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Re: [ptp-user] Failed to parse output of OpenMPI command
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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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