[petsc-users] DMPlex overlap
Matthew Knepley
knepley at gmail.com
Fri Apr 16 06:17:55 CDT 2021
On Fri, Apr 16, 2021 at 5:50 AM Nicolas Barral <
nicolas.barral at math.u-bordeaux.fr> wrote:
> On 31/03/2021 21:44, Matthew Knepley wrote:
> > On Wed, Mar 31, 2021 at 3:36 PM Nicolas Barral
> > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>> wrote:
> >
> > On 31/03/2021 21:24, Matthew Knepley wrote:
> > > Ok so that's worth clarifying, but my problem is that dm has a
> > > 0-overlap
> > > before DMPlexDistributeOverlap and odm has a 1-overlap even
> > though I
> > > passed "0". If I understand what you just wrote, adding "0"
> > more levels
> > > of overlap to 0-overlap, that should still be 0 overlap ?
> > >
> > > Yet when I look at the code of DMPlexDistributeOverlap,
> > you're flagging
> > > points to be added to the overlap whatever "k" is.
> > >
> > >
> > > Crap. There is a bug handling 0. Evidently, no one ever asks for
> > overlap 0.
> > > Will fix.
> > >
> > ok now I'm sure I understand what you explained :) Thanks Matt.
> >
> > Now we can look at the other question: I need to be able to pass the
> > non-overlapping mesh to the remesher. I can either maintain 2
> > plexes, or
> > trim the overlapping plex when I create the arrays I pass to the
> > remesher. I'm not sure which is the best/worst ?
> >
> >
> > I would start with two plexes since it is very easy.
>
> Hi Matt,
>
> I've been playing with two plexes, and am running in an unexpected
> issue. It seems that the vertices ordering of the new overlapping plex
> is not the same as the one of the original plex, which makes converting
> a Vec from one plex to the other difficult. Can you please confirm it's
> the case, and is there a way to convert the Vecs out of the box ?
>
Okay, we should get all the new cells at the end of the current cells, but
then we automatically create
the renumbering for the cones using the global vertex numbering. Thus it
looks like they could get
renumbered if the vertex of a new cell has a lower global number than some
existing vertex.
Whenever we move things around, we give back the PetscSF we built to do the
moving. The idea is
that you can use the returned SF to move anything that we did not, using
the same method we used to
move the internal things. For example, DMMigrate() takes an SF and moves
the internal mesh data,
cones + labels + coordinates. It calls DMPlexDistributeField() to move the
coordinate data. You can
call the same thing. If you have your two vectors+sections already created,
and you just want to go
back and forth, you can use PetscSFCreateSectionSF() (which you can store)
and SFBcast(). This is
done inside DMPlexDistributeField().
Does this make sense?
Thanks,
Matt
Else filtering the plex may be easier.
>
> Thanks
>
> --
> Nicolas
>
> >
> > Trimming the plex would essentially make another plex anyway, but it is
> > not hard using DMPlexFilter().
> >
> > Thanks,
> >
> > Matt
> >
> > Thanks
> >
> > --
> > Nicolas
> >
> >
> > > Thanks,
> > >
> > > Matt
> > >
> > > Sample code:
> > > static char help[] = "Tests plex distribution and
> overlaps.\n";
> > >
> > > #include <petsc/private/dmpleximpl.h>
> > >
> > > int main (int argc, char * argv[]) {
> > >
> > > DM dm, odm;
> > > MPI_Comm comm;
> > > PetscErrorCode ierr;
> > >
> > > ierr = PetscInitialize(&argc, &argv, NULL, help);if (ierr)
> > > return ierr;
> > > comm = PETSC_COMM_WORLD;
> > >
> > > ierr = DMPlexCreateBoxMesh(comm, 2, PETSC_TRUE, NULL,
> > NULL, NULL,
> > > NULL, PETSC_TRUE, &dm);CHKERRQ(ierr);
> > > ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
> > >
> > >
> > >
> > > ierr = PetscObjectSetName((PetscObject) dm, "DM
> > > before");CHKERRQ(ierr);
> > > ierr = DMViewFromOptions(dm, NULL,
> > "-before_dm_view");CHKERRQ(ierr);
> > > DMPlexDistributeOverlap(dm, 0, NULL, &odm);
> > > ierr = PetscObjectSetName((PetscObject) odm, "DM
> > > after");CHKERRQ(ierr);
> > > ierr = DMViewFromOptions(odm, NULL,
> > "-after_dm_view");CHKERRQ(ierr);
> > >
> > >
> > > ierr = DMDestroy(&dm);CHKERRQ(ierr);
> > > ierr = DMDestroy(&odm);CHKERRQ(ierr);
> > > ierr = PetscFinalize();
> > > return ierr;
> > > }
> > >
> > > % mpiexec -n 2 ./test_overlapV3 -dm_plex_box_faces 5,5
> > -dm_distribute
> > > -before_dm_view -after_dm_view
> > > DM Object: DM before 2 MPI processes
> > > type: plex
> > > DM before in 2 dimensions:
> > > 0-cells: 21 21
> > > 1-cells: 45 45
> > > 2-cells: 25 25
> > > Labels:
> > > depth: 3 strata with value/size (0 (21), 1 (45), 2 (25))
> > > celltype: 3 strata with value/size (0 (21), 1 (45), 3
> (25))
> > > marker: 1 strata with value/size (1 (21))
> > > Face Sets: 1 strata with value/size (1 (10))
> > > DM Object: DM after 2 MPI processes
> > > type: plex
> > > DM after in 2 dimensions:
> > > 0-cells: 29 29
> > > 1-cells: 65 65
> > > 2-cells: 37 37
> > > Labels:
> > > depth: 3 strata with value/size (0 (29), 1 (65), 2 (37))
> > > celltype: 3 strata with value/size (0 (29), 1 (65), 3
> (37))
> > > marker: 1 strata with value/size (1 (27))
> > > Face Sets: 1 strata with value/size (1 (13))
> > >
> > >
> > >
> > > >
> > > > Thanks,
> > > >
> > > > Matt
> > > >
> > > > Thanks,
> > > >
> > > > --
> > > > Nicolas
> > > >
> > > > >
> > > > > Thanks,
> > > > >
> > > > > Matt
> > > > >
> > > > > if (!dm) {printf("Big problem\n"); dm =
> odm;}
> > > > > else {DMDestroy(&odm);}
> > > > > ierr = PetscObjectSetName((PetscObject) dm,
> > "Initial
> > > > > DM");CHKERRQ(ierr);
> > > > > ierr = DMViewFromOptions(dm, NULL,
> > > > > "-initial_dm_view");CHKERRQ(ierr);
> > > > >
> > > > >
> > > > > ierr = DMDestroy(&dm);CHKERRQ(ierr);
> > > > > ierr = PetscFinalize();
> > > > > return ierr;
> > > > > }
> > > > >
> > > > > called with mpiexec -n 2 ./test_overlapV3
> > -initial_dm_view
> > > > > -dm_plex_box_faces 5,5 -dm_distribute
> > > > >
> > > > > gives:
> > > > > DM Object: Initial DM 2 MPI processes
> > > > > type: plex
> > > > > Initial DM in 2 dimensions:
> > > > > 0-cells: 29 29
> > > > > 1-cells: 65 65
> > > > > 2-cells: 37 37
> > > > > Labels:
> > > > > depth: 3 strata with value/size (0 (29), 1
> > (65), 2
> > > (37))
> > > > > celltype: 3 strata with value/size (0 (29),
> 1
> > > (65), 3 (37))
> > > > > marker: 1 strata with value/size (1 (27))
> > > > > Face Sets: 1 strata with value/size (1 (13))
> > > > >
> > > > > which is not what I expect ?
> > > > >
> > > > > Thanks,
> > > > >
> > > > > --
> > > > > Nicolas
> > > > >
> > > > > On 31/03/2021 19:02, Matthew Knepley wrote:
> > > > > > Alright, I think the problem had to do with
> > keeping
> > > track
> > > > of what
> > > > > DM you
> > > > > > were looking at. This code increases the
> > overlap of an
> > > > initial DM:
> > > > > >
> > > > > > static char help[] = "Tests plex
> > distribution and
> > > > overlaps.\n";
> > > > > >
> > > > > > #include <petsc/private/dmpleximpl.h>
> > > > > >
> > > > > > int main (int argc, char * argv[]) {
> > > > > >
> > > > > > DM dm, dm2;
> > > > > > PetscInt overlap;
> > > > > > MPI_Comm comm;
> > > > > > PetscErrorCode ierr;
> > > > > >
> > > > > > ierr = PetscInitialize(&argc, &argv, NULL,
> > > help);if (ierr)
> > > > > return ierr;
> > > > > > comm = PETSC_COMM_WORLD;
> > > > > >
> > > > > > ierr = DMPlexCreateBoxMesh(comm, 2,
> > PETSC_TRUE,
> > > NULL,
> > > > NULL, NULL,
> > > > > > NULL, PETSC_TRUE, &dm);CHKERRQ(ierr);
> > > > > > ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
> > > > > > ierr = PetscObjectSetName((PetscObject)
> > dm, "Initial
> > > > > DM");CHKERRQ(ierr);
> > > > > > ierr = DMViewFromOptions(dm, NULL,
> > > > > "-initial_dm_view");CHKERRQ(ierr);
> > > > > >
> > > > > > ierr = DMPlexGetOverlap(dm,
> > &overlap);CHKERRQ(ierr);
> > > > > > ierr = DMPlexDistributeOverlap(dm,
> > overlap+1, NULL,
> > > > > &dm2);CHKERRQ(ierr);
> > > > > > ierr = PetscObjectSetName((PetscObject)
> dm2,
> > > "More Overlap
> > > > > > DM");CHKERRQ(ierr);
> > > > > > ierr = DMViewFromOptions(dm2, NULL,
> > > > > "-over_dm_view");CHKERRQ(ierr);
> > > > > >
> > > > > > ierr = DMDestroy(&dm2);CHKERRQ(ierr);
> > > > > > ierr = DMDestroy(&dm);CHKERRQ(ierr);
> > > > > > ierr = PetscFinalize();
> > > > > > return ierr;
> > > > > > }
> > > > > >
> > > > > > and when we run it we get the expected result
> > > > > >
> > > > > > master *:~/Downloads/tmp/Nicolas$
> > > > /PETSc3/petsc/apple/bin/mpiexec
> > > > > -n 2
> > > > > > ./test_overlap -initial_dm_view
> > -dm_plex_box_faces 5,5
> > > > > -dm_distribute
> > > > > > -dm_distribute_overlap 1 -over_dm_view
> > > > > > DM Object: Initial DM 2 MPI processes
> > > > > > type: plex
> > > > > > Initial DM in 2 dimensions:
> > > > > > 0-cells: 29 29
> > > > > > 1-cells: 65 65
> > > > > > 2-cells: 37 37
> > > > > > Labels:
> > > > > > depth: 3 strata with value/size (0 (29),
> > 1 (65),
> > > 2 (37))
> > > > > > celltype: 3 strata with value/size (0
> (29), 1
> > > (65), 3 (37))
> > > > > > marker: 1 strata with value/size (1 (27))
> > > > > > Face Sets: 1 strata with value/size (1
> (13))
> > > > > > DM Object: More Overlap DM 2 MPI processes
> > > > > > type: plex
> > > > > > More Overlap DM in 2 dimensions:
> > > > > > 0-cells: 36 36
> > > > > > 1-cells: 85 85
> > > > > > 2-cells: 50 50
> > > > > > Labels:
> > > > > > depth: 3 strata with value/size (0 (36),
> > 1 (85),
> > > 2 (50))
> > > > > > celltype: 3 strata with value/size (0
> (36), 1
> > > (85), 3 (50))
> > > > > > marker: 1 strata with value/size (1 (40))
> > > > > > Face Sets: 1 strata with value/size (1
> (20))
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Matt
> > > > > >
> > > > > > On Wed, Mar 31, 2021 at 12:57 PM Matthew
> Knepley
> > > > > <knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>
> > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>>
> > > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>
> > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>>>
> > > > > > <mailto:knepley at gmail.com
> > <mailto:knepley at gmail.com>
> > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>>
> > > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>
> > > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>
> > <mailto:knepley at gmail.com <mailto:knepley at gmail.com>>>>>> wrote:
> > > > > >
> > > > > > Okay, let me show a really simple
> > example that
> > > gives
> > > > the expected
> > > > > > result before I figure out what is going
> > wrong for
> > > > you. This code
> > > > > >
> > > > > > static char help[] = "Tests plex
> > distribution and
> > > > overlaps.\n";
> > > > > >
> > > > > > #include <petsc/private/dmpleximpl.h>
> > > > > >
> > > > > > int main (int argc, char * argv[]) {
> > > > > > DM dm;
> > > > > > MPI_Comm comm;
> > > > > > PetscErrorCode ierr;
> > > > > >
> > > > > > ierr = PetscInitialize(&argc, &argv,
> > NULL,
> > > help);if
> > > > (ierr)
> > > > > return
> > > > > > ierr;
> > > > > > comm = PETSC_COMM_WORLD;
> > > > > >
> > > > > > ierr = DMPlexCreateBoxMesh(comm, 2,
> > > PETSC_TRUE, NULL,
> > > > > NULL, NULL,
> > > > > > NULL, PETSC_TRUE, &dm);CHKERRQ(ierr);
> > > > > > ierr =
> > DMSetFromOptions(dm);CHKERRQ(ierr);
> > > > > > ierr =
> > PetscObjectSetName((PetscObject) dm,
> > > "Initial
> > > > > > DM");CHKERRQ(ierr);
> > > > > > ierr = DMViewFromOptions(dm, NULL,
> > > > > "-initial_dm_view");CHKERRQ(ierr);
> > > > > > ierr = DMDestroy(&dm);CHKERRQ(ierr);
> > > > > > ierr = PetscFinalize();
> > > > > > return ierr;
> > > > > > }
> > > > > >
> > > > > > can do all the overlap tests. For
> > example, you
> > > can run
> > > > it naively
> > > > > > and get a serial mesh
> > > > > >
> > > > > > master *:~/Downloads/tmp/Nicolas$
> > > > > /PETSc3/petsc/apple/bin/mpiexec -n
> > > > > > 2 ./test_overlap -initial_dm_view
> > > -dm_plex_box_faces 5,5
> > > > > > DM Object: Initial DM 2 MPI processes
> > > > > > type: plex
> > > > > > Initial DM in 2 dimensions:
> > > > > > 0-cells: 36 0
> > > > > > 1-cells: 85 0
> > > > > > 2-cells: 50 0
> > > > > > Labels:
> > > > > > celltype: 3 strata with value/size (0
> > (36),
> > > 3 (50),
> > > > 1 (85))
> > > > > > depth: 3 strata with value/size (0
> > (36), 1
> > > (85), 2
> > > > (50))
> > > > > > marker: 1 strata with value/size (1
> (40))
> > > > > > Face Sets: 1 strata with value/size
> > (1 (20))
> > > > > >
> > > > > > Then run it telling Plex to distribute
> after
> > > creating
> > > > the mesh
> > > > > >
> > > > > > master *:~/Downloads/tmp/Nicolas$
> > > > > /PETSc3/petsc/apple/bin/mpiexec -n
> > > > > > 2 ./test_overlap -initial_dm_view
> > > -dm_plex_box_faces 5,5
> > > > > -dm_distribute
> > > > > > DM Object: Initial DM 2 MPI processes
> > > > > > type: plex
> > > > > > Initial DM in 2 dimensions:
> > > > > > 0-cells: 21 21
> > > > > > 1-cells: 45 45
> > > > > > 2-cells: 25 25
> > > > > > Labels:
> > > > > > depth: 3 strata with value/size (0
> > (21), 1
> > > (45), 2
> > > > (25))
> > > > > > celltype: 3 strata with value/size (0
> > (21),
> > > 1 (45),
> > > > 3 (25))
> > > > > > marker: 1 strata with value/size (1
> (21))
> > > > > > Face Sets: 1 strata with value/size
> > (1 (10))
> > > > > >
> > > > > > The get the same thing back with overlap
> = 0
> > > > > >
> > > > > > master *:~/Downloads/tmp/Nicolas$
> > > > > /PETSc3/petsc/apple/bin/mpiexec -n
> > > > > > 2 ./test_overlap -initial_dm_view
> > > -dm_plex_box_faces 5,5
> > > > > > -dm_distribute -dm_distribute_overlap 0
> > > > > > DM Object: Initial DM 2 MPI processes
> > > > > > type: plex
> > > > > > Initial DM in 2 dimensions:
> > > > > > 0-cells: 21 21
> > > > > > 1-cells: 45 45
> > > > > > 2-cells: 25 25
> > > > > > Labels:
> > > > > > depth: 3 strata with value/size (0
> > (21), 1
> > > (45), 2
> > > > (25))
> > > > > > celltype: 3 strata with value/size (0
> > (21),
> > > 1 (45),
> > > > 3 (25))
> > > > > > marker: 1 strata with value/size (1
> (21))
> > > > > > Face Sets: 1 strata with value/size
> > (1 (10))
> > > > > >
> > > > > > and get larger local meshes with overlap
> = 1
> > > > > >
> > > > > > master *:~/Downloads/tmp/Nicolas$
> > > > > /PETSc3/petsc/apple/bin/mpiexec -n
> > > > > > 2 ./test_overlap -initial_dm_view
> > > -dm_plex_box_faces 5,5
> > > > > > -dm_distribute -dm_distribute_overlap 1
> > > > > > DM Object: Initial DM 2 MPI processes
> > > > > > type: plex
> > > > > > Initial DM in 2 dimensions:
> > > > > > 0-cells: 29 29
> > > > > > 1-cells: 65 65
> > > > > > 2-cells: 37 37
> > > > > > Labels:
> > > > > > depth: 3 strata with value/size (0
> > (29), 1
> > > (65), 2
> > > > (37))
> > > > > > celltype: 3 strata with value/size (0
> > (29),
> > > 1 (65),
> > > > 3 (37))
> > > > > > marker: 1 strata with value/size (1
> (27))
> > > > > > Face Sets: 1 strata with value/size
> > (1 (13))
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Matt
> > > > > >
> > > > > > On Wed, Mar 31, 2021 at 12:22 PM Nicolas
> > Barral
> > > > > > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>
> > > > > >
> > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>>> wrote:
> > > > > >
> > > > > >
> > > > > >
> > > > > > @+
> > > > > >
> > > > > > --
> > > > > > Nicolas
> > > > > >
> > > > > > On 31/03/2021 17:51, Matthew Knepley
> > wrote:
> > > > > > > On Sat, Mar 27, 2021 at 9:27 AM
> > Nicolas
> > > Barral
> > > > > > >
> > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>
> > > > > >
> > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>>
> > > > > > >
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>
> > > > > >
> > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>
> > > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>
> > > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>
> > > <mailto:nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>>>>>>> wrote:
> > > > > > >
> > > > > > > Hi all,
> > > > > > >
> > > > > > > First, I'm not sure I
> understand
> > > what the
> > > > overlap
> > > > > > parameter in
> > > > > > > DMPlexDistributeOverlap does.
> I
> > > tried the
> > > > following:
> > > > > > generate a small
> > > > > > > mesh on 1 rank with
> > > DMPlexCreateBoxMesh, then
> > > > > distribute
> > > > > > it with
> > > > > > > DMPlexDistribute. At this
> point I
> > > have two nice
> > > > > > partitions, with shared
> > > > > > > vertices and no overlapping
> > cells.
> > > Then I call
> > > > > > DMPlexDistributeOverlap
> > > > > > > with the overlap parameter
> > set to 0
> > > or 1,
> > > > and get the
> > > > > > same resulting
> > > > > > > plex in both cases. Why is
> that ?
> > > > > > >
> > > > > > >
> > > > > > > The overlap parameter says how
> > many cell
> > > > adjacencies to go
> > > > > > out. You
> > > > > > > should not get the same
> > > > > > > mesh out. We have lots of
> > examples that use
> > > > this. If
> > > > > you send
> > > > > > your small
> > > > > > > example, I can probably
> > > > > > > tell you what is happening.
> > > > > > >
> > > > > >
> > > > > > Ok so I do have a small example on
> > that and the
> > > > DMClone
> > > > > thing I
> > > > > > set up
> > > > > > to understand! I attach it to the
> email.
> > > > > >
> > > > > > For the overlap, you can change the
> > overlap
> > > > constant at
> > > > > the top
> > > > > > of the
> > > > > > file. With OVERLAP=0 or 1, the
> > distributed
> > > > overlapping mesh
> > > > > > (shown using
> > > > > > -over_dm_view, it's DMover) are the
> > same, and
> > > > different
> > > > > from the
> > > > > > mesh
> > > > > > before distributing the overlap
> > (shown using
> > > > > -distrib_dm_view). For
> > > > > > larger overlap values they're
> different.
> > > > > >
> > > > > > The process is:
> > > > > > 1/ create a DM dm on 1 rank
> > > > > > 2/ clone dm into dm2
> > > > > > 3/ distribute dm
> > > > > > 4/ clone dm into dm3
> > > > > > 5/ distribute dm overlap
> > > > > >
> > > > > > I print all the DMs after each step.
> > dm has a
> > > > distributed
> > > > > > overlap, dm2
> > > > > > is not distributed, dm3 is
> > distributed but
> > > without
> > > > > overlap. Since
> > > > > > distribute and distributeOverlap
> > create new
> > > DMs, I
> > > > don't seem
> > > > > > have a
> > > > > > problem with the shallow copies.
> > > > > >
> > > > > >
> > > > > > > Second, I'm wondering what
> > would be
> > > a good
> > > > way to
> > > > > handle
> > > > > > two overlaps
> > > > > > > and associated local vectors.
> > In my
> > > adaptation
> > > > > code, the
> > > > > > remeshing
> > > > > > > library requires a
> > non-overlapping mesh,
> > > > while the
> > > > > > refinement criterion
> > > > > > > computation is based on
> hessian
> > > > computations, which
> > > > > > require a layer of
> > > > > > > overlap. What I can do is
> > clone the
> > > dm before
> > > > > > distributing the overlap,
> > > > > > > then manage two independent
> plex
> > > objects with
> > > > > their own
> > > > > > local sections
> > > > > > > etc. and copy/trim local
> vectors
> > > manually.
> > > > Is there a
> > > > > > more automatic
> > > > > > > way
> > > > > > > to do this ?
> > > > > > >
> > > > > > >
> > > > > > > DMClone() is a shallow copy, so
> that
> > > will not work.
> > > > > You would
> > > > > > maintain
> > > > > > > two different Plexes, overlapping
> > > > > > > and non-overlapping, with their
> > own sections
> > > > and vecs. Are
> > > > > > you sure you
> > > > > > > need to keep around the
> > non-overlapping one?
> > > > > > > Maybe if I understood what
> operations
> > > you want
> > > > to work, I
> > > > > > could say
> > > > > > > something more definitive.
> > > > > > >
> > > > > > I need to be able to pass the
> > > non-overlapping mesh
> > > > to the
> > > > > > remesher. I
> > > > > > can either maintain 2 plexes, or
> > trim the
> > > overlapping
> > > > > plex when
> > > > > > I create
> > > > > > the arrays I give to the remesher.
> > I'm not sure
> > > > which is the
> > > > > > best/worst ?
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > > > --
> > > > > > Nicolas
> > > > > >
> > > > > >
> > > > > > > Thanks,
> > > > > > >
> > > > > > > Matt
> > > > > > >
> > > > > > > Thanks
> > > > > > >
> > > > > > > --
> > > > > > > Nicolas
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > --
> > > > > > > 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/>
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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/>
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > 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/>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > 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/>
> > > >
> > > >
> > > >
> > > > --
> > > > 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/>
> > >
> > >
> > >
> > > --
> > > 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/>
> >
> >
> >
> > --
> > 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/>
>
>
--
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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