Dear everybody,
I have bug a bit into the code and I am able to add more information.
Il 02/12/22 12:48, Matteo Semplice ha scritto:
Hi.
I am sorry to take this up again, but further tests show that it's not
right yet.
Il 04/11/22 12:48, Matthew Knepley ha scritto:
On Fri, Nov 4, 2022 at 7:46 AM Matteo Semplice
<matteo.sempl...@uninsubria.it> wrote:
On 04/11/2022 02:43, Matthew Knepley wrote:
On Thu, Nov 3, 2022 at 8:36 PM Matthew Knepley
<knep...@gmail.com> wrote:
On Thu, Oct 27, 2022 at 11:57 AM Semplice Matteo
<matteo.sempl...@uninsubria.it> wrote:
Dear Petsc developers,
I am trying to use a DMSwarm to locate a cloud of points
with respect to a background mesh. In the real
application the points will be loaded from disk, but I
have created a small demo in which
* each processor creates Npart particles, all within
the domain covered by the mesh, but not all in the
local portion of the mesh
* migrate the particles
After migration most particles are not any more in the
DMSwarm (how many and which ones seems to depend on the
number of cpus, but it never happens that all particle
survive the migration process).
Thanks for sending this. I found the problem. Someone has
some overly fancy code inside DMDA to figure out the local
bounding box from the coordinates.
It is broken for DM_BOUNDARY_GHOSTED, but we never tested
with this. I will fix it.
Okay, I think this fix is correct
https://gitlab.com/petsc/petsc/-/merge_requests/5802
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Fpetsc%2Fpetsc%2F-%2Fmerge_requests%2F5802&data=05%7C01%7Cmatteo.semplice%40uninsubria.it%7Cf4d64b09df1f438437ad08dad45b342b%7C9252ed8bdffc401c86ca6237da9991fa%7C0%7C0%7C638055785720875500%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000%7C%7C%7C&sdata=ISLaLhhnYU4njkYfod%2F3tEiIOIV5uZvmiAlKZ2PvhmE%3D&reserved=0>
I incorporated your test as src/dm/impls/da/tests/ex1.c. Can you
take a look and see if this fixes your issue?
Yes, we have tested 2d and 3d, with various combinations of
DM_BOUNDARY_* along different directions and it works like a charm.
On a side note, neither DMSwarmViewXDMF nor DMSwarmMigrate seem
to be implemented for 1d: I get
[0]PETSC ERROR: No support for this operation for this object
type[0]PETSC ERROR: Support not provided for 1D
However, currently I have no need for this feature.
Finally, if the test is meant to stay in the source, you may
remove the call to DMSwarmRegisterPetscDatatypeField as in the
attached patch.
Thanks a lot!!
Thanks! Glad it works.
Matt
There are still problems when not using 1,2 or 4 cpus. Any other
number of cpus that I've tested does not work corectly.
I have now modified private_DMDALocatePointsIS_2D_Regular to print out
some debugging information. I see that this is called twice during
migration, once before and once after DMSwarmMigrate_DMNeighborScatter.
If I understand correctly, the second call to
private_DMDALocatePointsIS_2D_Regular should be able to locate all
particles owned by the rank but it fails for some of them because they
have been sent to the wrong rank (despite being well away from process
boundaries).
For example, running the example src/dm/impls/da/tests/ex1.c with Nx=21
(20x20 Q1 elements on [-1,1]X[-1,1]) with 3 processors,
- the particles (-0.191,-0.462) and (0.191,-0.462) are sent cpu2 instead
of cpu0
- those at (-0.287,-0.693)and (0.287,-0.693) are sent to cpu1 instead of
cpu0
- those at (0.191,0.462) and (-0.191,0.462) are sent to cpu0 instead of cpu2
(This is 2d and thus not affected by the 3d issue mentioned yesterday on
petsc-dev. Tests were made based on the release branch pulled out this
morning, i.e. on commit bebdc8d016f).
I attach the output separated by process.
If you have any hints, they would be appreciated.
Thanks
Matteo
... calling DMSwarmMigrate ...
=== private_DMDALocatePointsIS_2D_Regular
0] local domain (-1.000,-1.000) ... (1.000,-0.400)
0] local domain 20X6 cells with dx=(0.100,0.100)
0] locating particle 0 at (0.231,0.096)
0] locating particle 1 at (0.096,0.231)
0] locating particle 2 at (-0.096,0.231)
0] locating particle 3 at (-0.231,0.096)
0] locating particle 4 at (-0.231,-0.096)
0] locating particle 5 at (-0.096,-0.231)
0] locating particle 6 at (0.096,-0.231)
0] locating particle 7 at (0.231,-0.096)
=== DMSwarmMigrate_DMNeighborScatter
=== private_DMDALocatePointsIS_2D_Regular
0] local domain (-1.000,-1.000) ... (1.000,-0.400)
0] local domain 20X6 cells with dx=(0.100,0.100)
0] locating particle 0 at (0.191,0.462)
0] locating particle 1 at (-0.191,0.462)
0] locating particle 2 at (-0.191,-0.462)
0] ---->ok, particle 2 is in cell (8,5)-->108
0] locating particle 3 at (0.191,-0.462)
0] ---->ok, particle 3 is in cell (11,5)-->111
=== private_DMDALocatePointsIS_2D_Regular
1] local domain (-1.000,-0.400) ... (1.000,0.300)
1] local domain 20X7 cells with dx=(0.100,0.100)
1] locating particle 0 at (0.462,0.191)
1] ---->ok, particle 0 is in cell (14,11)-->114
1] locating particle 1 at (0.191,0.462)
1] locating particle 2 at (-0.191,0.462)
1] locating particle 3 at (-0.462,0.191)
1] ---->ok, particle 3 is in cell (5,11)-->105
1] locating particle 4 at (-0.462,-0.191)
1] ---->ok, particle 4 is in cell (5,8)-->45
1] locating particle 5 at (-0.191,-0.462)
1] locating particle 6 at (0.191,-0.462)
1] locating particle 7 at (0.462,-0.191)
1] ---->ok, particle 7 is in cell (14,8)-->54
=== DMSwarmMigrate_DMNeighborScatter
=== private_DMDALocatePointsIS_2D_Regular
1] local domain (-1.000,-0.400) ... (1.000,0.300)
1] local domain 20X7 cells with dx=(0.100,0.100)
1] locating particle 0 at (0.231,0.096)
1] ---->ok, particle 0 is in cell (12,10)-->92
1] locating particle 1 at (0.096,0.231)
1] ---->ok, particle 1 is in cell (10,12)-->130
1] locating particle 2 at (-0.096,0.231)
1] ---->ok, particle 2 is in cell (9,12)-->129
1] locating particle 3 at (-0.231,0.096)
1] ---->ok, particle 3 is in cell (7,10)-->87
1] locating particle 4 at (-0.231,-0.096)
1] ---->ok, particle 4 is in cell (7,9)-->67
1] locating particle 5 at (-0.096,-0.231)
1] ---->ok, particle 5 is in cell (9,7)-->29
1] locating particle 6 at (0.096,-0.231)
1] ---->ok, particle 6 is in cell (10,7)-->30
1] locating particle 7 at (0.231,-0.096)
1] ---->ok, particle 7 is in cell (12,9)-->72
1] locating particle 8 at (0.693,0.287)
1] ---->ok, particle 8 is in cell (16,12)-->136
1] locating particle 9 at (-0.693,0.287)
1] ---->ok, particle 9 is in cell (3,12)-->123
1] locating particle 10 at (-0.693,-0.287)
1] ---->ok, particle 10 is in cell (3,7)-->23
1] locating particle 11 at (-0.287,-0.693)
1] locating particle 12 at (0.287,-0.693)
1] locating particle 13 at (0.693,-0.287)
1] ---->ok, particle 13 is in cell (16,7)-->36
=== private_DMDALocatePointsIS_2D_Regular
2] local domain (-1.000,0.300) ... (1.000,1.000)
2] local domain 20X7 cells with dx=(0.100,0.100)
2] locating particle 0 at (0.693,0.287)
2] locating particle 1 at (0.287,0.693)
2] ---->ok, particle 1 is in cell (12,16)-->72
2] locating particle 2 at (-0.287,0.693)
2] ---->ok, particle 2 is in cell (7,16)-->67
2] locating particle 3 at (-0.693,0.287)
2] locating particle 4 at (-0.693,-0.287)
2] locating particle 5 at (-0.287,-0.693)
2] locating particle 6 at (0.287,-0.693)
2] locating particle 7 at (0.693,-0.287)
=== DMSwarmMigrate_DMNeighborScatter
=== private_DMDALocatePointsIS_2D_Regular
2] local domain (-1.000,0.300) ... (1.000,1.000)
2] local domain 20X7 cells with dx=(0.100,0.100)
2] locating particle 0 at (0.191,0.462)
2] ---->ok, particle 0 is in cell (11,14)-->31
2] locating particle 1 at (-0.191,0.462)
2] ---->ok, particle 1 is in cell (8,14)-->28
2] locating particle 2 at (-0.191,-0.462)
2] locating particle 3 at (0.191,-0.462)
