[petsc-users] Vec Ownership ranges with Global Section Offsets
Nicholas Arnold-Medabalimi
narnoldm at umich.edu
Fri Jan 6 09:09:58 CST 2023
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.
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
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