[petsc-users] DMPlex Halo Communication or Graph Partitioner Issue
Mike Michell
mi.mike1021 at gmail.com
Sun Feb 26 10:19:00 CST 2023
Which version of petsc you tested? With petsc 3.18.4, median duan volume
gives the same value with petsc from DMPlexComputeCellGeometryFVM().
> On Sat, Feb 25, 2023 at 3:11 PM Mike Michell <mi.mike1021 at gmail.com>
> wrote:
>
>> My apologies for the late follow-up. There was a time conflict.
>>
>> A simple example code related to the issue I mentioned is attached here.
>> The sample code does: (1) load grid on dm, (2) compute vertex-wise control
>> volume for each node in a median-dual way, (3) halo exchange among procs to
>> have complete control volume values, and (4) print out its field as a .vtu
>> file. To make sure, the computed control volume is also compared with
>> PETSc-computed control volume via DMPlexComputeCellGeometryFVM() (see lines
>> 771-793).
>>
>> Back to the original problem, I can get a proper control volume field
>> with PETSc 3.18.4, which is the latest stable release. However, if I use
>> PETSc from the main repo, it gives a strange control volume field.
>> Something is certainly strange around the parallel boundaries, thus I think
>> something went wrong with halo communication. To help understand, a
>> comparing snapshot is also attached. I guess a certain part of my code is
>> no longer compatible with PETSc unless there is a bug in the library. Could
>> I get comments on it?
>>
>
> I can run your example. The numbers I get for "median-dual volume" do not
> match the "PETSc volume", and the PETSc volume is correct. Moreover, the
> median-dual numbers change, which suggests a memory fault. I compiled it
> using address sanitizer, and it found an error:
>
> Number of physical boundary edge ... 4 0
> Number of physical and parallel boundary edge ... 4
> 0
> Number of parallel boundary edge ... 0 0
> Number of physical boundary edge ... 4 1
> Number of physical and parallel boundary edge ... 4
> 1
> Number of parallel boundary edge ... 0 1
> =================================================================
> ==36587==ERROR: AddressSanitizer: heap-buffer-overflow on address
> 0x603000022d40 at pc 0x0001068e12a8 bp 0x7ffee932cfd0 sp 0x7ffee932cfc8
> READ of size 8 at 0x603000022d40 thread T0
> =================================================================
> ==36588==ERROR: AddressSanitizer: heap-buffer-overflow on address
> 0x60300000f0f0 at pc 0x00010cf702a8 bp 0x7ffee2c9dfd0 sp 0x7ffee2c9dfc8
> READ of size 8 at 0x60300000f0f0 thread T0
> #0 0x10cf702a7 in MAIN__ test.F90:657
> #1 0x10cf768ee in main test.F90:43
> #0 0x1068e12a7 in MAIN__ test.F90:657
> #1 0x1068e78ee in main test.F90:43
> #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>
> 0x60300000f0f0 is located 0 bytes to the right of 32-byte region
> [0x60300000f0d0,0x60300000f0f0)
> allocated by thread T0 here:
> #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>
> 0x603000022d40 is located 0 bytes to the right of 32-byte region
> [0x603000022d20,0x603000022d40)
> allocated by thread T0 here:
> #0 0x114a7457f in wrap_malloc (libasan.5.dylib:x86_64+0x7b57f)
> #1 0x1068dba71 in MAIN__ test.F90:499
> #2 0x1068e78ee in main test.F90:43
> #3 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>
> SUMMARY: AddressSanitizer: heap-buffer-overflow test.F90:657 in MAIN__
> Shadow bytes around the buggy address:
>
> which corresponds to
>
> ! midpoint of median-dual face for inner face
> axrf(ifa,1) = 0.5d0*(yc(nc1)+yfc(ifa)) ! for nc1 cell
> axrf(ifa,2) = 0.5d0*(yc(nc2)+yfc(ifa)) ! for nc2 cell
>
> and these were allocated here
>
> allocate(xc(ncell))
> allocate(yc(ncell))
>
> Hopefully the error is straightforward to see now.
>
> Thanks,
>
> Matt
>
>
>> Thanks,
>> Mike
>>
>>
>>> On Mon, Feb 20, 2023 at 12:05 PM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Sat, Feb 18, 2023 at 12:00 PM Mike Michell <mi.mike1021 at gmail.com>
>>>> wrote:
>>>>
>>>>> As a follow-up, I tested:
>>>>>
>>>>> (1) Download tar for v3.18.4 from petsc gitlab (
>>>>> https://gitlab.com/petsc/petsc/-/tree/v3.18.4) has no issue on DMPlex
>>>>> halo exchange. This version works as I expect.
>>>>> (2) Clone main branch (git clone https://gitlab.com/petsc/petsc.git)
>>>>> has issues with DMPlex halo exchange. Something is suspicious about this
>>>>> main branch, related to DMPlex halo. The solution field I got is not
>>>>> correct. But it works okay with 1-proc.
>>>>>
>>>>> Does anyone have any comments on this issue? I am curious if other
>>>>> DMPlex users have no problem regarding halo exchange. FYI, I do not
>>>>> declare ghost layers for halo exchange.
>>>>>
>>>>
>>>> There should not have been any changes there and there are definitely
>>>> tests for this.
>>>>
>>>> It would be great if you could send something that failed. I could fix
>>>> it and add it as a test.
>>>>
>>>
>>> Just to follow up, we have tests of the low-level communication (Plex
>>> tests ex1, ex12, ex18, ex29, ex31), and then we have
>>> tests that use halo exchange for PDE calculations, for example SNES
>>> tutorial ex12, ex13, ex62. THe convergence rates
>>> should be off if the halo exchange were wrong. Is there any example
>>> similar to your code that is failing on your installation?
>>> Or is there a way to run your code?
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Thanks,
>>>>> Mike
>>>>>
>>>>>
>>>>>> Dear PETSc team,
>>>>>>
>>>>>> I am using PETSc for Fortran with DMPlex. I have been using this
>>>>>> version of PETSc:
>>>>>> >>git rev-parse origin
>>>>>> >>995ec06f924a86c4d28df68d1fdd6572768b0de1
>>>>>> >>git rev-parse FETCH_HEAD
>>>>>> >>9a04a86bf40bf893fb82f466a1bc8943d9bc2a6b
>>>>>>
>>>>>> There has been no issue, before the one with VTK viewer, which Jed
>>>>>> fixed today (
>>>>>> https://gitlab.com/petsc/petsc/-/merge_requests/6081/diffs?commit_id=27ba695b8b62ee2bef0e5776c33883276a2a1735
>>>>>> ).
>>>>>>
>>>>>> Since that MR has been merged into the main repo, I pulled the latest
>>>>>> version of PETSc (basically I cloned it from scratch). But if I use the
>>>>>> same configure option with before, and run my code, then there is an issue
>>>>>> with halo exchange. The code runs without error message, but it gives wrong
>>>>>> solution field. I guess the issue I have is related to graph partitioner or
>>>>>> halo exchange part. This is because if I run the code with 1-proc, the
>>>>>> solution is correct. I only updated the version of PETSc and there was no
>>>>>> change in my own code. Could I get any comments on the issue? I was
>>>>>> wondering if there have been many changes in halo exchange or graph
>>>>>> partitioning & distributing part related to DMPlex.
>>>>>>
>>>>>> Thanks,
>>>>>> Mike
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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/>
>>>>
>>>
>>>
>>> --
>>> 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/>
>>>
>>
>
> --
> 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/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20230226/492fe712/attachment-0001.html>
More information about the petsc-users
mailing list