[petsc-users] DMPlexDistribute question

[Yaakoub El Khamra]

Just sent credentials. I am also trying on stampede.


Regards
Yaakoub El Khamra


On Tue, Dec 31, 2013 at 11:44 AM, Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Dec 31, 2013 at 11:38 AM, Yaakoub El Khamra <
> yaakoub at tacc.utexas.edu> wrote:
>
>>
>> snes ex12 also hangs. Then I started trying all other examples, all MPI
>> examples hang. Basic MPI code and benchmarks appear to compile and run
>> fine. I recompiled PETSc and went carefully over the output, there are a
>> lot of warnings (even from a stable build)
>>
>> If I compile petsc with openmpi 1.7.3 and gcc 4.8.2 and the configure
>> line:
>>
>> /configure --with-mpi-compilers=yes --download-metis --download-parmetis
>> --download-fiat --with-fortran=yes --download-scientificpython
>> --download-f-blas-lapack=1  --download-triangle --download-chaco
>> --download-exodusii --download-netcdf --download-hdf5
>>
>> I get a lot of warnings from MPI that might significant. I can provide
>> access to the fedora 20 box where I am working.
>>
>
> Either send login info to petsc-maint at mcs.anl.gov, or get a stack trace
> of the hang using gdb.
>
>   Thanks,
>
>     Matt
>
>
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:159:5: warning:
>> ‘MPI_Keyval_create’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by
>> MPI_Comm_create_keyval in MPI-2.0 [-Wdeprecated-declarations]
>>      ierr =
>> MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_Tmp_keyval,0);CHKERRQ(ierr);
>>      ^
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:159:5: warning:
>> ‘OMPI_C_MPI_NULL_COPY_FN’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:828): MPI_NULL_COPY_FN is deprecated in
>> MPI-2.0 [-Wdeprecated-declarations]
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:162:3: warning:
>> ‘MPI_Attr_get’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by
>> MPI_Comm_get_attr in MPI-2.0 [-Wdeprecated-declarations]
>>    ierr =
>> MPI_Attr_get(comm,Petsc_Tmp_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr);
>>    ^
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:168:5: warning:
>> ‘MPI_Attr_put’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by
>> MPI_Comm_set_attr in MPI-2.0 [-Wdeprecated-declarations]
>>      ierr = MPI_Attr_put(comm,Petsc_Tmp_keyval,tagvalp);CHKERRQ(ierr);
>>      ^
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c: In function
>> ‘PetscSharedWorkingDirectory’:
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:282:5: warning:
>> ‘MPI_Keyval_create’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by
>> MPI_Comm_create_keyval in MPI-2.0 [-Wdeprecated-declarations]
>>      ierr =
>> MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelTmpShared,&Petsc_WD_keyval,0);CHKERRQ(ierr);
>>      ^
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:282:5: warning:
>> ‘OMPI_C_MPI_NULL_COPY_FN’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:828): MPI_NULL_COPY_FN is deprecated in
>> MPI-2.0 [-Wdeprecated-declarations]
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:285:3: warning:
>> ‘MPI_Attr_get’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by
>> MPI_Comm_get_attr in MPI-2.0 [-Wdeprecated-declarations]
>>    ierr =
>> MPI_Attr_get(comm,Petsc_WD_keyval,(void**)&tagvalp,(int*)&iflg);CHKERRQ(ierr);
>>    ^
>> /home/yye00/Work/Saswata/petsc/src/sys/fileio/fretrieve.c:291:5: warning:
>> ‘MPI_Attr_put’ is deprecated (declared at
>> /usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by
>> MPI_Comm_set_attr in MPI-2.0 [-Wdeprecated-declarations]
>>      ierr = MPI_Attr_put(comm,Petsc_WD_keyval,tagvalp);CHKERRQ(ierr);
>>
>>
>>
>> Regards
>> Yaakoub El Khamra
>>
>>
>> On Mon, Dec 30, 2013 at 10:58 PM, Matthew Knepley <knepley at gmail.com>wrote:
>>
>>> On Mon, Dec 30, 2013 at 7:34 PM, Yaakoub El Khamra <
>>> yaakoub at tacc.utexas.edu> wrote:
>>>
>>>>
>>>> If I create a dm with DMPlexCreateBoxMesh and immediately attempt to
>>>> distribute it with DMPlexDistribute, the call to DMPlexDistribute never
>>>> returns. I am working with a development checkout and the code looks as
>>>> follows:
>>>>
>>>>       call DMPlexCreateBoxMesh(PETSC_COMM_WORLD, 2, PETSC_TRUE, dm,
>>>>      $     ierr)
>>>>       CHKERRQ(ierr)
>>>>
>>>>       call DMPlexDistribute(dm, "chaco", 0,
>>>>      $ PETSC_NULL_OBJECT, distributedMesh, ierr)
>>>>       CHKERRQ(ierr)
>>>>
>>>> Any thoughts?
>>>>
>>>
>>> Can you run SNES ex12? It does exactly this and gets run in the nightly
>>> tests. I can run it in parallel
>>> with no problems. My guess is that something is going wrong with the
>>> Fortran binding. Can you
>>> get a stack trace for the hang? If not, can you send a full Fortran
>>> program which exhibits your problem?
>>>
>>>    Matt
>>>
>>>
>>>> Regards
>>>> Yaakoub El Khamra
>>>>
>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead.
>>> -- Norbert Wiener
>>>
>>
>>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
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