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

[Matthew Knepley]

On Thu, Jul 14, 2022 at 8:25 PM Bora Jeong <boraj1021 at gmail.com> wrote:

> Okay, I checked it and you are correct. In my case, simply, natural node
> index can be identified by stacking all the preceding processor's numbers
> of nodes for a particular processor, which is good due to simplicity.
> However, one serious question is why this is happening in my code? In other
> words, why the natural SF is not created during the mesh distribution? My
> code wants to have consistency in dealing with this natural indexing for
> several different kinds of mesh files. So there is a necessity to guarantee
> of consistency in this weird behavior.
>

I can't tell what is going on in your code unless I can run it. Do you have
a simple example?

  Thanks,

     Matt


> Best,
>
> On Thu, Jul 14, 2022 at 6:43 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Thu, Jul 14, 2022 at 5:47 PM Bora Jeong <boraj1021 at gmail.com> wrote:
>>
>>> 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
>>>
>>
>> Clearly NULL was returned, which means no natural SF was created.
>>
>>
>>> 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)
>>>
>>
>> The natural SF is created during mesh distribution. That has not happened
>> here. This means that
>> the order of cells is identical to the file it was read from.
>>
>>   Thanks,
>>
>>       Matt
>>
>>
>>> 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/>
>>>>
>>>
>>
>> --
>> 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/>
>>
>

-- 
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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