[petsc-users] Is it possible to keep track of original elements # after a call to DMPlexDistribute ?
Matthew Knepley
knepley at gmail.com
Wed Oct 20 17:55:58 CDT 2021
On Wed, Oct 20, 2021 at 3:06 PM Eric Chamberland <
Eric.Chamberland at giref.ulaval.ca> wrote:
> Hi Matthew,
>
> we tried to reproduce the error in a simple example.
>
> The context is the following: We hard coded the mesh and initial partition
> into the code (see sConnectivity and sInitialPartition) for 2 ranks and try
> to create a section in order to use the DMPlexNaturalToGlobalBegin function
> to retreive our initial element numbers.
>
> Now the call to DMPlexDistribute give different errors depending on what
> type of component we ask the field to be created. For our objective, we
> would like a global field to be created on elements only (like a P0
> interpolation).
>
> We now have the following error generated:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Petsc has generated inconsistent data
> [0]PETSC ERROR: Inconsistency in indices, 18 should be 17
> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.15.0, Mar 30, 2021
> [0]PETSC ERROR: ./bug on a named rohan by ericc Wed Oct 20 14:52:36 2021
> [0]PETSC ERROR: Configure options
> --prefix=/opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7 --with-mpi-compilers=1
> --with-mpi-dir=/opt/openmpi-4.1.0_gcc7 --with-cxx-dialect=C++14
> --with-make-np=12 --with-shared-libraries=1 --with-debugging=yes
> --with-memalign=64 --with-visibility=0 --with-64-bit-indices=0
> --download-ml=yes --download-mumps=yes --download-superlu=yes
> --download-hpddm=yes --download-slepc=yes --download-superlu_dist=yes
> --download-parmetis=yes --download-ptscotch=yes --download-metis=yes
> --download-strumpack=yes --download-suitesparse=yes --download-hypre=yes
> --with-blaslapack-dir=/opt/intel/oneapi/mkl/2021.1.1/env/../lib/intel64
> --with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/2021.1.1/env/..
> --with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/2021.1.1/env/..
> --with-scalapack=1
> --with-scalapack-include=/opt/intel/oneapi/mkl/2021.1.1/env/../include
> --with-scalapack-lib="-L/opt/intel/oneapi/mkl/2021.1.1/env/../lib/intel64
> -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64"
> [0]PETSC ERROR: #1 PetscSFCreateSectionSF() at
> /tmp/ompi-opt/petsc-3.15.0-debug/src/vec/is/sf/utils/sfutils.c:409
> [0]PETSC ERROR: #2 DMPlexCreateGlobalToNaturalSF() at
> /tmp/ompi-opt/petsc-3.15.0-debug/src/dm/impls/plex/plexnatural.c:184
> [0]PETSC ERROR: #3 DMPlexDistribute() at
> /tmp/ompi-opt/petsc-3.15.0-debug/src/dm/impls/plex/plexdistribute.c:1733
> [0]PETSC ERROR: #4 main() at bug_section.cc:159
> [0]PETSC ERROR: No PETSc Option Table entries
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> Hope the attached code is self-explaining, note that to make it short, we
> have not included the final part of it, just the buggy part we are
> encountering right now...
>
> Thanks for your insights,
>
> Thanks for making the example. I tweaked it slightly. I put in a test case
that just makes a parallel 7 x 10 quad mesh. This works
fine. Thus I think it must be something connected with the original mesh.
It is hard to get a handle on it without the coordinates.
Do you think you could put the coordinate array in? I have added the code
to load them (see attached file).
Thanks,
Matt
> Eric
> On 2021-10-06 9:23 p.m., Matthew Knepley wrote:
>
> On Wed, Oct 6, 2021 at 5:43 PM Eric Chamberland <
> Eric.Chamberland at giref.ulaval.ca> wrote:
>
>> Hi Matthew,
>>
>> we tried to use that. Now, we discovered that:
>>
>> 1- even if we "ask" for sfNatural creation with DMSetUseNatural, it is
>> not created because DMPlexCreateGlobalToNaturalSF looks for a "section":
>> this is not documented in DMSetUseNaturalso we are asking ourselfs: "is
>> this a permanent feature or a temporary situation?"
>>
> I think explaining this will help clear up a lot.
>
> What the Natural2Global map does is permute a solution vector into the
> ordering that it would have had prior to mesh distribution.
> Now, in order to do this permutation, I need to know the original (global)
> data layout. If it is not specified _before_ distribution, we
> cannot build the permutation. The section describes the data layout, so I
> need it before distribution.
>
> I cannot think of another way that you would implement this, but if you
> want something else, let me know.
>
>> 2- We then tried to create a "section" in different manners: we took the
>> code into the example petsc/src/dm/impls/plex/tests/ex15.c. However, we
>> ended up with a segfault:
>>
>> corrupted size vs. prev_size
>> [rohan:07297] *** Process received signal ***
>> [rohan:07297] Signal: Aborted (6)
>> [rohan:07297] Signal code: (-6)
>> [rohan:07297] [ 0] /lib64/libpthread.so.0(+0x13f80)[0x7f6f13be3f80]
>> [rohan:07297] [ 1] /lib64/libc.so.6(gsignal+0x10b)[0x7f6f109b718b]
>> [rohan:07297] [ 2] /lib64/libc.so.6(abort+0x175)[0x7f6f109b8585]
>> [rohan:07297] [ 3] /lib64/libc.so.6(+0x7e2f7)[0x7f6f109fb2f7]
>> [rohan:07297] [ 4] /lib64/libc.so.6(+0x857ea)[0x7f6f10a027ea]
>> [rohan:07297] [ 5] /lib64/libc.so.6(+0x86036)[0x7f6f10a03036]
>> [rohan:07297] [ 6] /lib64/libc.so.6(+0x861a3)[0x7f6f10a031a3]
>> [rohan:07297] [ 7] /lib64/libc.so.6(+0x88740)[0x7f6f10a05740]
>> [rohan:07297] [ 8] /lib64/libc.so.6(__libc_malloc+0x1b8)[0x7f6f10a070c8]
>> [rohan:07297] [ 9]
>> /lib64/libc.so.6(__backtrace_symbols+0x134)[0x7f6f10a8b064]
>> [rohan:07297] [10]
>> /home/mefpp_ericc/GIREF/bin/MEF++.dev(_Z12reqBacktraceRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x4e)[0x4538ce]
>> [rohan:07297] [11]
>> /home/mefpp_ericc/GIREF/bin/MEF++.dev(_Z15attacheDebuggerv+0x120)[0x4523c0]
>> [rohan:07297] [12]
>> /home/mefpp_ericc/GIREF/lib/libgiref_dev_Util.so(traitementSignal+0x612)[0x7f6f28f503a2]
>> [rohan:07297] [13] /lib64/libc.so.6(+0x3a210)[0x7f6f109b7210]
>>
>> [rohan:07297] [14]
>> /opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscTrMallocDefault+0x6fd)[0x7f6f22f1b8ed]
>> [rohan:07297] [15]
>> /opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscMallocA+0x5cd)[0x7f6f22f19c2d]
>> [rohan:07297] [16]
>> /opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(PetscSFCreateSectionSF+0xb48)[0x7f6f23268e18]
>> [rohan:07297] [17]
>> /opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(DMPlexCreateGlobalToNaturalSF+0x13b2)[0x7f6f241a5602]
>> [rohan:07297] [18]
>> /opt/petsc-3.15.0_debug_openmpi-4.1.0_gcc7/lib/libpetsc.so.3.15(DMPlexDistribute+0x39b1)[0x7f6f23fdca21]
>>
> I am not sure what happened here, but if you could send a sample code, I
> will figure it out.
>
>> If we do not create a section, the call to DMPlexDistribute is
>> successful, but DMPlexGetGlobalToNaturalSF return a null SF pointer...
>>
> Yes, it just ignores it in this case because it does not have a global
> layout.
>
>> Here are the operations we are calling ( this is almost the code we are
>> using, I just removed verifications and creation of the connectivity which
>> use our parallel structure and code):
>>
>> ===========
>>
>> PetscInt* lCells = 0;
>> PetscInt lNumCorners = 0;
>> PetscInt lDimMail = 0;
>> PetscInt lnumCells = 0;
>>
>> //At this point we create the cells for PETSc expected input for
>> DMPlexBuildFromCellListParallel and set lNumCorners, lDimMail and lnumCells
>> to correct values.
>> ...
>>
>> DM lDMBete = 0
>> DMPlexCreate(lMPIComm,&lDMBete);
>>
>> DMSetDimension(lDMBete, lDimMail);
>>
>> DMPlexBuildFromCellListParallel(lDMBete,
>> lnumCells,
>> PETSC_DECIDE,
>>
>> pLectureElementsLocaux.reqNbTotalSommets(),
>> lNumCorners,
>> lCells,
>> PETSC_NULL);
>>
>> DM lDMBeteInterp = 0;
>> DMPlexInterpolate(lDMBete, &lDMBeteInterp);
>> DMDestroy(&lDMBete);
>> lDMBete = lDMBeteInterp;
>>
>> DMSetUseNatural(lDMBete,PETSC_TRUE);
>>
>> PetscSF lSFMigrationSansOvl = 0;
>> PetscSF lSFMigrationOvl = 0;
>> DM lDMDistribueSansOvl = 0;
>> DM lDMAvecOverlap = 0;
>>
>> PetscPartitioner lPart;
>> DMPlexGetPartitioner(lDMBete, &lPart);
>> PetscPartitionerSetFromOptions(lPart);
>>
>> PetscSection section;
>> PetscInt numFields = 1;
>> PetscInt numBC = 0;
>> PetscInt numComp[1] = {1};
>> PetscInt numDof[4] = {1, 0, 0, 0};
>> PetscInt bcFields[1] = {0};
>> IS bcPoints[1] = {NULL};
>>
>> DMSetNumFields(lDMBete, numFields);
>>
>> DMPlexCreateSection(lDMBete, NULL, numComp, numDof, numBC, bcFields,
>> bcPoints, NULL, NULL, §ion);
>> DMSetLocalSection(lDMBete, section);
>>
>> DMPlexDistribute(lDMBete, 0, &lSFMigrationSansOvl,
>> &lDMDistribueSansOvl); // segfault!
>>
>> ===========
>>
>> So we have other question/remarks:
>>
>> 3- Maybe PETSc expect something specific that is missing/not verified:
>> for example, we didn't gave any coordinates since we just want to partition
>> and compute overlap for the mesh... and then recover our element numbers in
>> a "simple way"
>>
>> 4- We are telling ourselves it is somewhat a "big price to pay" to have
>> to build an unused section to have the global to natural ordering set ?
>> Could this requirement be avoided?
>>
> I don't think so. There would have to be _some_ way of describing your
> data layout in terms of mesh points, and I do not see how you could use
> less memory doing that.
>
>> 5- Are there any improvement towards our usages in 3.16 release?
>>
> Let me try and run the code above.
>
> Thanks,
>
> Matt
>
>> Thanks,
>>
>> Eric
>>
>>
>> On 2021-09-29 7:39 p.m., Matthew Knepley wrote:
>>
>> On Wed, Sep 29, 2021 at 5:18 PM Eric Chamberland <
>> Eric.Chamberland at giref.ulaval.ca> wrote:
>>
>>> Hi,
>>>
>>> I come back with _almost_ the original question:
>>>
>>> I would like to add an integer information (*our* original element
>>> number, not petsc one) on each element of the DMPlex I create with
>>> DMPlexBuildFromCellListParallel.
>>>
>>> I would like this interger to be distribruted by or the same way
>>> DMPlexDistribute distribute the mesh.
>>>
>>> Is it possible to do this?
>>>
>>
>> I think we already have support for what you want. If you call
>>
>> https://petsc.org/main/docs/manualpages/DM/DMSetUseNatural.html
>>
>> before DMPlexDistribute(), it will compute a PetscSF encoding the global
>> to natural map. You
>> can get it with
>>
>>
>> https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGetGlobalToNaturalSF.html
>>
>> and use it with
>>
>>
>> https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html
>>
>> Is this sufficient?
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> Thanks,
>>>
>>> Eric
>>>
>>> On 2021-07-14 1:18 p.m., Eric Chamberland wrote:
>>> > Hi,
>>> >
>>> > I want to use DMPlexDistribute from PETSc for computing overlapping
>>> > and play with the different partitioners supported.
>>> >
>>> > However, after calling DMPlexDistribute, I noticed the elements are
>>> > renumbered and then the original number is lost.
>>> >
>>> > What would be the best way to keep track of the element renumbering?
>>> >
>>> > a) Adding an optional parameter to let the user retrieve a vector or
>>> > "IS" giving the old number?
>>> >
>>> > b) Adding a DMLabel (seems a wrong good solution)
>>> >
>>> > c) Other idea?
>>> >
>>> > Of course, I don't want to loose performances with the need of this
>>> > "mapping"...
>>> >
>>> > Thanks,
>>> >
>>> > Eric
>>> >
>>> --
>>> Eric Chamberland, ing., M. Ing
>>> Professionnel de recherche
>>> GIREF/Université Laval
>>> (418) 656-2131 poste 41 22 42
>>>
>>>
>>
>> --
>> 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/>
>>
>> --
>> Eric Chamberland, ing., M. Ing
>> Professionnel de recherche
>> GIREF/Université Laval
>> (418) 656-2131 poste 41 22 42
>>
>>
>
> --
> 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/>
>
> --
> Eric Chamberland, ing., M. Ing
> Professionnel de recherche
> GIREF/Université Laval
> (418) 656-2131 poste 41 22 42
>
>
--
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/20211020/1ffd8500/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: ex44.c
Type: application/octet-stream
Size: 5243 bytes
Desc: not available
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20211020/1ffd8500/attachment-0001.obj>
More information about the petsc-users
mailing list