On 12/2/25 15:02, Matthew Knepley wrote:

On Mon, Dec 1, 2025 at 8:22 AM Aldo Bonfiglioli <aldo.bonfiglioli@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

https://www.cse.buffalo.edu/~knepley/

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@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: http://docenti.unibas.it/site/home/docente.html?m=002423