Thanks for the quick reply!
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?
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?
Really appreciate it.
On 12/12/2017 03:54 PM, Matthew Knepley wrote:
Barry wrote this, so he probably knows how to fix it.
Another option is to use DMPlex for your mesh. It will give you the
dual if you want.
Thanks,
Matt
On Tue, Dec 12, 2017 at 3:44 PM, Jordan Wagner <[email protected]
<mailto:[email protected]>> wrote:
Hi,
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.
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?
Thanks very much for any tips.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or
-on_error_attach_debugger
[0]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
<http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple
Mac OS X to find memory corruption errors
[0]PETSC ERROR: PetscMallocValidate: error detected at
PetscSignalHandlerDefault() line 145 in
/home/jordan/petsc/src/sys/error/signal.c
[0]PETSC ERROR: Memory [id=0(16)] at address 0x1b4cb80 is
corrupted (probably write past end of array)
[0]PETSC ERROR: Memory originally allocated in
MatConvertFrom_MPIAdj() line 444 in
/home/jordan/petsc/src/mat/impls/adj/mpi/mpiadj.c
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Memory corruption:
http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
<http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind>
[0]PETSC ERROR:
[0]PETSC ERROR: See
http://www.mcs.anl.gov/petsc/documentation/faq.html
<http://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble
shooting.
[0]PETSC ERROR: Petsc Release Version 3.8.2, unknown
[0]PETSC ERROR: ./preprocess.exe on a arch-linux2-c-debug named
jordan-nest by jordan Tue Dec 12 14:40:02 2017
[0]PETSC ERROR: Configure options --with-shared-libraries=1
--download-metis --download-parmetis
[0]PETSC ERROR: #1 PetscMallocValidate() line 146 in
/home/jordan/petsc/src/sys/memory/mtr.c
[0]PETSC ERROR: #2 PetscSignalHandlerDefault() line 145 in
/home/jordan/petsc/src/sys/error/signal.c
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which
their experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/%7Emk51/>
