[petsc-users] Write/read a DMForest to/from a file

Mark Adams mfadams at lbl.gov
Fri Dec 30 16:46:34 CST 2022 

Oh, right, you need to convert to a Plex and then write.

I've never read a Forest but you will read in a Plex and I would think just
convert to a Forest.

Mark

On Fri, Dec 30, 2022 at 9:29 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Fri, Dec 30, 2022 at 5:59 AM Berend van Wachem <
> berend.vanwachem at ovgu.de> wrote:
>
>> Dear Mark,
>>
>> Yes, I have tried that. That will only work if I convert the DMForest to
>> a DMPlex first, and then write the DMPlex to file. But then, I cannot
>> read in a DMForest when I want to continue the calculations later on.
>>
>> Below is the code I use to write a DMPlex to file. When I call this
>> routine with a DMForest, I get the error:
>>
>
> This is true. I am going to have to look at this with Toby. I will get
> back to you.
>
>   THanks,
>
>      Matt
>
>
>> [0]PETSC ERROR: Invalid argument
>> [0]PETSC ERROR: Wrong type of object: Parameter # 1
>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.18.2, Nov 28, 2022
>> [0]PETSC ERROR: ./bin/write_periodic on a linux-gcc-dev named
>> multiflow.multiflow.org by berend Fri Dec 30 11:54:51 2022
>> [0]PETSC ERROR: Configure options --with-clean --download-metis=yes
>> --download-parmetis=yes --download-hdf5 --download-p4est
>> --download-triangle --download-tetgen --with-zlib-lib=/usr/lib64/libz.a
>> --with-zlib-include=/usr/include --with-mpi=yes --with-mpi-dir=/usr
>> --with-mpiexec=/usr/bin/mpiexec --download-slepc=yes --download-fftw=yes
>> [0]PETSC ERROR: #1 PetscSectionGetChart() at
>> /usr/local/petsc-3.18.2/src/vec/is/section/interface/section.c:592
>> [0]PETSC ERROR: #2 DMPlexGetChart() at
>> /usr/local/petsc-3.18.2/src/dm/impls/plex/plex.c:2702
>> [0]PETSC ERROR: #3 DMPlexGetDepthStratum() at
>> /usr/local/petsc-3.18.2/src/dm/impls/plex/plex.c:4882
>> [0]PETSC ERROR: #4 DMPlexCreatePointNumbering() at
>> /usr/local/petsc-3.18.2/src/dm/impls/plex/plex.c:8303
>> [0]PETSC ERROR: #5 DMPlexTopologyView() at
>> /usr/local/petsc-3.18.2/src/dm/impls/plex/plex.c:1854
>> [0]PETSC ERROR: #6 WriteDMAndVectortoHDF5File() at
>> /home/berend/git/Code/petsc-dmplex-restart-test/src/createandwrite.c:176
>> [0]PETSC ERROR: #7 main() at
>> /home/berend/git/Code/petsc-dmplex-restart-test/src/createandwrite.c:555
>>
>> The code I use to write is:
>>
>> PetscErrorCode WriteDMAndVectortoHDF5File(DM dm, Vec *DataVector, const
>> char *HDF5file)
>> {
>>    PetscViewer H5Viewer;
>>    PetscErrorCode ierr;
>>    DM dmCopy;
>>    PetscSection sectionCopy;
>>    PetscInt i;
>>    PetscScalar *xVecArray;
>>    PetscInt numPoints, numPointsCopy;
>>    Vec vectorCopy;
>>    PetscScalar *array;
>>
>>    PetscFunctionBegin;
>>    ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, HDF5file,
>> FILE_MODE_WRITE, &H5Viewer);
>>    CHKERRQ(ierr);
>>    ierr = PetscObjectSetName((PetscObject) dm, "DM");
>>    CHKERRQ(ierr);
>>    ierr = PetscViewerPushFormat(H5Viewer, PETSC_VIEWER_HDF5_PETSC);
>>    CHKERRQ(ierr);
>>    ierr = DMPlexTopologyView(dm, H5Viewer);
>>    CHKERRQ(ierr);
>>    ierr = DMPlexLabelsView(dm, H5Viewer);
>>    CHKERRQ(ierr);
>>    ierr = DMPlexCoordinatesView(dm, H5Viewer);
>>    CHKERRQ(ierr);
>>    ierr = PetscViewerPopFormat(H5Viewer);
>>    CHKERRQ(ierr);
>>
>>    ierr = DMClone(dm, &dmCopy);
>>    CHKERRQ(ierr);
>>    ierr = PetscObjectSetName((PetscObject) dmCopy, "DM");
>>    CHKERRQ(ierr);
>>    ierr = DMGetLocalSection(dm, &sectionCopy);
>>    CHKERRQ(ierr);
>>    ierr = DMSetLocalSection(dmCopy, sectionCopy);
>>    CHKERRQ(ierr);
>>
>>    /* Write the section to the file */
>>    ierr = DMPlexSectionView(dm, H5Viewer, dmCopy);
>>    CHKERRQ(ierr);
>>
>>    ierr = DMGetGlobalVector(dmCopy, &vectorCopy);
>>    CHKERRQ(ierr);
>>
>>    /*** We have to copy the vector into the new vector ... ***/
>>    ierr = VecGetArray(vectorCopy, &array);
>>    CHKERRQ(ierr);
>>    ierr = VecGetLocalSize(*DataVector, &numPoints);
>>    CHKERRQ(ierr);
>>    ierr = VecGetLocalSize(vectorCopy, &numPointsCopy);
>>    CHKERRQ(ierr);
>>    assert(numPoints == numPointsCopy);
>>    ierr = VecGetArray(*DataVector, &xVecArray);
>>    CHKERRQ(ierr);
>>
>>    for (i = 0; i < numPoints; i++) /* Loop over all internal cells */
>>    {
>>      array[i] = xVecArray[i];
>>    }
>>
>>    ierr = VecRestoreArray(vectorCopy, &array);
>>    CHKERRQ(ierr);
>>    ierr = VecRestoreArray(*DataVector, &xVecArray);
>>    CHKERRQ(ierr);
>>
>>    ierr = PetscObjectSetName((PetscObject) vectorCopy, "DataVector");
>>    CHKERRQ(ierr);
>>
>>    /* Write the vector to the file */
>>    ierr = DMPlexGlobalVectorView(dm, H5Viewer, dmCopy, vectorCopy);
>>    CHKERRQ(ierr);
>>
>>    /* Close the file */
>>    ierr = PetscViewerDestroy(&H5Viewer);
>>    CHKERRQ(ierr);
>>
>>    ierr = DMDestroy(&dmCopy);
>>    CHKERRQ(ierr);
>>    /*** End of writing ****/
>>    PetscFunctionReturn(0);
>> }
>>
>>
>>
>>
>>
>> On 29/12/2022 21:54, Mark Adams wrote:
>> > Have you tried using the DMForest as you would use a DMPLex?
>> > That should work. Forst has extra stuff but it just makes a Plex and
>> the
>> > end of the day.
>> >
>> > On Tue, Dec 27, 2022 at 5:21 AM Berend van Wachem
>> > <berend.vanwachem at ovgu.de <mailto:berend.vanwachem at ovgu.de>> wrote:
>> >
>> >     Dear Petsc-team/users,
>> >
>> >     I am trying to save a DMForest which has been used for a calculation
>> >     (so
>> >     refined/coarsened in places) to a file and later read it from the
>> file
>> >     to continue a calculation with.
>> >     My question is: how do I do this? I've tried a few things, such as
>> >     using
>> >     DMView and DMLoad, and saving the BaseDM, but that doesn't seem to
>> save
>> >     the refining/coarsening which has taken place in the initial
>> >     calculation.
>> >     I haven't been able to find any example or documentation for this.
>> Any
>> >     pointers or examples would be very much appreciated!
>> >
>> >     Best regards, Berend.
>> >
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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