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:
[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, §ionCopy);
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
<[email protected] <mailto:[email protected]>> 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.
