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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 or something else, to build a mesh that combine different element types into a single
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<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>
<p>Thanks,</p>
<p>Eric<br>
</p>
<div class="moz-cite-prefix">On 2021-09-23 11:30, Hapla Vaclav
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BB7104B9-EB9F-4F1A-A62F-A4AD9CD6F294@erdw.ethz.ch">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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 class="">
<div class=""><br class="">
</div>
<div class=""><a href="https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/4350__;!!G_uCfscf7eWS!fgngRI84CI_6fHdWdRiVbv0bvraQkhXyV396Uo5y2mORbR4DjlMYrHTqX0p22Ysp8t9yJPhCL1E3fkbWxmIZpQp6dYhcdaKz9_yUIGas$" class="moz-txt-link-freetext" moz-do-not-send="true">https://gitlab.com/petsc/petsc/-/merge_requests/4350</a></div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Vaclav</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 23 Sep 2021, at 16:53, Eric Chamberland
<<a href="mailto:Eric.Chamberland@giref.ulaval.ca"
class="moz-txt-link-freetext" moz-do-not-send="true">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">
<p class="">Hi,</p>
<p class="">oh, that's a great news!</p>
<p class="">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 class="">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 class="">
</p>
<p class="">Thanks for the follow-up! :)<br class="">
</p>
<p class="">Eric<br class="">
</p>
<p class=""><br class="">
</p>
<div class="moz-cite-prefix">On 2021-09-22 7:20 a.m.,
Matthew Knepley wrote:<br class="">
</div>
<blockquote type="cite"
cite="mid:CAMYG4G=mUTVCuayh4_kqfjEoNT_XEt6+FF24jF2KhLu0nWb8tw@mail.gmail.com"
class="">
<div dir="ltr" class="">
<div dir="ltr" class="">On Wed, Sep 22, 2021 at
3:04 AM Karin&NiKo <<a
href="mailto:niko.karin@gmail.com"
moz-do-not-send="true"
class="moz-txt-link-freetext">niko.karin@gmail.com</a>>
wrote:<br class="">
</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" class="">Dear Matthew,
<div class=""><br class="">
</div>
<div class="">This is great news!</div>
<div class="">For my part, I would be mostly
interested in the parallel input
interface. Sorry for that... </div>
<div class="">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 class=""> 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 class=""><br class="">
</div>
<div class="">An MED interface does exist. I
stopped using it for two reasons:</div>
<div class=""><br class="">
</div>
<div class=""> 1) The code was not portable and
the build was failing on different
architectures. I had to manually fix it.</div>
<div class=""><br class="">
</div>
<div class=""> 2) The boundary markers did not
provide global information, so that parallel
reading was much harder.</div>
<div class=""><br class="">
</div>
<div class="">Feel free to update my MED reader
to a better design.</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class=""> </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" class="">
<div class="">Best regards,</div>
<div class="">Nicolas</div>
<div class=""><br class="">
</div>
</div>
<br class="">
<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" moz-do-not-send="true"
class="moz-txt-link-freetext">knepley@gmail.com</a>>
a écrit :<br class="">
</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" class="">
<div dir="ltr" class="">On Tue, Sep 21,
2021 at 10:31 AM Karin&NiKo <<a
href="mailto:niko.karin@gmail.com"
target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">niko.karin@gmail.com</a>>
wrote:<br class="">
</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" class="">Dear Eric,
dear Matthew,
<div class=""><br class="">
</div>
<div class="">I share Eric's
desire to be able to manipulate
meshes composed of different
types of elements in a PETSc's
DMPlex. </div>
<div class="">Since this
discussion, is there anything
new on this feature for the
DMPlex object or am I missing
something?</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Thanks for finding this!</div>
<div class=""><br class="">
</div>
<div class="">Okay, I did a rewrite of
the Plex internals this summer. It
should now be possible to
interpolate a mesh with any</div>
<div class="">number of cell types,
partition it, redistribute it, and
many other manipulations.</div>
<div class=""><br class="">
</div>
<div class="">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 class="">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 class="">parallel I/O. This will
make parallel reading and writing
for checkpointing possible,
supporting topology, geometry,
fields and</div>
<div class="">layouts, for many
meshes in one HDF5 file. I think we
will finish in November.</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Matt</div>
<div class=""> </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" class="">
<div class="">Thanks,</div>
<div class="">Nicolas</div>
</div>
<br class="">
<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"
moz-do-not-send="true"
class="moz-txt-link-freetext">Eric.Chamberland@giref.ulaval.ca</a>>
a écrit :<br class="">
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div class="">
<p class="">Hi,<br class="">
</p>
<div class="">On 2021-07-14
3:14 p.m., Matthew Knepley
wrote:<br class="">
</div>
<blockquote type="cite"
class="">
<div dir="ltr" class="">
<div dir="ltr" class="">On
Wed, Jul 14, 2021 at
1:25 PM Eric Chamberland
<<a
href="mailto:Eric.Chamberland@giref.ulaval.ca" target="_blank"
moz-do-not-send="true"
class="moz-txt-link-freetext">Eric.Chamberland@giref.ulaval.ca</a>>
wrote:<br class="">
</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 class="">
<br class="">
while playing with
DMPlexBuildFromCellListParallel,
I noticed we have to <br
class="">
specify "numCorners"
which is a fixed
value, then gives a
fixed number <br
class="">
of nodes for a series
of elements.<br
class="">
<br class="">
How can I then add,
for example, triangles
and quadrangles into a
DMPlex?<br class="">
</blockquote>
<div class=""><br
class="">
</div>
<div class="">You can't
with that function. It
would be much mich
more complicated if
you could, and I am
not sure</div>
<div class="">it is
worth it for that
function. The reason
is that you would need
index information to
offset into the</div>
<div class="">connectivity
list, and that would
need to be replicated
to some extent so that
all processes know
what</div>
<div class="">the others
are doing. Possible,
but complicated.</div>
<div class=""><br
class="">
</div>
<div class="">Maybe I
can help suggest
something for what you
are trying to do?</div>
</div>
</div>
</blockquote>
<p class="">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 class="">When we directly
use
ParMETIS_V3_PartMeshKway, we
give two arrays to describe
the elements which allows
mixed elements.</p>
<p class="">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 class="">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 class="">Thanks,</p>
<p class="">Eric<br class="">
</p>
<p class=""><br class="">
</p>
<blockquote type="cite"
class="">
<div dir="ltr" class="">
<div class="gmail_quote">
<div class=""><br
class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br
class="">
</div>
<div class=""> Matt</div>
<div class=""><br
class="">
</div>
<div class=""> </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 class="">
<br class="">
Eric<br class="">
<br class="">
-- <br class="">
Eric Chamberland,
ing., M. Ing<br
class="">
Professionnel de
recherche<br class="">
GIREF/Université Laval<br
class="">
(418) 656-2131 poste
41 22 42<br class="">
<br class="">
</blockquote>
</div>
<br class="" clear="all">
<div class=""><br class="">
</div>
-- <br class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr"
class="">
<div class="">
<div dir="ltr"
class="">
<div class="">What
most
experimenters
take for
granted before
they begin
their
experiments is
infinitely
more
interesting
than any
results to
which their
experiments
lead.<br
class="">
-- Norbert
Wiener</div>
<div class=""><br
class="">
</div>
<div class=""><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fgngRI84CI_6fHdWdRiVbv0bvraQkhXyV396Uo5y2mORbR4DjlMYrHTqX0p22Ysp8t9yJPhCL1E3fkbWxmIZpQp6dYhcdaKz9w0270gm$" target="_blank" moz-do-not-send="true" class="">https://www.cse.buffalo.edu/~knepley/</a><br
class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre cols="72" class="">--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42</pre>
</div>
</blockquote>
</div>
</blockquote>
</div>
<br class="" clear="all">
<div class=""><br class="">
</div>
-- <br class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">What most
experimenters take for
granted before they begin
their experiments is
infinitely more
interesting than any
results to which their
experiments lead.<br
class="">
-- Norbert Wiener</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fgngRI84CI_6fHdWdRiVbv0bvraQkhXyV396Uo5y2mORbR4DjlMYrHTqX0p22Ysp8t9yJPhCL1E3fkbWxmIZpQp6dYhcdaKz9w0270gm$" target="_blank" moz-do-not-send="true" class="">https://www.cse.buffalo.edu/~knepley/</a><br
class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
<br class="" clear="all">
<div class=""><br class="">
</div>
-- <br class="">
<div dir="ltr" class="gmail_signature">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">
<div dir="ltr" class="">
<div class="">What most experimenters
take for granted before they begin
their experiments is infinitely more
interesting than any results to
which their experiments lead.<br
class="">
-- Norbert Wiener</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fgngRI84CI_6fHdWdRiVbv0bvraQkhXyV396Uo5y2mORbR4DjlMYrHTqX0p22Ysp8t9yJPhCL1E3fkbWxmIZpQp6dYhcdaKz9w0270gm$" target="_blank" moz-do-not-send="true" class="">https://www.cse.buffalo.edu/~knepley/</a><br
class="">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<pre class="moz-signature" 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 class="">
</div>
</div>
</blockquote>
<pre class="moz-signature" 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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