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

[Matthew Knepley]

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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