[petsc-users] Petsc Section in DMPlex

Nicholas Arnold-Medabalimi narnoldm at umich.edu
Thu Dec 8 02:04:16 CST 2022 

Hi Matt

I think I've gotten it just about there. I'm just having an issue with the
VecISCopy. I have an IS built that matches size correctly to map from the
full state to the filtered state. The core issue I think, is should the
expanded IS the ownership range of the vector subtracted out. Looking at
the implementation, it looks like VecISCopy takes care of that for me.
(Line 573 in src/vec/vec/utils/projection.c) But I could be mistaken.

The error I am getting is:
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: Only owned values supported


Here is what I am currently doing.

call DMPlexFilter(dmplex_full, iBlankLabel, 1, dmplex_filtered,ierr)
call DMPlexGetSubpointIS(dmplex_filtered, subpointsIS,ierr)

! adds section to dmplex_filtered and allocates vec_filtered using
DMCreateGlobalVector
call addSectionToDMPlex(dmplex_filtered,vec_filtered)

! Get Sections for dmplex_filtered and dmplex_full
call DMGetGlobalSection(dmplex_filtered,filteredfieldSection,ierr)
call DMGetGlobalSection(dmplex_full,fullfieldSection,ierr)



call ISGetIndicesF90(subpointsIS, subPointKey,ierr)
ExpandedIndexSize = 0
do i = 1, size(subPointKey)
    call PetscSectionGetDof(fullfieldSection, subPointKey(i), dof,ierr)
    ExpandedIndexSize = ExpandedIndexSize + dof
enddo


!Create expandedIS from offset sections of full and filtered sections
allocate(ExpandedIndex(ExpandedIndexSize))
call VecGetOwnershipRange(vec_full,oStart,oEnd,ierr)
do i = 1, size(subPointKey)
    call PetscSectionGetOffset(fullfieldSection, subPointKey(i),
offset,ierr)
    call PetscSectionGetDof(fullfieldSection, subPointKey(i), dof,ierr)
    !offset=offset-oStart   !looking at VecIScopy it takes care of this
subtraction (not sure)
    do j = 1, (dof)
        ExpandedIndex((i-1)*dof+j) = offset+j
    end do
enddo

call ISCreateGeneral(PETSC_COMM_WORLD, ExpandedIndexSize, ExpandedIndex,
PETSC_COPY_VALUES, expandedIS,ierr)
call ISRestoreIndicesF90(subpointsIS, subPointKey,ierr)
deallocate(ExpandedIndex)


call VecGetLocalSize(vec_full,sizeVec,ierr)
write(*,*) sizeVec
call VecGetLocalSize(vec_filtered,sizeVec,ierr)
write(*,*) sizeVec
call ISGetLocalSize(expandedIS,sizeVec,ierr)
write(*,*) sizeVec
call PetscSynchronizedFlush(PETSC_COMM_WORLD,ierr)


call VecISCopy(vec_full,expandedIS,SCATTER_REVERSE,vec_filtered,ierr)


Thanks again for the great help.

Sincerely
Nicholas


On Wed, Dec 7, 2022 at 9:29 PM Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Dec 7, 2022 at 9:21 PM Nicholas Arnold-Medabalimi <
> narnoldm at umich.edu> wrote:
>
>> Thank you for the help.
>>
>> I think the last piece of the puzzle is how do I create the "expanded IS"
>> from the subpoint IS using the section?
>>
>
> Loop over the points in the IS. For each point, get the dof and offset
> from the Section. Make a new IS that has all the
> dogs, namely each run [offset, offset+dof).
>
>   Thanks,
>
>      Matt
>
>
>> Sincerely
>> Nicholas
>>
>>
>> On Wed, Dec 7, 2022 at 7:06 AM Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> 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/>
>>>
>>
>>
>> --
>> 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
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