[petsc-users] Is it possible to keep track of original elements # after a call to DMPlexDistribute ?
Matthew Knepley
knepley at gmail.com
Tue Oct 26 15:35:42 CDT 2021
On Tue, Oct 26, 2021 at 1:35 PM Eric Chamberland <
Eric.Chamberland at giref.ulaval.ca> wrote:
> Here is a screenshot of the partition I hard coded (top) and
> vertices/element numbers (down):
>
> I have not yet modified the ex44.c example to properly assign the
> coordinates...
>
> (but I would not have done it like it is in the last version because the
> sCoords array is the global array with global vertices number)
>
> I will have time to do this tomorrow...
>
> Maybe I can first try to reproduce all this with a smaller mesh?
>
That might make it easier to find a problem.
Thanks!
Matt
> Eric
> On 2021-10-26 9:46 a.m., Matthew Knepley wrote:
>
> Okay, I ran it. Something seems off with the mesh. First, I cannot simply
> explain the partition. The number of shared vertices and edges
> does not seem to come from a straight cut. Second, the mesh look scrambled
> on output.
>
> Thanks,
>
> Matt
>
> On Sun, Oct 24, 2021 at 11:49 PM Eric Chamberland <
> Eric.Chamberland at giref.ulaval.ca> wrote:
>
>> Hi Matthew,
>>
>> ok, I started back from your ex44.c example and added the global array of
>> coordinates. I just have to code the creation of the local coordinates now.
>>
>> Eric
>> On 2021-10-20 6:55 p.m., Matthew Knepley wrote:
>>
>> 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/>
>>
>> --
>> 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/>
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