[petsc-users] Trouble when viewing a subDM in vtk format

[Matthew Knepley]

On Mon, Dec 1, 2025 at 8:22 AM Aldo Bonfiglioli <aldo.bonfiglioli at unibas.it>
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=002423__;!!G_uCfscf7eWS!eXE2csxUb1J5bnRosf9LIGxLs17TdstMxQcGs0mbXFroRjzLN81jVmeAWfMr41X8JGEuVm286lVTmDgmi5s1zfsfegJNuWVVWTM$
>


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