[petsc-users] Petsc Section in DMPlex

Matthew Knepley knepley at gmail.com
Wed Dec 7 06:05:39 CST 2022 

On Wed, Dec 7, 2022 at 6:51 AM Nicholas Arnold-Medabalimi <
narnoldm at umich.edu> wrote:

> Hi
>
> Thank you so much for your patience. One thing to note: I don't have any
> need to go back from the filtered distributed mapping back to the full but
> it is good to know.
>
> One aside question.
> 1) Is natural and global ordering the same in this context?
>

No.


> As far as implementing what you have described.
>
> When I call ISView on the generated SubpointIS, I get an unusual error
> which I'm not sure how to interpret. (this case is running on 2 ranks and
> the filter label has points located on both ranks of the original DM.
> However, if I manually get the indices (the commented lines), it seems to
> not have any issues.
> call DMPlexFilter(dmplex_full, iBlankLabel, 1, dmplex_filtered,ierr)
> call DMPlexGetSubpointIS(dmplex_filtered, subpointsIS,ierr)
> !call ISGetIndicesF90(subpointsIS, subPointKey,ierr)
> !write(*,*) subPointKey
> !call ISRestoreIndicesF90(subpointsIS, subPointKey,ierr)
> call ISView(subpointsIS,PETSC_VIEWER_STDOUT_WORLD,ierr)
>
> [1]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [1]PETSC ERROR: Arguments must have same communicators
> [1]PETSC ERROR: Different communicators in the two objects: Argument # 1
> and 2 flag 3
> [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [1]PETSC ERROR: Petsc Development GIT revision: v3.18.1-320-g7810d690132
>  GIT Date: 2022-11-20 20:25:41 -0600
> [1]PETSC ERROR: Configure options with-fc=mpiifort with-mpi-f90=mpiifort
> --download-triangle --download-parmetis --download-metis --with-debugging=1
> --download-hdf5 --prefix=/home/narnoldm/packages/petsc_install
> [1]PETSC ERROR: #1 ISView() at
> /home/narnoldm/packages/petsc/src/vec/is/is/interface/index.c:1629
>

The problem here is the subpointsIS is a _serial_ object, and you are using
a parallel viewer. You can use PETSC_VIEWER_STDOUT_SELF,
or you can pull out the singleton viewer from STDOUT_WORLD if you want them
all to print in order.


> As far as the overall process you have described my question on first
> glance is do I have to allocate/create the vector that is output by
> VecISCopy before calling it, or does it create the vector automatically?
>

You create both vectors. I would do it using DMCreateGlobalVector() from
both DMs.


> I think I would need to create it first using a section and Setting the
> Vec in the filtered DM?
>

Setting the Section in the filtered DM.


> And I presume in this case I would be using the scatter reverse option to
> go from the full set to the reduced set?
>

Yes

  Thanks

     Matt


> Sincerely
> Nicholas
>
>
>
>
>
>
> Sincerely
> Nick
>
> On Wed, Dec 7, 2022 at 6:00 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Wed, Dec 7, 2022 at 3:35 AM Nicholas Arnold-Medabalimi <
>> narnoldm at umich.edu> wrote:
>>
>>> Hi Matthew
>>>
>>> Thank you for the help. This clarified a great deal.
>>>
>>> I have a follow-up question related to DMPlexFilter. It may be better to
>>> describe what I'm trying to achieve.
>>>
>>> I have a general mesh I am solving which has a section with cell center
>>> finite volume states, as described in my initial email. After calculating
>>> some metrics, I tag a bunch of cells with an identifying Label and use
>>> DMFilter to generate a new DM which is only that subset of cells.
>>> Generally, this leads to a pretty unbalanced DM so I then plan to use
>>> DMPlexDIstribute to balance that DM across the processors. The coordinates
>>> pass along fine, but the state(or I should say Section) does not at least
>>> as far as I can tell.
>>>
>>> Assuming I can get a filtered DM I then distribute the DM and state
>>> using the method you described above and it seems to be working ok.
>>>
>>> The last connection I have to make is the transfer of information from
>>> the full mesh to the "sampled" filtered mesh. From what I can gather I
>>> would need to get the mapping of points using DMPlexGetSubpointIS and then
>>> manually copy the values from the full DM section to the filtered DM? I
>>> have the process from full->filtered->distributed all working for the
>>> coordinates so its just a matter of transferring the section correctly.
>>>
>>> I appreciate all the help you have provided.
>>>
>>
>> Let's do this in two steps, which makes it easier to debug. First, do not
>> redistribute the submesh. Just use DMPlexGetSubpointIS()
>> to get the mapping of filtered points to points in the original mesh.
>> Then create an expanded IS using the Section which makes
>> dofs in the filtered mesh to dofs in the original mesh. From this use
>>
>>   https://petsc.org/main/docs/manualpages/Vec/VecISCopy/
>>
>> to move values between the original vector and the filtered vector.
>>
>> Once that works, you can try redistributing the filtered mesh. Before
>> calling DMPlexDistribute() on the filtered mesh, you need to call
>>
>>   https://petsc.org/main/docs/manualpages/DM/DMSetUseNatural/
>>
>> When you redistribute, it will compute a mapping back to the original
>> layout. Now when you want to transfer values, you
>>
>>   1) Create a natural vector with DMCreateNaturalVec()
>>
>>   2) Use DMGlobalToNaturalBegin/End() to move values from the filtered
>> vector to the natural vector
>>
>>   3) Use VecISCopy() to move values from the natural vector to the
>> original vector
>>
>> Let me know if you have any problems.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Sincerely
>>> Nicholas
>>>
>>>
>>>
>>> On Mon, Nov 28, 2022 at 6:19 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Sun, Nov 27, 2022 at 10:22 PM Nicholas Arnold-Medabalimi <
>>>> narnoldm at umich.edu> wrote:
>>>>
>>>>> Hi Petsc Users
>>>>>
>>>>> I have a question about properly using PetscSection to assign state
>>>>> variables to a DM. I have an existing DMPlex mesh distributed on 2
>>>>> processors. My goal is to have state variables set to the cell centers. I
>>>>> then want to call DMPlexDistribute, which I hope will balance the mesh
>>>>> elements and hopefully transport the state variables to the hosting
>>>>> processors as the cells are distributed to a different processor count or
>>>>> simply just redistributing after doing mesh adaption.
>>>>>
>>>>> Looking at the DMPlex User guide, I should be able to achieve this
>>>>> with a single field section using SetDof and assigning the DOF to the
>>>>> points corresponding to cells.
>>>>>
>>>>
>>>> Note that if you want several different fields, you can clone the DM
>>>> first for this field
>>>>
>>>>   call DMClone(dm,dmState,ierr)
>>>>
>>>> and use dmState in your calls below.
>>>>
>>>>
>>>>>
>>>>> call DMPlexGetHeightStratum(dm,0,c0,c1,ierr)
>>>>> call DMPlexGetChart(dm,p0,p1,ierr)
>>>>> call PetscSectionCreate(PETSC_COMM_WORLD,section,ierr)
>>>>> call PetscSectionSetNumFields(section,1,ierr) call
>>>>> PetscSectionSetChart(section,p0,p1,ierr)
>>>>> do i = c0, (c1-1)
>>>>>     call PetscSectionSetDof(section,i,nvar,ierr)
>>>>> end do
>>>>> call PetscSectionSetup(section,ierr)
>>>>> call DMSetLocalSection(dm,section,ierr)
>>>>>
>>>>
>>>> In the loop, I would add a call to
>>>>
>>>>   call PetscSectionSetFieldDof(section,i,0,nvar,ierr)
>>>>
>>>> This also puts in the field breakdown. It is not essential, but nicer.
>>>>
>>>>
>>>>> From here, it looks like I can access and set the state vars using
>>>>>
>>>>> call DMGetGlobalVector(dmplex,state,ierr)
>>>>> call DMGetGlobalSection(dmplex,section,ierr)
>>>>> call VecGetArrayF90(state,stateVec,ierr)
>>>>> do i = c0, (c1-1)
>>>>> call PetscSectionGetOffset(section,i,offset,ierr)
>>>>> stateVec(offset:(offset+nvar))=state_i(:) !simplified assignment
>>>>> end do
>>>>> call VecRestoreArrayF90(state,stateVec,ierr)
>>>>> call DMRestoreGlobalVector(dmplex,state,ierr)
>>>>>
>>>>> To my understanding, I should be using Global vector since this is a
>>>>> pure assignment operation and I don't need the ghost cells.
>>>>>
>>>>
>>>> Yes.
>>>>
>>>> But the behavior I am seeing isn't exactly what I'd expect.
>>>>>
>>>>> To be honest, I'm somewhat unclear on a few things
>>>>>
>>>>> 1) Should be using nvar fields with 1 DOF each or 1 field with nvar
>>>>> DOFs or what the distinction between the two methods are?
>>>>>
>>>>
>>>> We have two divisions in a Section. A field can have a number of
>>>> components. This is intended to model a vector or tensor field.
>>>> Then a Section can have a number of fields, such as velocity and
>>>> pressure for a Stokes problem. The division is mainly to help the
>>>> user, so I would use the most natural one.
>>>>
>>>>
>>>>> 2) Adding a print statement after the offset assignment I get (on rank
>>>>> 0 of 2)
>>>>> cell           1 offset           0
>>>>>  cell           2 offset          18
>>>>>  cell           3 offset          36
>>>>> which is expected and works but on rank 1 I get
>>>>>  cell           1 offset        9000
>>>>>  cell           2 offset        9018
>>>>>  cell           3 offset        9036
>>>>>
>>>>> which isn't exactly what I would expect. Shouldn't the offsets reset
>>>>> at 0 for the next rank?
>>>>>
>>>>
>>>> The local and global sections hold different information. This is the
>>>> source of the confusion. The local section does describe a local
>>>> vector, and thus includes overlap or "ghost" dofs. The global section
>>>> describes a global vector. However, it is intended to deliver
>>>> global indices, and thus the offsets give back global indices. When you
>>>> use VecGetArray*() you are getting out the local array, and
>>>> thus you have to subtract the first index on this process. You can get
>>>> that from
>>>>
>>>>   VecGetOwnershipRange(v, &rstart, &rEnd);
>>>>
>>>> This is the same whether you are using DMDA or DMPlex or any other DM.
>>>>
>>>>
>>>>> 3) Does calling DMPlexDistribute also distribute the section data
>>>>> associated with the DOF, based on the description in DMPlexDistribute it
>>>>> looks like it should?
>>>>>
>>>>
>>>> No. By default, DMPlexDistribute() only distributes coordinate data. I
>>>> you want to distribute your field, it would look something like this:
>>>>
>>>> DMPlexDistribute(dm, 0, &sfDist, &dmDist);
>>>> VecCreate(comm, &stateDist);
>>>> VecSetDM(sateDist, dmDist);
>>>> PetscSectionCreate(comm &sectionDist);
>>>> DMSetLocalSection(dmDist, sectionDist);
>>>> DMPlexDistributeField(dmDist, sfDist, section, state, sectionDist,
>>>> stateDist);
>>>>
>>>> We do this in src/dm/impls/plex/tests/ex36.c
>>>>
>>>>   THanks,
>>>>
>>>>      Matt
>>>>
>>>> I'd appreciate any insight into the specifics of this usage. I expect I
>>>>> have a misconception on the local vs global section. Thank you.
>>>>>
>>>>> Sincerely
>>>>> Nicholas
>>>>>
>>>>> --
>>>>> Nicholas Arnold-Medabalimi
>>>>>
>>>>> Ph.D. Candidate
>>>>> Computational Aeroscience Lab
>>>>> University of Michigan
>>>>>
>>>>
>>>>
>>>> --
>>>> 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/>
>>>>
>>>
>>>
>>> --
>>> Nicholas Arnold-Medabalimi
>>>
>>> Ph.D. Candidate
>>> Computational Aeroscience Lab
>>> University of Michigan
>>>
>>
>>
>> --
>> 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/>
>>
>
>
> --
> Nicholas Arnold-Medabalimi
>
> Ph.D. Candidate
> Computational Aeroscience Lab
> University of Michigan
>


-- 
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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