[petsc-users] PetscSF Object on Distributed DMPlex for Halo Data Exchange

Matthew Knepley knepley at gmail.com
Tue May 31 09:34:41 CDT 2022 

On Tue, May 31, 2022 at 10:26 AM Mike Michell <mi.mike1021 at gmail.com> wrote:

> Thank you. But, it seems that PetscSFCreateSectionSF() also requires
> petscsf.h file. Which header file I should include to call
> PetscSFCreateSectionSF() from Fortran?
>

I will have to write a binding. I will send you the MR when I finish.

  THanks,

    Matt


> Thanks,
> Mike
>
>
> On Tue, May 31, 2022 at 10:04 AM Mike Michell <mi.mike1021 at gmail.com>
>> wrote:
>>
>>> As a follow-up question on your example, is it possible to call
>>> PetscSFCreateRemoteOffsets() from Fortran?
>>>
>>> My code is written in .F90 and in "petsc/finclude/" there is no
>>> petscsf.h so that the code currently cannot find
>>> PetscSFCreateRemoteOffsets().
>>>
>>
>> I believe if you pass in NULL for remoteOffsets, that function will be
>> called internally.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks,
>>> Mike
>>>
>>>
>>> I will also point out that Toby has created a nice example showing how
>>>> to create an SF for halo exchange between local vectors.
>>>>
>>>>   https://gitlab.com/petsc/petsc/-/merge_requests/5267
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>> On Sun, May 22, 2022 at 9:47 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Sun, May 22, 2022 at 4:28 PM Mike Michell <mi.mike1021 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Thanks for the reply. The diagram makes sense and is helpful for
>>>>>> understanding 1D representation.
>>>>>>
>>>>>> However, something is still unclear. From your diagram, the number of
>>>>>> roots per process seems to vary according to run arguments, such as
>>>>>> "-dm_distribute_overlap", because "the number of roots for a DMPlex is the
>>>>>> number of mesh points in the local portion of the mesh (cited from your
>>>>>> answer to my question (1))" will end up change according to that argument.
>>>>>> However, from my mock-up code, number of roots is independent to
>>>>>> -dm_distribute_overlap argument. The summation of "number of roots" through
>>>>>> processes was always equal to number of physical vertex on my mesh, if I
>>>>>> define the section layout on vertex with 1DOF. But in your diagram example,
>>>>>> the summation of "nroots" is larger than the actual number of mesh points,
>>>>>> which is 13.
>>>>>>
>>>>>
>>>>> I do not understand your question. Notice the -dm_distribute_overlap
>>>>> does _not_ change the owned points for any process. It only puts in new
>>>>> leaves, so it also never
>>>>> changes the roots for this way of using the SF.
>>>>>
>>>>>
>>>>>> Also, it is still unclear how to get the size of "roots" from the
>>>>>> PetscSection & PetscSF on distributed DMPlex?
>>>>>>
>>>>>
>>>>> For an SF mapping ghost dofs in a global vector, the number of roots
>>>>> is just the size of the local portion of the vector.
>>>>>
>>>>>
>>>>>> In your diagram, how can you tell your code and make it allocate the
>>>>>> "nroots=7 for P0, nroots=9 for P1, and nroots=7 for P2" arrays before you
>>>>>> call PetscSFBcastBegin/End()? It seems that we need to define arrays having
>>>>>> the size of nroots & nleaves before calling PetscSFBcastBegin/End().
>>>>>>
>>>>>
>>>>> I just want to note that this usage is different from the canonical
>>>>> usage in Plex. It is fine to do this, but this will not match what I do in
>>>>> the library if you look.
>>>>> In Plex, I distinguish two linear spaces:
>>>>>
>>>>>   1) Global space: This is the vector space for the solvers. Each
>>>>> point is uniquely represented and owned by some process
>>>>>
>>>>>   2) Local space: This is the vector space for assembly. Some points
>>>>> are represented multiple times.
>>>>>
>>>>> I create an SF that maps from the global space (roots) to the local
>>>>> space (leaves), and it is called in DMGlobalToLocal() (and
>>>>> associated functions). This
>>>>> is more natural in FEM. You seem to want an SF that maps between
>>>>> global vectors. This will also work. The roots would be the local dofs, and
>>>>> the leaves
>>>>> would be shared dofs.
>>>>>
>>>>>   Does this make sense?
>>>>>
>>>>>      Thanks,
>>>>>
>>>>>        Matt
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>> Mike
>>>>>>
>>>>>> Here's a diagram of a 1D mesh with overlap and 3 partitions, showing
>>>>>>> what the petscsf data is for each.  The number of roots is the number of
>>>>>>> mesh points in the local representation, and the number of leaves is the
>>>>>>> number of mesh points that are duplicates of mesh points on other
>>>>>>> processes.  With that in mind, answering your questions
>>>>>>>
>>>>>>> > (1) It seems that the "roots" means the number of vertex not
>>>>>>> considering overlap layer, and "leaves" seems the number of distributed
>>>>>>> vertex for each processor that includes overlap layer. Can you acknowledge
>>>>>>> that this is correct understanding? I have tried to find clearer examples
>>>>>>> from PETSc team's articles relevant to Star Forest, but I am still unclear
>>>>>>> about the exact relation & graphical notation of roots & leaves in SF if
>>>>>>> it's the case of DMPlex solution arrays.
>>>>>>>
>>>>>>> No, the number of roots for a DMPlex is the number of mesh points in
>>>>>>> the local portion of the mesh
>>>>>>>
>>>>>>> > (2) If it is so, there is an issue that I cannot define "root
>>>>>>> data" and "leave data" generally. I am trying to following
>>>>>>> "src/vec/is/sf/tutorials/ex1f.F90", however, in that example, size of roots
>>>>>>> and leaves are predefined as 6. How can I generalize that? Because I can
>>>>>>> get size of leaves using DAG depth(or height), which is equal to number of
>>>>>>> vertices each proc has. But, how can I get the size of my "roots" region
>>>>>>> from SF? Any example about that? This question is connected to how can I
>>>>>>> define "rootdata" for "PetscSFBcastBegin/End()".
>>>>>>>
>>>>>>> Does the diagram help you generalize?
>>>>>>>
>>>>>>> > (3) More importantly, with the attached PetscSection & SF layout,
>>>>>>> my vector is only resolved for the size equal to "number of roots" for each
>>>>>>> proc, but not for the overlapping area(i.e., "leaves"). What I wish to do
>>>>>>> is to exchange (or reduce) the solution data between each proc, in the
>>>>>>> overlapping region. Can I get some advices why my vector does not encompass
>>>>>>> the "leaves" regime? Is there any example doing similar things?
>>>>>>> Going back to my first response: if you use a section to say how
>>>>>>> many pieces of data are associated with each local mesh point, then a
>>>>>>> PetscSF is constructed that requires no more manipulation from you.
>>>>>>>
>>>>>>>
>>>>>>> On Sun, May 22, 2022 at 10:47 AM Mike Michell <mi.mike1021 at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Thank you for the reply.
>>>>>>>> The PetscSection and PetscSF objects are defined as in the attached
>>>>>>>> mock-up code (Q_PetscSF_1.tar). 1-DOF is defined on vertex as my solution
>>>>>>>> is determined on each vertex with 1-DOF from a finite-volume method.
>>>>>>>>
>>>>>>>> As follow up questions:
>>>>>>>> (1) It seems that the "roots" means the number of vertex not
>>>>>>>> considering overlap layer, and "leaves" seems the number of distributed
>>>>>>>> vertex for each processor that includes overlap layer. Can you acknowledge
>>>>>>>> that this is correct understanding? I have tried to find clearer examples
>>>>>>>> from PETSc team's articles relevant to Star Forest, but I am still unclear
>>>>>>>> about the exact relation & graphical notation of roots & leaves in SF if
>>>>>>>> it's the case of DMPlex solution arrays.
>>>>>>>>
>>>>>>>> (2) If it is so, there is an issue that I cannot define "root data"
>>>>>>>> and "leave data" generally. I am trying to following
>>>>>>>> "src/vec/is/sf/tutorials/ex1f.F90", however, in that example, size of roots
>>>>>>>> and leaves are predefined as 6. How can I generalize that? Because I can
>>>>>>>> get size of leaves using DAG depth(or height), which is equal to number of
>>>>>>>> vertices each proc has. But, how can I get the size of my "roots" region
>>>>>>>> from SF? Any example about that? This question is connected to how can I
>>>>>>>> define "rootdata" for "PetscSFBcastBegin/End()".
>>>>>>>>
>>>>>>>> (3) More importantly, with the attached PetscSection & SF layout,
>>>>>>>> my vector is only resolved for the size equal to "number of roots" for each
>>>>>>>> proc, but not for the overlapping area(i.e., "leaves"). What I wish to do
>>>>>>>> is to exchange (or reduce) the solution data between each proc, in the
>>>>>>>> overlapping region. Can I get some advices why my vector does not encompass
>>>>>>>> the "leaves" regime? Is there any example doing similar things?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Mike
>>>>>>>>
>>>>>>>>
>>>>>>>>> On Fri, May 20, 2022 at 4:45 PM Mike Michell <
>>>>>>>>> mi.mike1021 at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Thanks for the reply.
>>>>>>>>>>
>>>>>>>>>> > "What I want to do is to exchange data (probably just
>>>>>>>>>> MPI_Reduce)" which confuses me, because halo exchange is a point-to-point
>>>>>>>>>> exchange and not a reduction.  Can you clarify?
>>>>>>>>>> PetscSFReduceBegin/End seems to be the function that do reduction
>>>>>>>>>> for PetscSF object. What I intended to mention was either reduction or
>>>>>>>>>> exchange, not specifically intended "reduction".
>>>>>>>>>>
>>>>>>>>>> As a follow-up question:
>>>>>>>>>> Assuming that the code has its own local solution arrays (not
>>>>>>>>>> Petsc type), and if the plex's DAG indices belong to the halo region are
>>>>>>>>>> the only information that I want to know (not the detailed section
>>>>>>>>>> description, such as degree of freedom on vertex, cells, etc.). I have
>>>>>>>>>> another PetscSection for printing out my solution.
>>>>>>>>>> Also if I can convert that DAG indices into my local cell/vertex
>>>>>>>>>> index, can I just use the PetscSF object created from DMGetPointSF(),
>>>>>>>>>> instead of "creating PetscSection + DMGetSectionSF()"? In other words, can
>>>>>>>>>> I use the PetscSF object declared from DMGetPointSF() for the halo
>>>>>>>>>> communication?
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> No, because that point SF will index information by point number.
>>>>>>>>> You would need to build a new SF that indexes your dofs. The steps you would
>>>>>>>>> go through are exactly the same as you would if you just told us
>>>>>>>>> what the Section is that indexes your data.
>>>>>>>>>
>>>>>>>>>   Thanks,
>>>>>>>>>
>>>>>>>>>      Matt
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> Mike
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> The PetscSF that is created automatically is the "point sf" (
>>>>>>>>>>> https://petsc.org/main/docs/manualpages/DM/DMGetPointSF/): it
>>>>>>>>>>> says which mesh points (cells, faces, edges and vertices) are duplicates of
>>>>>>>>>>> others.
>>>>>>>>>>>
>>>>>>>>>>> In a finite volume application we typically want to assign
>>>>>>>>>>> degrees of freedom just to cells: some applications may only have one
>>>>>>>>>>> degree of freedom, others may have multiple.
>>>>>>>>>>>
>>>>>>>>>>> You encode where you want degrees of freedom in a PetscSection
>>>>>>>>>>> and set that as the section for the DM in DMSetLocalSection() (
>>>>>>>>>>> https://petsc.org/release/docs/manualpages/DM/DMSetLocalSection.html
>>>>>>>>>>> )
>>>>>>>>>>>
>>>>>>>>>>> (A c example of these steps that sets degrees of freedom for
>>>>>>>>>>> *vertices* instead of cells is `src/dm/impls/plex/tutorials/ex7.c`)
>>>>>>>>>>>
>>>>>>>>>>> After that you can call DMGetSectionSF() (
>>>>>>>>>>> https://petsc.org/main/docs/manualpages/DM/DMGetSectionSF/) to
>>>>>>>>>>> the the PetscSF that you want for halo exchange: the one for your solution
>>>>>>>>>>> variables.
>>>>>>>>>>>
>>>>>>>>>>> After that, the only calls you typically need in a finite volume
>>>>>>>>>>> code is PetscSFBcastBegin() to start a halo exchange and PetscSFBcastEnd()
>>>>>>>>>>> to complete it.
>>>>>>>>>>>
>>>>>>>>>>> You say
>>>>>>>>>>>
>>>>>>>>>>> > What I want to do is to exchange data (probably just
>>>>>>>>>>> MPI_Reduce)
>>>>>>>>>>>
>>>>>>>>>>> which confuses me, because halo exchange is a point-to-point
>>>>>>>>>>> exchange and not a reduction.  Can you clarify?
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, May 20, 2022 at 8:35 PM Mike Michell <
>>>>>>>>>>> mi.mike1021 at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Dear PETSc developer team,
>>>>>>>>>>>>
>>>>>>>>>>>> Hi, I am using DMPlex for a finite-volume code and trying to
>>>>>>>>>>>> understand the usage of PetscSF. What is a typical procedure for doing halo
>>>>>>>>>>>> data exchange at parallel boundary using PetscSF object on DMPlex? Is there
>>>>>>>>>>>> any example that I can refer to usage of PetscSF with distributed DMPlex?
>>>>>>>>>>>>
>>>>>>>>>>>> Assuming to use the attached mock-up code and mesh, if I give
>>>>>>>>>>>> "-dm_distribute_overlap 1 -over_dm_view" to run the code, I can see a
>>>>>>>>>>>> PetscSF object is already created, although I have not called
>>>>>>>>>>>> "PetscSFCreate" in the code. How can I import & use that PetscSF already
>>>>>>>>>>>> created by the code to do the halo data exchange?
>>>>>>>>>>>>
>>>>>>>>>>>> What I want to do is to exchange data (probably just
>>>>>>>>>>>> MPI_Reduce) in a parallel boundary region using PetscSF and its functions.
>>>>>>>>>>>> I might need to have an overlapping layer or not.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>> Mike
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> 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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