<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Dec 20, 2017 at 11:08 AM, Yann JOBIC <span dir="ltr"><<a href="mailto:yann.jobic@univ-amu.fr" target="_blank">yann.jobic@univ-amu.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="m_-7806503419130730542m_-2865967129517278233moz-cite-prefix">On 12/19/2017 05:50 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">On Tue, Dec 19, 2017 at 11:40 AM,
Yann JOBIC <span dir="ltr"><<a href="mailto:yann.jobic@univ-amu.fr" target="_blank">yann.jobic@univ-amu.fr</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
We want to extract the cell connectivity from a DMPlex. We
have no problem for a sequential run.<br>
</blockquote>
<div><br>
</div>
<div>Do you want it on disk? If so, you can just DMView()
for HDF5. That outputs the connectivity in a global
numbering.</div>
<div>I can show you the calls I use inside if you want. </div>
</div>
</div>
</div>
</blockquote>
I looked at the code, specifically
DMPlexWriteTopology_Vertices_H<wbr>DF5_Static<br>
cellIS should have what i want. <br>
However it seems that it is not the case. Do i look at the right
spot in the code ?<br></div></blockquote><div><br></div><div>cellIS has the entire connectivity. You sound like you want cell-vertex only. You could get that by just</div><div><br></div><div> DMPlexUninterpolate(dm, &udm);</div><div> <get your cellIS from udm></div><div> DMDestroy(&udm);</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
I also looked at DMPlexGetCellNumbering, which does exactly what i
want for the global numbering of Cells, even if the ordering is
different for different number of processors.<br></div></blockquote><div><br></div><div>Yes.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
When i use DMPlexGetVertexNumbering, i've got negative values, which
is correctly handeled by DMPlexWriteTopology_Vertices_H<wbr>DF5_Static,
but i really don't understand this part.<br></div></blockquote><div><br></div><div>There are no shared cells in your partition, so you get all positive numbers. You have shared vertices, so the negative numbers are for vertices</div><div>you do not own. If the negative number is n, the corresponding global number is -(n+1). Notice that the transformation is 1-1 and its square is I.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
I succeed in having the coordinates, but maybe not in the right
order. I reused DMPlexWriteCoordinates_HDF5_St<wbr>atic, which create a
Vec of vertex coordinates, but i couldn't understand the order of
vertex coordinate linked (or not) with
DMPlexWriteTopology_Vertices_H<wbr>DF5_Static. The number of local
coordinates is also strange, and does not correspond to the cell's
topology. <br></div></blockquote><div><br></div><div>It matches the order of the global numbering.</div><div><br></div><div> Thanks</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000">
Thanks for the help!<br>
<br>
Regards,<br>
<br>
Yann<br>
<br>
<br>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_extra">
<div class="gmail_quote">
<div>I usually put</div>
<div><br>
</div>
<div> DMViewFromOptions(dm, NULL, "-dm_view")</div>
<div><br>
</div>
<div>Then</div>
<div><br>
</div>
<div> -dm_view hdf5:mesh.h5</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
However for parallel ones, we need to get the node
numbering in the global ordering, as when we distribute
the mesh, we only have local nodes, and thus local
numbering.<br>
<br>
It seems that we should use DMGetLocalToGlobalMapping (we
are using Fortran with Petsc 3.8p3). However, we get the
running error :<br>
<br>
[0]PETSC ERROR: No support for this operation for this
object type<br>
[0]PETSC ERROR: DM can not create LocalToGlobalMapping<br>
<br>
Is it the right way to do it ?<br>
<br>
Many thanks,<br>
<br>
Regards,<br>
<br>
Yann<br>
<br>
</blockquote>
</div>
<br>
<br clear="all"><span class="m_-7806503419130730542HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_-7806503419130730542m_-2865967129517278233gmail_signature" data-smartmail="gmail_signature">
<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="http://www.caam.rice.edu/%7Emk51/" target="_blank">https://www.cse.buffalo.edu/~k<wbr>nepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></div>
</div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="m_-7806503419130730542gmail_signature" data-smartmail="gmail_signature"><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="http://www.caam.rice.edu/~mk51/" target="_blank">https://www.cse.buffalo.edu/~<wbr>knepley/</a><br></div></div></div></div></div>
</div></div>