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 < [email protected]> 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 < [email protected]> 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 [email protected]
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 < [email protected]> 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 < [email protected]> 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.ht...
and use it with
https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.ht...
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/>
