[petsc-users] Doubt about mesh size distribution in DMDACreate3d using periodic boundary conditions

Wed Nov 20 11:56:27 CST 2024

I mean that if the dimensions of the cube are 1x1x1 (for example). And I want 10 elements per edge, the discretization size must be 0.1 constant over the whole cube edge.

This is not in the code, I just impose the number of elements per edge.

Thank you,
Miguel

On 20 Nov 2024, at 18:52, Barry Smith <bsmith at petsc.dev> wrote:

  What do you mean by discretization size, and how do I see it in the code?

  Barry

On Nov 20, 2024, at 12:48 PM, MIGUEL MOLINOS PEREZ <mmolinos at us.es> wrote:

Sorry, I meant that the discretisation size is not constant across the edges of the cube.

Miguel

On 20 Nov 2024, at 18:36, Barry Smith <bsmith at petsc.dev> wrote:

   I am sorry, I don't understand the problem. When I run by default with -da_view I get

Processor [0] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 0 2
Processor [1] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 3, Y range of indices: 0 2, Z range of indices: 0 2
Processor [2] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 2 3, Z range of indices: 0 2
Processor [3] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 3, Y range of indices: 2 3, Z range of indices: 0 2
Processor [4] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 2 3
Processor [5] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 3, Y range of indices: 0 2, Z range of indices: 2 3
Processor [6] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 2 3, Z range of indices: 2 3
Processor [7] M 3 N 3 P 3 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 3, Y range of indices: 2 3, Z range of indices: 2 3

which seems right because you are trying to have three cells in each direction. The distribution has to be uneven, hence 0 2 and 2 3

When I change the code to use ndiv_mesh_* = 4 and run with periodic or not I get

$ PETSC_OPTIONS="" mpiexec -n 8 ./atoms-3D -dm_view
DM Object: 8 MPI processes
  type: da
Processor [0] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 0 2
Processor [1] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 4, Y range of indices: 0 2, Z range of indices: 0 2
Processor [2] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 2 4, Z range of indices: 0 2
Processor [3] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 4, Y range of indices: 2 4, Z range of indices: 0 2
Processor [4] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 0 2, Z range of indices: 2 4
Processor [5] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 4, Y range of indices: 0 2, Z range of indices: 2 4
Processor [6] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 0 2, Y range of indices: 2 4, Z range of indices: 2 4
Processor [7] M 4 N 4 P 4 m 2 n 2 p 2 w 1 s 1
X range of indices: 2 4, Y range of indices: 2 4, Z range of indices: 2 4

so it is splitting as expected each rank gets a 2 by 2 by 2 set of indices.

Could you please let me know what the problem is that I should be seeing.

  Barry

On Nov 20, 2024, at 7:06 AM, MIGUEL MOLINOS PEREZ <mmolinos at us.es> wrote:

Dear Barry,

Please, find attached to this email a minimal example of the problem. Run it using 8 MPI processes.

Thanks,
Miguel

On 20 Nov 2024, at 11:48, Miguel Molinos <mmolinos at us.es> wrote:

Hi Bary:

I will check the example you suggest. Anyhow, I’ll send a reproducible example ASAP.

Thanks,
Miguel

On 19 Nov 2024, at 18:55, Barry Smith <bsmith at petsc.dev> wrote:

   I modify src/dm/tests/ex25.c and always see a nice even split when possible with both DM_BOUNDARY_NONE and DM_BOUNDARY_PERIODIC

    Can you please send a reproducible example?

    Thanks

     Barry

On Nov 19, 2024, at 6:14 AM, MIGUEL MOLINOS PEREZ <mmolinos at us.es> wrote:

Dear all:

It seems that if I mesh a cubic domain with “DMDACreate3d” using 8 bricks for discretization and with periodic boundaries, each of the bricks has a different size. In contrast, if I use DM_BOUNDARY_NONE, all 8 bricks have the same size.

I have used this together with the DMSWarm discretization. And as you can see the number of particles per rank is not evenly distributed:
210 420 366 732 420 840 732 1464

Am I missing something?

Thanks,
Miguel

<Screenshot 2024-11-19 at 10.56.36.png>

<atoms-3D.cpp><Mg-hcp-cube-x17-x10-x10.dump>

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