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

Fri Jul 15 07:17:34 CDT 2022

A sample code for loading dm and declaring Natural SF from a sphere mesh is
attached here. PetscSFView() returns NULL from sf_nat.

Best

On Fri, Jul 15, 2022 at 6:39 AM Matthew Knepley <knepley at gmail.com> wrote:

> 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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