[petsc-users] DMPlexDistribute question

[Yaakoub El Khamra]

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.

/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/usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by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/usr/include/openmpi-x86_64/mpi.h:1201): MPI_Attr_get is superseded by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/usr/include/openmpi-x86_64/mpi.h:1203): MPI_Attr_put is superseded by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/usr/include/openmpi-x86_64/mpi.h:1506): MPI_Keyval_create is superseded by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
>
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