dolfin team mailing list archive

["Johannes Ring" <johannr@xxxxxxxxx>]

On Thu, August 14, 2008 09:42, Anders Logg wrote:
> On Thu, Aug 14, 2008 at 08:39:25AM +0100, Garth N. Wells wrote:
>>
>>
>> Johannes Ring wrote:
>> > On Thu, August 14, 2008 08:52, Garth N. Wells wrote:
>> >>
>> >> Anders Logg wrote:
>> >>> On Wed, Aug 13, 2008 at 08:03:39PM +0100, Garth N. Wells wrote:
>> >>>> I'm experiencing a puzzling problem wth pyDOLFIN and MPI again.
>> >>>>
>> >>>> When I do
>> >>>>
>> >>>>      python file.py
>> >>>>
>> >>>> where file.py is just
>> >>>>
>> >>>>      from dolfin import *
>> >>>>
>> >>>>      object = Function("/tmp/fileKFnQpl.xml")
>> >>>>      plot(object)
>> >>>>      interactive()
>> >>>>
>> >>>> I see a plot as expected, and get
>> >>>>
>> >>>>      Plot active, press 'q' to continue.
>> >>>>
>> >>>> After pressing 'q', I get
>> >>>>
>> >>>>      *** An error occurred in MPI_Attr_get
>> >>>>      *** after MPI was finalized
>> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
>> >>>>      [gnw20pc:2277] Abort before MPI_INIT completed successfully;
>> not
>> >>>> able to guarantee that all other processes were killed!
>> >>>>      *** An error occurred in MPI_Comm_rank
>> >>>>      *** after MPI was finalized
>> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
>> >>>>      *** An error occurred in MPI_Type_free
>> >>>>      *** after MPI was finalized
>> >>>>      *** MPI_ERRORS_ARE_FATAL (goodbye)
>> >>>>      Segmentation fault
>> >>>>
>> >>>> Somehow, Python appears to be calling MPI_Finalize before DOLFIN
>> gets a
>> >>>> chance to finalise things correctly. Any ideas/experience on how
>> Python
>> >>>> interacts with MPI? I've commented out MPI_Finalize() in DOLFIN to
>> be
>> >>>> sure that DOLFIN is not calling it.
>> >>>>
>> >>>> Garth
>> >>> Would it help if we just call MPI_Finalized to check before
>> >>> finalizing? We can add a wrapper for it just like for
>> MPI_Initialized.
>> >>>
>> >> I've added some annoying debug output to SubSystemsManager. Can you
>> tell
>> >> me what you see when running
>> >>
>> >>      from dolfin import *
>> >>      x = PETScVector(10)
>> >>
>> >> When I run it, the first line of output is
>> >>
>> >>      MPI status in initPETSc() 1
>> >>
>> >> which indicates that MPI_Initialize is saying that MPI has been
>> >> initialised before PETSc is initialised, but we haven't initialise
>> it.
>> >> The same code in C++ gives
>> >>
>> >>      MPI status in initPETSc() 0
>> >>
>> >> which is the expected result.
>> >
>> > I get
>> >
>> >>>> from dolfin import *
>> >>>> x = PETScVector(10)
>> > MPI status in initPETSc() 0
>> > [simula-x61:17855] mca: base: component_find: unable to open osc
>> pt2pt:
>> > file not found (ignored)
>> > MPI status in initMPI() 1
>> >
>> > Have you compiled Trilinos with MPI support? It seems to be the same
>> > problems I had with my Ubuntu packages for Trilinos on 64bit. Turning
>> off
>> > MPI support for Trilinos fixed the problem for me.
>> >
>>
>> Yes, Trilinos with MPI support was the culprit, even though I disabled
>> Trilinos (enableTrilinos=no). Trilinos must be placing some files in
>> /usr/local/lib/ which cause a problem which is nasty. Just removing
>> Trilinos did the trick. Thanks!
>>
>> Garth
>
> What about the annoying
>
>   mca: base: component_find: unable to open osc pt2pt: file not found
> (ignored)
>
> ?

I'm not sure how to remove it.

Johannes

> --
> Anders
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