPI 1.4, and it looks like this will be back
>>>>> ported
>>>>> to
>>>>> 1.3.4.
>>>>>
>>>>> I found another problem with RSE interpreting XML escape sequences,
>>>>> which
>>>>> may have also been causing problems when using DStore connections (but
>>>>> not
>>>>> ssh connections). I've implemented a work around for this, but it's
>>>>> really
>>>>> an RSE bug that needs to be fixed.
>>>>>
>>>>> I've checked in the changes if you'd like to give it a go. Let me know
>>>>> if
>>>>> you still have problems.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Greg
>>>>>
>>>>> On Aug 13, 2009, at 12:23 PM, Matthew Fotzler wrote:
>>>>>
>>>>>> Hey Greg,
>>>>>>
>>>>>> I setup NAMD to see if I would have the same problem. I'm still
>>>>>> getting the same error, but I also get a little output in the PTP
>>>>>> Runtime perspective. Here's the debug output in context:
>>>>>>
>>>>>> <stdout rank=
>>>>>> RTS job #50331652: "0">Info: 1 NAMD 2.7b1 Linux-x86_64 1
>>>>>> 4pcnuggets rdt-test
</stdout>
>>>>>> <stdout rank="0">Inf
>>>>>> RTS job #50331652: o: Running on 1 processors.
</stdout>
>>>>>> <stdout rank="0">Info: Charm++/Converse parallel runtime
>>>>>> RTS job #50331652: startup completed at 0.00456786 s
</st
>>>>>> dout>
>>>>>> <stdout rank="0">Info: 1.49565 MB of memory in use
>>>>>> RTS job #50331652: based on CmiMemoryUsage
</stdout>
>>>>>> <stdout rank="0">Info: Changed directory to src
</stdou
>>>>>> RTS job #50331652: t>
>>>>>> <stdout rank="0">Info: Configuration file is alanin
</stdout>
>>>>>> <stdout rank="0">TCL: Suspendi
>>>>>> RTS job #50331652: ng until startup complete.
</stdout>
>>>>>>
>>>>>> The last line of output I see in the PTP Runtime view is "Info:
>>>>>> Running on 1 processors."
>>>>>>
>>>>>> I updated my PTP from CVS this morning and I'm still using OpenMPI
>>>>>> 1.4a1r21763.
>>>>>>
>>>>>> Matthew
>>>>>>
>>>>>> On Fri, Aug 7, 2009 at 3:09 PM, Matthew Fotzler<incongruous@xxxxxxxxx>
>>>>>> wrote:
>>>>>>>
>>>>>>> Greg,
>>>>>>>
>>>>>>> I'm using RSE for the connection as well as the resource manager. Is
>>>>>>> there anything I can do to help find the problem?
>>>>>>>
>>>>>>> Matthew
>>>>>>>
>>>>>>> On Fri, Aug 7, 2009 at 2:56 PM, Greg Watson<g.watson@xxxxxxxxxxxx>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Hi Matthew,
>>>>>>>>
>>>>>>>> I don't think the output you're seeing is the problem. I haven't
>>>>>>>> been
>>>>>>>> able
>>>>>>>> to reproduce it yet either.
>>>>>>>>
>>>>>>>> Are you using Remote Tools or RSE for the connection?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Greg
>>>>>>>>
>>>>>>>> On Aug 6, 2009, at 10:46 AM, Matthew Fotzler wrote:
>>>>>>>>
>>>>>>>>> Hey Greg,
>>>>>>>>>
>>>>>>>>> Sure. The output is quite large, so I hope sending as an
>>>>>>>>> attachment
>>>>>>>>> is okay. debug.log is the debug output eclipse gives me when I try
>>>>>>>>> to
>>>>>>>>> run the job through PTP, and ompi.log is the output I get when I
>>>>>>>>> run
>>>>>>>>> from a terminal.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>> Matthew
>>>>>>>>>
>>>>>>>>> On Wed, Aug 5, 2009 at 1:32 PM, Greg Watson<g.watson@xxxxxxxxxxxx>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> Hi Matthew,
>>>>>>>>>>
>>>>>>>>>> If there's a newline between "</std" and "out>" then it is likely
>>>>>>>>>> to
>>>>>>>>>> be
>>>>>>>>>> the
>>>>>>>>>> problem as XML names cannot contain whitespace. Can you send the
>>>>>>>>>> actual
>>>>>>>>>> output from POP at this point?
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Greg
>>>>>>>>>>
>>>>>>>>>> On Aug 5, 2009, at 12:48 PM, Matthew Fotzler wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> I'm using PTP 3.0 from CVS and OpenMPI 1.4a1r21763 (yesterday's
>>>>>>>>>>> nightly build). I'm trying to run the Parallel Ocean Program
>>>>>>>>>>> remotely
>>>>>>>>>>> and am receiving the following:
>>>>>>>>>>>
>>>>>>>>>>> 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:575)
>>>>>>>>>>> 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 element type "stdout" must be
>>>>>>>>>>> terminated by the matching end-tag "</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:232)
>>>>>>>>>>>
>>>>>>>>>>> Looking at the debug output, I see some lines that look like:
>>>>>>>>>>>
>>>>>>>>>>> RTS job #100663327: <stdout
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> rank="0">------------------------------------------------------------------------
</std
>>>>>>>>>>> RTS job #100663327:
>>>>>>>>>>>
>>>>>>>>>>> RTS job #100663327: out>
>>>>>>>>>>>
>>>>>>>>>>> I'm not sure if these are the culprit or not. Any ideas what
>>>>>>>>>>> might
>>>>>>>>>>> be
>>>>>>>>>>> causing this?
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>> Matthew Fotzler
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> ptp-user mailing list
>>>>>>>>>>> ptp-user@xxxxxxxxxxx
>>>>>>>>>>> https://dev.eclipse.org/mailman/listinfo/ptp-user
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> ptp-user mailing list
>>>>>>>>>> ptp-user@xxxxxxxxxxx
>>>>>>>>>> https://dev.eclipse.org/mailman/listinfo/ptp-user
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> <debug.log><ompi.log>_______________________________________________
>>>>>>>>> ptp-user mailing list
>>>>>>>>> ptp-user@xxxxxxxxxxx
>>>>>>>>> https://dev.eclipse.org/mailman/listinfo/ptp-user
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> ptp-user mailing list
>>>>>>>> ptp-user@xxxxxxxxxxx
>>>>>>>> https://dev.eclipse.org/mailman/listinfo/ptp-user
>>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
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>>>>>
>>>>> _______________________________________________
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