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

Bora Jeong boraj1021 at gmail.com
Fri Jul 15 17:10:35 CDT 2022 

Thank you for the reply.
In that example, it seems that the sizes of each array are known values and
are provided to PetscSFSetGraph() at line 63. How does it change if those
sizes are unknown? When a mesh file is loaded to a dm and define PetscSF,
those sizes might be unknown.

In my test,
If pointers are defined as
   PetscInt, pointer                   :: iroots(:)
   type(PetscSFNode), pointer :: ileaves(:)

And then call PetscSFGetGraph() as,
   call PetscSFGetGraph(sf_nat, nroots, nleaves, iroots, ileaves,
ierr);CHKERRA(ierr)

I got this error message:
   forrtl: severe (408): fort: (7): Attempt to use pointer IROOTS when it
is not associated with a target

If a target vector with an arbitrary size is associated with the pointers,
there is no error message. However, the proper size of target vectors is
unclear to me. Is it number of processors? or number roots for each
processor? anything else?

Best

On Fri, Jul 15, 2022 at 3:53 PM Matthew Knepley <knepley at gmail.com> wrote:

> 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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