<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Tue, Dec 12, 2017 at 7:30 PM, Jordan Wagner <span dir="ltr"><<a href="mailto:j.wagner@rice.edu" target="_blank">j.wagner@rice.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p>Thanks for the quick reply! <br>
</p>
<p>I have been reviewing DMPlex for a few weeks. It looks awesome (I
like topology :) ); great work. I planned on implementing it in my
code sooner or later. The problem for me, however, is that I am
mainly using multi-section CGNS meshes in my code. This currently
isn't supported in DMPlexCreateCGNS. Though, I guess I could just
use DMPlexCreateFromCellList. Would that be the route you would
recommend for creating a DMPlex with a connectivity matrix that I
have extracted myself from the cgns file?<br>
</p>
<p></p></div></blockquote><div>Yes, I think that is the best way. That is what I do in the CGNS code I believe. We have much more complete support for ExodusII and Gmsh (and MED). </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF"><p>I've been somewhat contemplating trying to add multi-section
capability to the DMPlexCreateCGNS function; however, I figured
there was a good reason why this wasn't already done and assumed
would take me way longer than you guys who are much more
knowledgeable. Would this be something worth thinking more about?
</p></div></blockquote><div>Actually, it is not done because a) I know very little about CGNS, b) no one has ever requested it and c) we got requests for other formats. I believe it would not be that</div><div>hard and we could help you. Most of the ExodusII support was done by a user (Blaise Bourdin) and the GMsh support by Lisandro and Stefano, and the MED support</div><div>by Michael Lange, so most of this stuff is not from me.</div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
<p>Really appreciate it.<br>
</p>
<br>
<div class="m_-3584301775419722269moz-cite-prefix">On 12/12/2017 03:54 PM, Matthew Knepley
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Barry wrote this, so he probably knows how to fix
it.
<div><br>
</div>
<div>Another option is to use DMPlex for your mesh. It will give
you the dual if you want.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div> Matt</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Dec 12, 2017 at 3:44 PM, Jordan
Wagner <span dir="ltr"><<a href="mailto:j.wagner@rice.edu" target="_blank">j.wagner@rice.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I am trying to use the function MatMeshToCellGraph. I
currently have a matrix that holds the cell connectivity of
simplex elements. So it is a numCells x 3 matrix where the
row corresponds to the cell number and the column is a
vertex of that cell. To use this function, it appears I need
to get the corresponding adjacency matrix.<br>
<br>
I found the function MatConvert, which I was hoping could be
the function I am looking for, but I keep getting a memory
error when using it, which I have added at the bottom. Is
this the correct function to use to convert my cell
connectivity matrix, or do I need to loop through to get the
proper offsets (i,j) needed to create the adjacency matrix
with MatCreateMPIAdj, as is done in ex11.c?<br>
<br>
Thanks very much for any tips.<br>
<br>
<br>
[0]PETSC ERROR: ------------------------------<wbr>------------------------------<wbr>------------<br>
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range<br>
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger<br>
[0]PETSC ERROR: or see <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html#valgrind</a><br>
[0]PETSC ERROR: or try <a href="http://valgrind.org" rel="noreferrer" target="_blank">http://valgrind.org</a>
on GNU/linux and Apple Mac OS X to find memory corruption
errors<br>
[0]PETSC ERROR: PetscMallocValidate: error detected at
PetscSignalHandlerDefault() line 145 in
/home/jordan/petsc/src/sys/err<wbr>or/signal.c<br>
[0]PETSC ERROR: Memory [id=0(16)] at address 0x1b4cb80 is
corrupted (probably write past end of array)<br>
[0]PETSC ERROR: Memory originally allocated in
MatConvertFrom_MPIAdj() line 444 in
/home/jordan/petsc/src/mat/imp<wbr>ls/adj/mpi/mpiadj.c<br>
[0]PETSC ERROR: --------------------- Error Message
------------------------------<wbr>------------------------------<wbr>--<br>
[0]PETSC ERROR: Memory corruption: <a href="http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/installation.html<wbr>#valgrind</a><br>
[0]PETSC ERROR:<br>
[0]PETSC ERROR: See <a href="http://www.mcs.anl.gov/petsc/documentation/faq.html" rel="noreferrer" target="_blank">http://www.mcs.anl.gov/petsc/d<wbr>ocumentation/faq.html</a>
for trouble shooting.<br>
[0]PETSC ERROR: Petsc Release Version 3.8.2, unknown<br>
[0]PETSC ERROR: ./preprocess.exe on a arch-linux2-c-debug
named jordan-nest by jordan Tue Dec 12 14:40:02 2017<br>
[0]PETSC ERROR: Configure options --with-shared-libraries=1
--download-metis --download-parmetis<br>
[0]PETSC ERROR: #1 PetscMallocValidate() line 146 in
/home/jordan/petsc/src/sys/mem<wbr>ory/mtr.c<br>
[0]PETSC ERROR: #2 PetscSignalHandlerDefault() line 145 in
/home/jordan/petsc/src/sys/err<wbr>or/signal.c<br>
<br>
<br>
<br>
</blockquote>
</div>
<br>
<br clear="all"><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
-- <br>
<div class="m_-3584301775419722269gmail_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/~<wbr>knepley/</a><br>
</div>
</div>
</div>
</div>
</div>
</font></span></div>
</blockquote>
<br>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_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/~knepley/</a><br></div></div></div></div></div>
</div></div>