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<div class="moz-cite-prefix">On 12/2/25 15:02, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMYG4G=6C+u6u7dQ1TgW2BMc5cU52b66Uc7W6XFLukZgRx7TAw@mail.gmail.com">
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<div dir="ltr">On Mon, Dec 1, 2025 at 8:22 AM Aldo Bonfiglioli
<<a href="mailto:aldo.bonfiglioli@unibas.it"
moz-do-not-send="true" class="moz-txt-link-freetext">aldo.bonfiglioli@unibas.it</a>>
wrote:</div>
<div class="gmail_quote gmail_quote_container">
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear
developers,<br>
<br>
I wrote a code that extracts subDMs corresponding to the
various strata <br>
in the Face Sets.<br>
<br>
I run into troubles when I view a subDM or a Vec attached to
the subDM <br>
using the VTK format.<br>
<br>
More precisely, the problem only occurs on more than one
processor when <br>
the rank=0 processor has no points on a given subDM.<br>
<br>
For instance, when the attached reproducer is run on 2
procs, the <br>
u_01.vtu file (global u Vec mapped to the subDM
corresponding to stratum=1)<br>
<br>
only includes the header, but no data. All other u_0?.vtu
files can <br>
successfully be loaded and viewed in paraview.<br>
<br>
The problem does NOT arise when I view the same objects in
HDF5 format.<br>
<br>
However, my problem in using the HDF5 lies in the fact that:<br>
<br>
while the hdf5 file obtained with DMView can be
post-processed with <br>
"petsc/lib/petsc/bin/petsc_gen_xdmf.py" to create a xmf file
readable by <br>
paraview<br>
</blockquote>
<div><br>
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<div>Hi Aldo,</div>
<div><br>
</div>
<div>Sorry about this, I would like to make it more intuitive.
First, the solution (I think)</div>
<div><br>
</div>
<div> -dm_plex_view_hdf5_storage_version 1.1.0</div>
<div><br>
</div>
<div>will write the Viz field by default, so that PAraview
will see it. Can you try this?</div>
<div><br>
</div>
<div>Why do we need this? I have now made version-controlled
output formats. There is something about</div>
<div>this in the manual, but not enough. Paraview only
supports vertex-based fields and cell-based fields</div>
<div>(at least that I understand), so we need to write a
separate copy of the field (since Plex supports any</div>
<div>layout). Lots of people do not want a separate copy,
since they are checkpointing, so we control this</div>
<div>with a format (PETSC_VIEWER_HDF5_VIZ). You can pass this
for specific output, or use the format</div>
<div>version that does it automatically.</div>
<div><br>
</div>
<div>Let me know if this works.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
I do not know how to view the field(s) associated with the
DM when the <br>
hdf5 file is obtained from VecView.<br>
<br>
The reproducer compiles with the latest petsc release.<br>
<br>
Thanks,<br>
<br>
Aldo<br>
<br>
-- <br>
Dr. Aldo Bonfiglioli<br>
Associate professor of Fluid Mechanics<br>
Dipartimento di Ingegneria<br>
Universita' della Basilicata<br>
V.le dell'Ateneo Lucano, 10 85100 Potenza ITALY<br>
tel:+39.0971.205203 fax:+39.0971.205215<br>
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<br>
</blockquote>
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<span class="gmail_signature_prefix">-- </span><br>
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<div>What most experimenters take for granted before
they begin their experiments is infinitely more
interesting than any results to which their
experiments lead.<br>
-- Norbert Wiener</div>
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<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!Zla-FYPeT9khxXRG5MuCbh6NLunsaK0ljFdIlNk-3XDnbGEJPBARoshmLdtN7p3kHgPJbQDyNgvHIi-GT6IyAxxdaZ2jObGUdDk$" target="_blank" moz-do-not-send="true">https://www.cse.buffalo.edu/~knepley/</a><br>
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</blockquote>
<p>Matt,</p>
<p>use of the option "-dm_plex_view_hdf5_storage_version 1.1.0" is
indeed necessary,</p>
<p>but I also realized, thanks to a suggestion from
<a class="moz-txt-link-abbreviated" href="mailto:matteo.semplice@uninsubria.it">matteo.semplice@uninsubria.it</a>, that I have to View BOTH the dm and
vec in the same hdf5 file, i.e.</p>
<p>
<blockquote type="cite">
<span style="font-family:monospace"><span
style="color:#1818b2;background-color:#ffffff;">!</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#1818b2;background-color:#ffffff;">!
dump the dm+u to the same HDF5 file</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#1818b2;background-color:#ffffff;">!</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<br>
<span style="color:#000000;background-color:#ffffff;">filename
</span><span style="color:#af5f00;background-color:#ffffff;">=</span><span
style="color:#000000;background-color:#ffffff;"> </span><span
style="color:#b21818;background-color:#ffffff;">"test.h5"</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, </span><span
style="color:#18b2b2;background-color:#ffffff;">trim</span><span
style="color:#000000;background-color:#ffffff;">(filename),
FILE_MODE_WRITE, viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(DMView(dm, viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(PetscViewerDestroy(viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, </span><span
style="color:#18b2b2;background-color:#ffffff;">trim</span><span
style="color:#000000;background-color:#ffffff;">(filename),
FILE_MODE_APPEND, viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(VecView(u, viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<span style="color:#000000;background-color:#ffffff;">
PetscCall(PetscViewerDestroy(viewer, ierr))</span><span
style="color:#000000;background-color:#ffffff;">
</span><br>
<br>
<br>
</span>
</blockquote>
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).</p>
<p>I was probably misled by the fact that a single VecView in VTK
format gives both the mesh and solution in the same file.</p>
<p>Does this make sense?</p>
<p>Final question:</p>
<p>is it possible to specify, using command line options or the
options db, that vecview should be appended to an existing file?</p>
<p>Thanks,</p>
<p>Aldo </p>
<pre class="moz-signature" cols="72">--
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: <a class="moz-txt-link-freetext" href="https://urldefense.us/v3/__http://docenti.unibas.it/site/home/docente.html?m=002423__;!!G_uCfscf7eWS!Zla-FYPeT9khxXRG5MuCbh6NLunsaK0ljFdIlNk-3XDnbGEJPBARoshmLdtN7p3kHgPJbQDyNgvHIi-GT6IyAxxdaZ2jJl4AAbM$">http://docenti.unibas.it/site/home/docente.html?m=002423</a></pre>
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