[petsc-users] Petsc Section in DMPlex

Matthew Knepley knepley at gmail.com
Thu Dec 8 06:27:02 CST 2022 

On Thu, Dec 8, 2022 at 3:04 AM Nicholas Arnold-Medabalimi <
narnoldm at umich.edu> wrote:

> 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.
>

It is a good question. We have tried to give guidance on the manpage:

  The index set identifies entries in the global vector. Negative indices
are skipped; indices outside the ownership range of vfull will raise an
error.

which means that it expects _global_ indices, and you have retrieved the
global section, so that matches.
The calculation of the index size looks right to me, and so does the index
calculation.

I would put a check in the loop, making sure that the calculated indices
lie within [oStart, oEnd). The global
section is designed to ensure that. It is not clear why one would lie
outside.

When I am debugging, I run a very small problem, and print out all the
sections.

  Thanks,

     Matt


> 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
>


-- 
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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