[petsc-users] DMPlex: a Mapping Array between Natural and Distributed Cell Index

[Bora Jeong]

Thank you for the comments. I have these errors when I call PetscSFView()
after DMGetNaturalSF()

[2]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[2]PETSC ERROR: Null argument, when expecting valid pointer
[2]PETSC ERROR: Null Pointer: Parameter # 1
[2]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[2]PETSC ERROR: Petsc Release Version 3.17.0, unknown
[2]PETSC ERROR: #1 PetscSFView() at
[2]PETSC ERROR: #2 User provided function() at User file:0
Abort(85) on node 2 (rank 0 in comm 16): application called
MPI_Abort(MPI_COMM_SELF, 85) - process 0


Below is the structure to load a mesh file from gmsh;

  call DMCreate(PETSC_COMM_WORLD, dm, ierr);CHKERRA(ierr)
  call DMSetType(dm, plex, ierr);CHKERRA(ierr)
  call DMSetUseNatural(dm, PETSC_TRUE, ierr);CHKERRA(ierr)
  call DMSetFromOptions(dm, ierr);CHKERRA(ierr)
  call DMGetNaturalSF(dm, sf_nat, ierr);CHKERRA(ierr)
  call PetscSFView(sf_nat, PETSC_VIEWER_STDOUT_WORLD, ierr);CHKERRA(ierr)

Best

On Thu, Jul 14, 2022 at 10:49 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Jul 13, 2022 at 10:17 PM Bora Jeong <boraj1021 at gmail.com> wrote:
>
>> Dear petsc team,
>>
>> I am a user of DMPlex for a finite volume code and there is a necessity
>> to know global index of each cell. Here the global index means the indexing
>> that can be found from a mesh file itself without distribution over
>> processors. It seems petsc community denotes this indexing term as
>> "natural".
>>
>> What I want to do is to create a local array (not petsc vector but just
>> an array variable in the program) to map distributed cell ID to natual cell
>> ID, for example, an array "A";
>> A(distributed_node_ID) = natural_node_ID
>>
>> There are some petsc functions to support mapping between global and
>> natural vectors. However, I just need to define the array "A" as above
>> example. To achieve this, what is a proper/smart way? In other words, how
>> can I extract the natural_cell_ID from a distributed local_cell_ID?
>>
>> I turned on DMSetUseNatural(DM, PETSC_TRUE) before distribution, but
>> after this, defining all the required section and star forest objects to
>> get natural and global vectors seems not that direct way for my purpose,
>> which is just to extract the above mapping array "A". Can I get any
>> comments about it?
>>
>
> There is only one thing created, the sfNatural PetscSF object, which you
> can get with DMGetNaturalSF(). The roots of this SF are
> the global numbers of dofs stored in PETSc vectors, and the leaves are
> natural numbers for these dofs. Thus, when we map global
> vectors to natural vectors in DMPlexGlobalToNaturalBegin/End(), we
> call PetscSFBcastBegin/End(). Mapping natural to global we call
> PetscSFReduceBegin/End(). You could pull the information out of the SF
> using PetscSFGetGraph() if you want.
>
>   Thanks,
>
>     Matt
>
>
>> Regards
>> Mo
>>
>
>
> --
> 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.cse.buffalo.edu/~knepley/>
>
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