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

Matthew Knepley knepley at gmail.com
Fri Jul 15 15:52:54 CDT 2022 

On Fri, Jul 15, 2022 at 2:25 PM Bora Jeong <boraj1021 at gmail.com> wrote:

> Thank you for the comments. Updated sample code is attached here;
> DMPlexDistribute() is explicitly called and by defining a section before
> mesh distribution, a Natural SF was able to be defined as found from
> PetscSFView().
>
> However, I am still struggling to call PetscSFGetGraph()
> https://petsc.org/main/docs/manualpages/PetscSF/PetscSFGetGraph/
> due to data type definition of ilocal and iremote. What is the proper size
> allocation for those two variables? Does this size for the number of
> processors? or the number of vertex?
>

Since we need to pass back arrays, you need to pass us in F90 pointers.
Here is an example of doing such a thing:


https://gitlab.com/petsc/petsc/-/blob/main/src/vec/is/sf/tutorials/ex1f.F90#L94

  Thanks,

      Matt


> Best
>
> On Fri, Jul 15, 2022 at 9:09 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Fri, Jul 15, 2022 at 8:46 AM Bora Jeong <boraj1021 at gmail.com> wrote:
>>
>>> Okay, I got it what's happening. First, this very bright functionality
>>> of petsc (the natural-global converting) needs to be documented in a better
>>> way for sure. Currently, it is very difficult to use/follow this features
>>> as an external user. Hope this will move forward in a better way.
>>>
>>> Then next question is if I load/distribute mesh just like I am doing
>>> right now shown in the sample code, can I assume that my code does not
>>> create natural sf during the distribution(always)? In other words, can I
>>> always get the natural order of each node by simply stacking the preceding
>>> processor's number of node? For example, for proc=0, natural node ID might
>>> be just 1 to nnode_proc_0,
>>> for proc=1, it might be {nnode_proc_0 + 1 to nnode_proc_0 +
>>> nnode_proc_1} and so on.
>>>
>>> Does that always make sense in this case?
>>>
>>
>> No, but if you call DMPlexDistribute() yourself, rather than having it
>> called automatically by DMSetFromOptions(), you can
>> preserve the mapping:
>>
>>   https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexDistribute/
>>
>> The SF returned maps the original point distribution, which is in the
>> same order as the file, to the redistributed points, which are determined
>> by the mesh partitioner.
>>
>>   Thanks,
>>
>>       Matt
>>
>>
>>> Best
>>>
>>>
>>> On Fri, Jul 15, 2022 at 8:07 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> 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/>
>>>>
>>>
>>
>> --
>> 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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