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
> > <[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>
> <mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>
> > > <mailto:[email protected]
<mailto:[email protected]> <mailto:[email protected]
<mailto:[email protected]>>
> <mailto:[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>>>> 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
> > > <[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>
> > > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>>> wrote:
> > >
> > >
> > >
> > > @+
> > >
> > > --
> > > Nicolas
> > >
> > > On 31/03/2021 17:51, Matthew Knepley wrote:
> > > > On Sat, Mar 27, 2021 at 9:27 AM Nicolas
Barral
> > > > <[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>
> > > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>>
> > > >
<mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>
> > > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>
> > <mailto:[email protected]
<mailto:[email protected]>
> <mailto:[email protected]
<mailto:[email protected]>>>>>> 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/>
