[yt-users] TimeSeriesData.piter() exiting early

Matthew Turk matthewturk at gmail.com
Thu Dec 6 14:40:04 PST 2012


Hi John and Nathan,

There's a barrier-at-end option with parallel_objects; could that also
fix this, if we had it for piter as well?

-Matt

On Thu, Dec 6, 2012 at 5:38 PM, John Wise <jwise at physics.gatech.edu> wrote:
> Hi Nathan,
>
> I've run into a problem like this before on pleiades.  I've solved it by
> manually calling MPI.Finalize() at the end of the script.
>
> from mpi4py import MPI
> [...script...]
> MPI.Finalize()
>
> This will allow all of the processors to finish before exiting the script.
> If you don't call MPI_Finalize, then it will exit once processor 0 exits.
> I've only seen this behavior with SGI's MPI.
>
> John
>
>
>
> On 12/06/2012 03:37 PM, Nathan Goldbaum wrote:
>>
>> Hi all,
>>
>> I'm processing some simulations that i have stored on Pleiades at NASA
>> Ames.  This machine using SGI's version of MPI so it's possible that this
>> issue is isolated to this MPI.
>>
>> When I ts.piter() on this machine, it will sometimes die early, before all
>> of the parameter files have been processed, with the following error:
>>
>> MPI: MPI_COMM_WORLD rank 7 has terminated without calling MPI_Finalize()
>> MPI: aborting job
>>
>> This particular script saves a bunch of plots to disk.  Taking a look at
>> the list of plots that have been saved, it seems that it got about halfway
>> through before dying.  The first ~third of the plots are all on disk, most
>> of the middle ~third are saved although there are some missing plots, and
>> the last ~third haven't been saved at all.
>>
>> Any ideas what's going wrong here?  Is there something simple I can do to
>> fix it?  This isn't game-ending since I can always process my data in serial
>> but it is a bit annoying.
>>
>> Cheers,
>>
>> Nathan
>>
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>>
>
> --
> John Wise
> Assistant Professor of Physics
> Center for Relativistic Astrophysics, Georgia Tech
>
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