On 12/2/25 15:02, Matthew Knepley wrote:
On Mon, Dec 1, 2025 at 8:22 AM Aldo Bonfiglioli <[email protected]> wrote:
Dear developers,
I wrote a code that extracts subDMs corresponding to the various strata in the Face Sets.
I run into troubles when I view a subDM or a Vec attached to the subDM using the VTK format.
More precisely, the problem only occurs on more than one processor when the rank=0 processor has no points on a given subDM.
For instance, when the attached reproducer is run on 2 procs, the u_01.vtu file (global u Vec mapped to the subDM corresponding to stratum=1)
only includes the header, but no data. All other u_0?.vtu files can successfully be loaded and viewed in paraview.
The problem does NOT arise when I view the same objects in HDF5 format.
However, my problem in using the HDF5 lies in the fact that:
while the hdf5 file obtained with DMView can be post-processed with "petsc/lib/petsc/bin/petsc_gen_xdmf.py" to create a xmf file readable by paraview
Hi Aldo,
Sorry about this, I would like to make it more intuitive. First, the solution (I think)
-dm_plex_view_hdf5_storage_version 1.1.0
will write the Viz field by default, so that PAraview will see it. Can you try this?
Why do we need this? I have now made version-controlled output formats. There is something about this in the manual, but not enough. Paraview only supports vertex-based fields and cell-based fields (at least that I understand), so we need to write a separate copy of the field (since Plex supports any layout). Lots of people do not want a separate copy, since they are checkpointing, so we control this with a format (PETSC_VIEWER_HDF5_VIZ). You can pass this for specific output, or use the format version that does it automatically.
Let me know if this works.
Thanks,
Matt
I do not know how to view the field(s) associated with the DM when the hdf5 file is obtained from VecView.
The reproducer compiles with the latest petsc release.
Thanks,
Aldo
-- Dr. Aldo Bonfiglioli Associate professor of Fluid Mechanics Dipartimento di Ingegneria Universita' della Basilicata V.le dell'Ateneo Lucano, 10 85100 Potenza ITALY tel:+39.0971.205203 fax:+39.0971.205215 web: https://urldefense.us/v3/__http://docenti.unibas.it/site/home/docente.html?m...
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Matt, use of the option "-dm_plex_view_hdf5_storage_version 1.1.0" is indeed necessary, but I also realized, thanks to a suggestion from [email protected], that I have to View BOTH the dm and vec in the same hdf5 file, i.e.
! ! dump the dm+u to the same HDF5 file !
filename ="test.h5" PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, trim(filename), FILE_MODE_WRITE, viewer, ierr)) PetscCall(DMView(dm, viewer, ierr)) PetscCall(PetscViewerDestroy(viewer, ierr)) PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, trim(filename), FILE_MODE_APPEND, viewer, ierr)) PetscCall(VecView(u, viewer, ierr)) PetscCall(PetscViewerDestroy(viewer, ierr))
Once test.h5 has been processed with "petsc_gen_xdmf.py", I can load the xmf file in paraview e see the solution (there is NO solution unless -dm_plex_view_hdf5_storage_version 1.1.0 is in the options db). I was probably misled by the fact that a single VecView in VTK format gives both the mesh and solution in the same file. Does this make sense? Final question: is it possible to specify, using command line options or the options db, that vecview should be appended to an existing file? Thanks, Aldo -- Dr. Aldo Bonfiglioli Associate professor of Fluid Mechanics Dipartimento di Ingegneria Universita' della Basilicata V.le dell'Ateneo Lucano, 10 85100 Potenza ITALY tel:+39.0971.205203 fax:+39.0971.205215 web:https://urldefense.us/v3/__http://docenti.unibas.it/site/home/docente.html?m...