Dear Vaclav, Lawrence, Koki,
Thanks for your help! Following your advice and following your example
(https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5)
we are able to save and load the DM with a wrapped Vector in h5 format
(PETSC_VIEWER_HDF5_PETSC) successfully.
For saving, we use something similar to:
DMPlexTopologyView(dm, viewer);
DMClone(dm, &sdm);
...
DMPlexSectionView(dm, viewer, sdm);
DMGetLocalVector(sdm, &vec);
...
DMPlexLocalVectorView(dm, viewer, sdm, vec);
and for loading:
DMCreate(PETSC_COMM_WORLD, &dm);
DMSetType(dm, DMPLEX);
...
PetscViewerPushFormat(viewer, PETSC_VIEWER_HDF5_PETSC);
DMPlexTopologyLoad(dm, viewer, &sfO);
DMPlexLabelsLoad(dm, viewer);
DMPlexCoordinatesLoad(dm, viewer);
PetscViewerPopFormat(viewer);
...
PetscSFCompose(sfO, sfDist, &sf);
...
DMClone(dm, &sdm);
DMPlexSectionLoad(dm, viewer, sdm, sf, &globalDataSF, &localDataSF);
DMGetLocalVector(sdm, &vec);
...
DMPlexLocalVectorLoad(dm, viewer, sdm, localDataSF, vec);
This works fine for non-periodic DMs but for periodic cases the line:
DMPlexCoordinatesLoad(dm, H5Viewer);
delivers the error message: invalid argument and the number of loaded
coordinates does not match the number of vertices.
Is this a known shortcoming, or have we forgotten something to load
periodic DMs?
Best regards,
Berend.
On 9/22/21 20:59, Hapla Vaclav wrote:
To avoid confusions here, Berend seems to be specifically demanding XDMF
(PETSC_VIEWER_HDF5_XDMF). The stuff we are now working on is parallel
checkpointing in our own HDF5 format (PETSC_VIEWER_HDF5_PETSC), I will
make a series of MRs on this topic in the following days.
For XDMF, we are specifically missing the ability to write/load DMLabels
properly. XDMF uses specific cell-local numbering for faces for
specification of face sets, and face-local numbering for specification
of edge sets, which is not great wrt DMPlex design. And ParaView doesn't
show any of these properly so it's hard to debug. Matt, we should talk
about this soon.
Berend, for now, could you just load the mesh initially from XDMF and
then use our PETSC_VIEWER_HDF5_PETSC format for subsequent saving/loading?
Thanks,
Vaclav
On 17 Sep 2021, at 15:46, Lawrence Mitchell <[email protected]
<mailto:[email protected]>> wrote:
Hi Berend,
On 14 Sep 2021, at 12:23, Matthew Knepley <[email protected]
<mailto:[email protected]>> wrote:
On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem
<[email protected] <mailto:[email protected]>> wrote:
Dear PETSc-team,
We are trying to save and load distributed DMPlex and its associated
physical fields (created with DMCreateGlobalVector) (Uvelocity,
VVelocity, ...) in HDF5_XDMF format. To achieve this, we do the
following:
1) save in the same xdmf.h5 file:
DMView( DM , H5_XDMF_Viewer );
VecView( UVelocity, H5_XDMF_Viewer );
2) load the dm:
DMPlexCreateFromfile(PETSC_COMM_WORLD, Filename, PETSC_TRUE, DM);
3) load the physical field:
VecLoad( UVelocity, H5_XDMF_Viewer );
There are no errors in the execution, but the loaded DM is distributed
differently to the original one, which results in the incorrect
placement of the values of the physical fields (UVelocity etc.) in the
domain.
This approach is used to restart the simulation with the last saved DM.
Is there something we are missing, or there exists alternative routes to
this goal? Can we somehow get the IS of the redistribution, so we can
re-distribute the vector data as well?
Many thanks, best regards,
Hi Berend,
We are in the midst of rewriting this. We want to support saving
multiple meshes, with fields attached to each,
and preserving the discretization (section) information, and allowing
us to load up on a different number of
processes. We plan to be done by October. Vaclav and I are doing this
in collaboration with Koki Sagiyama,
David Ham, and Lawrence Mitchell from the Firedrake team.
The core load/save cycle functionality is now in PETSc main. So if
you're using main rather than a release, you can get access to it now.
This section of the manual shows an example of how to do
thingshttps://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5
<https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5>
Let us know if things aren't clear!
Thanks,
Lawrence
