dolfin team mailing list archive

["Johannes Ring" <johannr@xxxxxxxxx>]

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.

Johannes