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?"
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]
If we do not create a section, the call to DMPlexDistribute is
successful, but DMPlexGetGlobalToNaturalSF return a null SF pointer...
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?
5- Are there any improvement towards our usages in 3.16 release?
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]
<mailto:[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
<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
<https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGetGlobalToNaturalSF.html>
and use it with
https://petsc.org/main/docs/manualpages/DMPLEX/DMPlexGlobalToNaturalBegin.html
<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
