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

Matthew Knepley knepley at gmail.com
Fri Jul 15 08:07:38 CDT 2022 

On Fri, Jul 15, 2022 at 7:17 AM Bora Jeong <boraj1021 at gmail.com> wrote:

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

The Global-to-Natural mapping relates global dofs to natural dofs. Thus, in
order to compute this mapping the DM has to know
about the dof layout before distribution. This means you need to setup a
local section before distributing, as we do for example in
Plex test ex15. This makes things more complicated since everything cannot
be packaged up into DMSetFromOptions(), but we need
user input so I do not see a simpler way to do things.

  Thanks,

    Matt


> 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/>
>>
>

-- 
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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