[petsc-users] Vec Ownership ranges with Global Section Offsets
Matthew Knepley
knepley at gmail.com
Fri Jan 6 09:59:08 CST 2023
On Fri, Jan 6, 2023 at 10:41 AM Nicholas Arnold-Medabalimi <
narnoldm at umich.edu> wrote:
> Hi Matt
>
> I appreciate the help. The section view is quite extensive because each
> cell has 55 dofs located at the cells and on certain faces. I've appended
> the first of these which corresponds with the output in the first email, to
> save space. The following 54 are exactly the same but offset incremented by
> 1. (or negative 1 for negative offsets)
>
Okay, from the output it is clear that this vector does not match your
global section. Did you get stateVec by calling DMCreateGlobalVector()?
Thanks,
Matt
> Thanks for your time
> Nicholas
>
> On Fri, Jan 6, 2023 at 10:23 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Fri, Jan 6, 2023 at 10:10 AM Nicholas Arnold-Medabalimi <
>> narnoldm at umich.edu> wrote:
>>
>>> Hi Matt
>>>
>>> I apologize for any lack of clarity in the initial email.
>>>
>>> looking at the initial output on rank 1
>>> write(*,*) "cell",i,"offset",offset,'oStart',oStart, offset-oStart
>>> cell 0 offset 2475 oStart 2640 -165
>>> cell 1 offset 2530 oStart 2640 -110
>>> cell 2 offset 2585 oStart 2640 -55
>>> cell 3 offset 2640 oStart 2640 0
>>> .....
>>> cell 15 offset -771 oStart 2640 -3411
>>>
>>>
>>> cell 15 provides a negative offset because it is the overlap cell (that
>>> is unowned)
>>> The remained of cells are all owned. However, the first 3 cells (0,1,2)
>>> return an offset that is less than the starting ownership range. I would
>>> expect cell 0 to start at offset 2640 at minimum.
>>>
>>
>> Send the output for this section
>>
>> call PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> Sincerely
>>> Nicholas
>>>
>>>
>>>
>>>
>>> On Fri, Jan 6, 2023 at 10:05 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Fri, Jan 6, 2023 at 9:56 AM Nicholas Arnold-Medabalimi <
>>>> narnoldm at umich.edu> wrote:
>>>>
>>>>> Apologies. If it helps, there is one cell of overlap in this small
>>>>> test case for a 2D mesh that is 1 cell in height and a number of cells in
>>>>> length. .
>>>>>
>>>>> process 0
>>>>> Petsc VecGetLocalSize 2750
>>>>> size(stateVecV) 2750
>>>>>
>>>>> process 1
>>>>> Petsc VecGetLocalSize 2640
>>>>> size(stateVecV) 2640
>>>>>
>>>>
>>>> The offsets shown below are well-within these sizes. I do not
>>>> understand the problem.
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> On Fri, Jan 6, 2023 at 9:51 AM Matthew Knepley <knepley at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> On Fri, Jan 6, 2023 at 9:37 AM Nicholas Arnold-Medabalimi <
>>>>>> narnoldm at umich.edu> wrote:
>>>>>>
>>>>>>> Hi Matt
>>>>>>>
>>>>>>> I made a typo on the line statVecV(offset) = <set to something> in
>>>>>>> my example, I agree. (I wrote that offhand since the actual assignment is
>>>>>>> much larger) I should be statVecV(offset+1) = <assignment> so I'm confident
>>>>>>> it's not a 1 0 indexing thing.
>>>>>>>
>>>>>>> My question is more related to what is happening in the offsets. c0
>>>>>>> and c1 are pulled using DMplexgetheight stratum, so they are zero-indexed
>>>>>>> (which is why I loop from c0 to (c1-1)).
>>>>>>>
>>>>>>> For the size inquiries. on processor 0
>>>>>>> Petsc VecGetSize(stateVec) 5390
>>>>>>>
>>>>>>
>>>>>> I need to see VecGetLocalSize()
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>>
>>>>>>> size(stateVecV) 2640
>>>>>>>
>>>>>>> on processor 1
>>>>>>> Petsc VecGetSize 5390
>>>>>>> size(stateVecV) 2750
>>>>>>>
>>>>>>> It's quite weird to me that processor one can have a positive offset
>>>>>>> that is less than its starting ownership index (in the initial email
>>>>>>> output).
>>>>>>>
>>>>>>> Thanks for the assistance
>>>>>>> Nicholas
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Jan 6, 2023 at 9:20 AM Matthew Knepley <knepley at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> On Fri, Jan 6, 2023 at 2:28 AM Nicholas Arnold-Medabalimi <
>>>>>>>> narnoldm at umich.edu> wrote:
>>>>>>>>
>>>>>>>>> Hi Petsc Users,
>>>>>>>>>
>>>>>>>>> I'm working with a dmplex system with a subsampled mesh
>>>>>>>>> distributed with an overlap of 1.
>>>>>>>>>
>>>>>>>>> I'm encountering unusual situations when using
>>>>>>>>> VecGetOwnershipRange to adjust the offset received from a global section.
>>>>>>>>> The logic of the following code is first to get the offset needed to index
>>>>>>>>> a global vector while still being able to check if it is an overlapped cell
>>>>>>>>> and skip if needed while counting the owned cells.
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> call DMGetGlobalSection(dmplex,section,ierr)
>>>>>>>>> call VecGetArrayF90(stateVec,stateVecV,ierr)
>>>>>>>>> call VecGetOwnershipRange(stateVec,oStart,oEnd,ierr)
>>>>>>>>> do i = c0, (c1-1)
>>>>>>>>>
>>>>>>>>> call PetscSectionGetOffset(section,i,offset,ierr)
>>>>>>>>> write(*,*) "cell",i,"offset",offset,'oStart',oStart, offset-
>>>>>>>>> oStart
>>>>>>>>>
>>>>>>>>> if(offset<0) then
>>>>>>>>> cycle
>>>>>>>>> endif
>>>>>>>>> offset=offset-oStart
>>>>>>>>> plexcells=plexcells+1
>>>>>>>>> stateVecV(offset)= <set to something> enddo
>>>>>>>>>
>>>>>>>>> I'm noticing some very weird results that I've appended below. The
>>>>>>>>> GetOffset documentation notes that a negative offset indicates an unowned
>>>>>>>>> point (which I use to cycle). However, the offset subtraction with oStart
>>>>>>>>> will yield an illegal index for the Vector access. I see that on the
>>>>>>>>> documentation for GetOwnershipRange, it notes that this may be
>>>>>>>>> "ill-defined" but I wanted to see if this is type of ill-defined I can
>>>>>>>>> expect or there is just something terribly wrong with my PetscSection.(both
>>>>>>>>> the Vec and Section were produced from DMPlexDistributeField so should by
>>>>>>>>> definition have synchronized section information) I was wondering if there
>>>>>>>>> is a possible output and/or the best way to index the vector. I'm thinking
>>>>>>>>> of subtracting the offset of cell 0 perhaps?
>>>>>>>>>
>>>>>>>>
>>>>>>>> Can you show your vector sizes? Are you sure it is not the fact
>>>>>>>> that F90 arrays use 1-based indices, but these are 0-based offsets?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>> on rank 0
>>>>>>>>>
>>>>>>>>> cell 0 offset 0 oStart 0 0
>>>>>>>>> cell 1 offset 55 oStart 0 55
>>>>>>>>> cell 2 offset 110 oStart 0 110
>>>>>>>>> cell 3 offset 165 oStart 0 165
>>>>>>>>> cell 4 offset 220 oStart 0 220
>>>>>>>>> cell 5 offset 275 oStart 0 275
>>>>>>>>> cell 6 offset 330 oStart 0 330
>>>>>>>>> cell 7 offset 385 oStart 0 385
>>>>>>>>> cell 8 offset 440 oStart 0 440
>>>>>>>>> cell 9 offset 495 oStart 0 495
>>>>>>>>> cell 10 offset 550 oStart 0 550
>>>>>>>>> cell 11 offset 605 oStart 0 605
>>>>>>>>> cell 12 offset 660 oStart 0 660
>>>>>>>>> cell 13 offset 715 oStart 0 715
>>>>>>>>>
>>>>>>>>> and on rank one
>>>>>>>>> cell 0 offset 2475 oStart 2640 -165
>>>>>>>>> cell 1 offset 2530 oStart 2640 -110
>>>>>>>>> cell 2 offset 2585 oStart 2640 -55
>>>>>>>>> cell 3 offset 2640 oStart 2640 0
>>>>>>>>> cell 4 offset 2695 oStart 2640 55
>>>>>>>>> cell 5 offset 2750 oStart 2640 110
>>>>>>>>> cell 6 offset 2805 oStart 2640 165
>>>>>>>>> cell 7 offset 2860 oStart 2640 220
>>>>>>>>> cell 8 offset 2915 oStart 2640 275
>>>>>>>>> cell 9 offset 2970 oStart 2640 330
>>>>>>>>> cell 10 offset 3025 oStart 2640 385
>>>>>>>>> cell 11 offset 3080 oStart 2640 440
>>>>>>>>> cell 12 offset 3135 oStart 2640 495
>>>>>>>>> cell 13 offset 3190 oStart 2640 550
>>>>>>>>> cell 14 offset 3245 oStart 2640 605
>>>>>>>>> cell 15 offset -771 oStart 2640 -3411
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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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