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

[Aldo Bonfiglioli]

On 12/2/25 15:02, Matthew Knepley wrote:
> 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$
>
>
>
>
> -- 
> What most experimenters take for granted before they begin their 
> experiments is infinitely more interesting than any results to which 
> their experiments lead.
> -- Norbert Wiener
>
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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 
matteo.semplice at uninsubria.it, 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=002423__;!!G_uCfscf7eWS!Zla-FYPeT9khxXRG5MuCbh6NLunsaK0ljFdIlNk-3XDnbGEJPBARoshmLdtN7p3kHgPJbQDyNgvHIi-GT6IyAxxdaZ2jJl4AAbM$ 
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