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On Wed, Jul 31, 2024 at 4: 16 PM Eric Chamberland <Eric. Chamberland@ giref. ulaval. ca> wrote: Hi Vaclav, Okay, I am coming back with this question after some time. . . ;) I am just wondering if it is now possible to call DMPlexBuildFromCellListParallel
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<div dir="ltr"><div dir="ltr">On Wed, Jul 31, 2024 at 4:16 PM Eric Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca">Eric.Chamberland@giref.ulaval.ca</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><u></u>
<div>
<p>Hi Vaclav,</p>
<p>Okay, I am coming back with this question after some time... ;)</p>
<p>I am just wondering if it is now possible to call
DMPlexBuildFromCellListParallel or something else, to build a mesh
that combine different element types into a single DMPlex (in
parallel of course) ?</p></div></blockquote><div>1) Meshes with different cell types are fully functional, and some applications have been using them for a while now.</div><div><br></div><div>2) The Firedrake I/O methods support these hybrid meshes. </div><div><br></div><div>3) You can, for example, read in a GMsh or ExodusII file with different cell types.</div><div><br></div><div>However, there is no direct interface like DMPlexBuildFromCellListParallel(). If you plan on creating meshes by hand, I can build that for you.</div><div>No one so far has wanted that. Rather they want to read in a mesh in some format, or alter a base mesh by inserting other cell types.</div><div><br></div><div>So, what is the motivating use case?</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
<p>Thanks,</p>
<p>Eric<br>
</p>
<div>On 2021-09-23 11:30, Hapla Vaclav
wrote:<br>
</div>
<blockquote type="cite">
Note there will soon be a generalization of
DMPlexBuildFromCellListParallel() around, as a side product of our
current collaborative efforts with Firedrake guys. It will take a
PetscSection instead of relying on the blocksize [which is indeed
always constant for the given dataset]. Stay tuned.
<div>
<div><br>
</div>
<div><a href="https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/4350__;!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oBuRbcJg$" target="_blank">https://gitlab.com/petsc/petsc/-/merge_requests/4350</a></div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Vaclav</div>
<div>
<div><br>
<blockquote type="cite">
<div>On 23 Sep 2021, at 16:53, Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:</div>
<br>
<div>
<div>
<p>Hi,</p>
<p>oh, that's a great news!</p>
<p>In our case we have our home-made
file-format, invariant to the number of processes
(thanks to MPI_File_set_view), that uses collective,
asynchronous MPI I/O native calls for unstructured
hybrid meshes and fields .</p>
<p>So our needs are not for reading meshes
but only to fill an hybrid DMPlex with
DMPlexBuildFromCellListParallel (or something else
to come?)... to exploit petsc partitioners and
parallel overlap computation...<br>
</p>
<p>Thanks for the follow-up! :)<br>
</p>
<p>Eric<br>
</p>
<p><br>
</p>
<div>On 2021-09-22 7:20 a.m.,
Matthew Knepley wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On Wed, Sep 22, 2021 at
3:04 AM Karin&NiKo <<a href="mailto:niko.karin@gmail.com" target="_blank">niko.karin@gmail.com</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear Matthew,
<div><br>
</div>
<div>This is great news!</div>
<div>For my part, I would be mostly
interested in the parallel input
interface. Sorry for that... </div>
<div>Indeed, in our application,
we already have a parallel mesh data
structure that supports hybrid meshes with
parallel I/O and distribution (based on
the MED format). We would like to use a
DMPlex to make parallel mesh adaptation.</div>
<div> As a matter of fact, all our
meshes are in the MED format. We could
also contribute to extend the interface of
DMPlex with MED (if you consider it could
be usefull).</div>
</div>
</blockquote>
<div><br>
</div>
<div>An MED interface does exist. I
stopped using it for two reasons:</div>
<div><br>
</div>
<div> 1) The code was not portable and
the build was failing on different
architectures. I had to manually fix it.</div>
<div><br>
</div>
<div> 2) The boundary markers did not
provide global information, so that parallel
reading was much harder.</div>
<div><br>
</div>
<div>Feel free to update my MED reader
to a better design.</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">
<div dir="ltr">
<div>Best regards,</div>
<div>Nicolas</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Le mar. 21
sept. 2021 à 21:56, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>>
a écrit :<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div dir="ltr">On Tue, Sep 21,
2021 at 10:31 AM Karin&NiKo <<a href="mailto:niko.karin@gmail.com" target="_blank">niko.karin@gmail.com</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear Eric,
dear Matthew,
<div><br>
</div>
<div>I share Eric's
desire to be able to manipulate
meshes composed of different
types of elements in a PETSc's
DMPlex. </div>
<div>Since this
discussion, is there anything
new on this feature for the
DMPlex object or am I missing
something?</div>
</div>
</blockquote>
<div><br>
</div>
<div>Thanks for finding this!</div>
<div><br>
</div>
<div>Okay, I did a rewrite of
the Plex internals this summer. It
should now be possible to
interpolate a mesh with any</div>
<div>number of cell types,
partition it, redistribute it, and
many other manipulations.</div>
<div><br>
</div>
<div>You can read in some
formats that support hybrid meshes.
If you let me know how you plan to
read it in, we can make it work.</div>
<div>Right now, I don't want
to make input interfaces that no one
will ever use. We have a project,
joint with Firedrake, to finalize</div>
<div>parallel I/O. This will
make parallel reading and writing
for checkpointing possible,
supporting topology, geometry,
fields and</div>
<div>layouts, for many
meshes in one HDF5 file. I think we
will finish in November.</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">
<div dir="ltr">
<div>Thanks,</div>
<div>Nicolas</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">Le mer.
21 juil. 2021 à 04:25, Eric
Chamberland <<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">Eric.Chamberland@giref.ulaval.ca</a>>
a écrit :<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi,<br>
</p>
<div>On 2021-07-14
3:14 p.m., Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">On
Wed, Jul 14, 2021 at
1:25 PM Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:<br>
</div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Hi,<br>
<br>
while playing with
DMPlexBuildFromCellListParallel,
I noticed we have to <br>
specify "numCorners"
which is a fixed
value, then gives a
fixed number <br>
of nodes for a series
of elements.<br>
<br>
How can I then add,
for example, triangles
and quadrangles into a
DMPlex?<br>
</blockquote>
<div><br>
</div>
<div>You can't
with that function. It
would be much mich
more complicated if
you could, and I am
not sure</div>
<div>it is
worth it for that
function. The reason
is that you would need
index information to
offset into the</div>
<div>connectivity
list, and that would
need to be replicated
to some extent so that
all processes know
what</div>
<div>the others
are doing. Possible,
but complicated.</div>
<div><br>
</div>
<div>Maybe I
can help suggest
something for what you
are trying to do?</div>
</div>
</div>
</blockquote>
<p>Yes: we are trying
to partition our parallel
mesh with PETSc functions.
The mesh has been read in
parallel so each process
owns a part of it, but we
have to manage mixed
elements types.</p>
<p>When we directly
use
ParMETIS_V3_PartMeshKway, we
give two arrays to describe
the elements which allows
mixed elements.</p>
<p>So, how would I
read my mixed mesh in
parallel and give it to
PETSc DMPlex so I can use a
PetscPartitioner with
DMPlexDistribute ?</p>
<p>A second goal we
have is to use PETSc to
compute the overlap, which
is something I can't find in
PARMetis (and any other
partitionning library?)</p>
<p>Thanks,</p>
<p>Eric<br>
</p>
<p><br>
</p>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_quote">
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div><br>
</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">
Thanks,<br>
<br>
Eric<br>
<br>
-- <br>
Eric Chamberland,
ing., M. Ing<br>
Professionnel de
recherche<br>
GIREF/Université Laval<br>
(418) 656-2131 poste
41 22 42<br>
<br>
</blockquote>
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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>
<div><br>
</div>
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</blockquote>
<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
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<div dir="ltr">
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<div>
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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>
<div><br>
</div>
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<div dir="ltr">
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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>
<div><br>
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<div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oMwy-ztx$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
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<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</blockquote>
<pre cols="72">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
</blockquote></div><br clear="all"><div><br></div><span class="gmail_signature_prefix">-- </span><br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><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><div><br></div><div><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oMwy-ztx$" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>