[petsc-users] DMView and DMLoad

[Hapla Vaclav]

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 <wence at gmx.li<mailto:wence at gmx.li>> wrote:

Hi Berend,

On 14 Sep 2021, at 12:23, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:

On Tue, Sep 14, 2021 at 5:15 AM Berend van Wachem <berend.vanwachem at ovgu.de<mailto:berend.vanwachem at ovgu.de>> 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 things https://petsc.org/main/docs/manual/dmplex/#saving-and-loading-data-with-hdf5

Let us know if things aren't clear!

Thanks,

Lawrence

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