Re: [ptp-dev] IOException Pipe closed

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Re: [ptp-dev] IOException Pipe closed

From: Greg Watson <g.watson@xxxxxxxxxxxx>
Date: Mon, 20 Jul 2009 16:03:12 -0700
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Hi Matthew,

This is a problem with the XML output from Open MPI. It has now beenfixed in their trunk (1.4) and should be in the next release version(1.3.4).


Regards,

Greg

On Jul 16, 2009, at 1:47 PM, Matthew Fotzler wrote:

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, orhas 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 ofptp).
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 atstep
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, GregWatson<g.watson@xxxxxxxxxxxx> wrote:
Hi Matthew,
Please make sure there are no plugins from older builds in youreclipseplugins folder. Also, I'd suggest starting with a clean workspaceand
creating a new resource manager.

If neither of those things work, please create the file
"<install_dir>/eclipse/Eclipse.app/Contents/MacOS/.options" withthe
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 sameproblem. Is
there a different build I should try?

Thanks,
Matthew
On Wed, Jul 15, 2009 at 2:22 PM, GregWatson<g.watson@xxxxxxxxxxxx>
wrote:
Matthew,
Which build of PTP 3.0 are you using?Please try the latest andlet 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 amnowreceiving a different error. Do you have any ideas what mightbe
causing this?
org.eclipse.core.runtime.CoreException: Failed to parse outputof 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? Olderversions
cause
a
problem if the program output contains a "<" or "&" characterwhich
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 gettingsomeconsole output, but not all of it. Then the process isterminated
abruptly and there are 2 errors logged.
org.eclipse.core.runtime.CoreException: Failed to parseoutput 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 mustconsist
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)
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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
  - 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

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