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

[Matthew Knepley]

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 <j.wagner at rice.edu> 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/d
> ocumentation/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/err
> or/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/d
> ocumentation/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
>
>
>
>


-- 
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/~mk51/>
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