[petsc-users] Function to convert a dense matrix holding the cell connectivity to a MPIADJ for use with MatMeshToCellGraph

[Jordan Wagner]

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
[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
[0]PETSC ERROR:
[0]PETSC ERROR: See 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