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

Mon, 15 Dec 2025 00:44:15 -0800 

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:
    
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--

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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 
[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

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