[petsc-users] DMPlexCreateSection crashed with larger number of processors

[Mike Michell]

What I did to avoid the crash is to provide bcPointIS from "call
DMGetStratumIS(dm_geom, "depth", dim, bcPointIS(1),ierr);CHKERRA(ierr)",
instead of "marker" for calling DMGetStratumIS().
The petscsection building part is
from src/dm/impls/plex/tutorials/ex1f90.F90 (See line 72).


> On Sat, Jul 9, 2022 at 8:34 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Fri, Jul 8, 2022 at 7:41 PM Mike Michell <mi.mike1021 at gmail.com>
>> wrote:
>>
>>> As a follow-up, just "depth" default label was provided to avoid NULL
>>> PETScIS, and it seems working.
>>>
>>
>> Ah, "depth" is definitely required and is produced by DMPlexStratify(). I
>> will put in a check for this so that you get a good error message.
>>
>
> I cannot find an instance of an IS being pulled from the depth label here.
> Do you have something I can run that shows this fault?
>
>   Thanks,
>
>      Matt
>
>
>>   Thanks!
>>
>>      Matt
>>
>>
>>> Thanks,
>>> Mike
>>>
>>>
>>>> It looks like NULL PETScIS is obtained from DMGetStratumIS() which is
>>>> shown in the previously attached code. Currently, "marker" label is used to
>>>> define default bcPointIS pointer with numBC=1 through DMGetStratumIS(), and
>>>> it seems that if a certain proc does not have any boundary from this
>>>> "marker" label, the DMPlexCreateSection() crashes.
>>>>
>>>> The PETSc's manual page for DMPlexCreateSection() says "bcPoints" is an
>>>> IS holding points to which each boundary condition applies. So, by
>>>> including no boundary for a certain distributed mesh block, it looks very
>>>> natural that this function crashes. How can I not to pass a NULL PETScIS in
>>>> this case? Is there any specific way for that (or a trick)?
>>>>
>>>> Thanks,
>>>> Mike
>>>>
>>>>
>>>>> On Wed, Jul 6, 2022 at 3:42 PM Mike Michell <mi.mike1021 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> I am passing NULL for IS Permutation as;
>>>>>>
>>>>>> call
>>>>>> DMPlexCreateSection(dm_geom,nolabel,pNumComp,pNumDof,numBC,pBcField,pBcCompIS,pBcPointIS,PETSC_NULL_IS,section,ierr)
>>>>>>
>>>>>> Should I define non-NULL IS Permutation before I call
>>>>>> DMPlexCreateSection() to avoid the issue?
>>>>>>
>>>>>
>>>>> No, the problem is not the perm argument. To be sure, we should get a
>>>>> stack trace with line numbers (use a debug build). To me it looked
>>>>> like you passed a NULL IS to DMAddBoundary().
>>>>>
>>>>>   Thanks,
>>>>>
>>>>>     Matt
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>> Mike
>>>>>>
>>>>>>
>>>>>> On Wed, Jul 6, 2022 at 12:57 PM Mike Michell <mi.mike1021 at gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Hi, I am using DMPlex for a FVM code written in Fortran that uses
>>>>>>>> DMPlexCreateSection() to prepare an output file in vtu format. A domain of
>>>>>>>> interest has around 5000 node points and with small number of processors
>>>>>>>> (such as nproc=3), the DMPlexCreateSection() works fine. However, if a
>>>>>>>> larger number of procs (such as nproc=20) is used,  DMPlexCreateSection()
>>>>>>>> crashes with error message below. It looks very similar problem in a
>>>>>>>> previous PETSc user inquiry: " [petsc-dev] DMPlexCreateSection
>>>>>>>> crash in a no-boundary corner case
>>>>>>>> <https://lists.mcs.anl.gov/pipermail/petsc-dev/2013-November/014049.html>
>>>>>>>> "
>>>>>>>>
>>>>>>>
>>>>>>> Yes, the recommendation is not to pass a NULL PetscIS to the
>>>>>>> AddBoundary() routine. Are you doing this?
>>>>>>>
>>>>>>>   Thanks,
>>>>>>>
>>>>>>>      Matt
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> When I call DMPlexCreateSection(), a nullified pointer
>>>>>>>> "nolabel(:)=>NULL()" is provided. What is a possible solution to this
>>>>>>>> problem? It looks like there is a problem with a processor that does not
>>>>>>>> have any boundaries. A piece of the source code is attached to show how
>>>>>>>> the  DMPlexCreateSection() is used in the code.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Mike
>>>>>>>>
>>>>>>>> [16]PETSC ERROR: --------------------- Error Message
>>>>>>>> --------------------------------------------------------------
>>>>>>>> [16]PETSC ERROR: Null argument, when expecting valid pointer
>>>>>>>> [16]PETSC ERROR: Null Pointer: Parameter # 1
>>>>>>>> [16]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>>>>> shooting.
>>>>>>>> [16]PETSC ERROR: Petsc Release Version 3.17.0, unknown
>>>>>>>> [16]PETSC ERROR: #1 ISGetLocalSize() at
>>>>>>>> [16]PETSC ERROR: #2 DMPlexCreateSectionBCDof() at
>>>>>>>> [16]PETSC ERROR: #3 DMPlexCreateSection() at
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> 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/>
>>
>
>
> --
> 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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