[petsc-users] Is it possible to keep track of original elements # after a call to DMPlexDistribute ?
Matthew Knepley
knepley at gmail.com
Wed Oct 27 10:14:27 CDT 2021
On Wed, Oct 27, 2021 at 8:29 AM Eric Chamberland <
Eric.Chamberland at giref.ulaval.ca> wrote:
> Hi Matthew,
>
> the smallest mesh which crashes the code is a 2x5 mesh:
>
> See the modified ex44.c
>
> With smaller meshes(2x2, 2x4, etc), it passes... But it bugs latter when
> I try to use DMPlexNaturalToGlobalBegin but let's keep that other problem
> for later...
>
> Thanks a lot for helping digging into this! :)
>
I have made a small fix in this branch
https://gitlab.com/petsc/petsc/-/commits/knepley/fix-plex-g2n
It seems to run for me. Can you check it?
Thanks,
Matt
> Eric
>
> (sorry if you received this for a 2nd times, I have trouble with my mail)
> On 2021-10-26 4:35 p.m., Matthew Knepley wrote:
>
> 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/>
>
> --
> 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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