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

Mike Michell mi.mike1021 at gmail.com
Tue May 31 09:25:50 CDT 2022 

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

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/>
>
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