[petsc-users] dmplex extrude in parallel

[Bhargav Subramanya]

Dear Matt,

Thanks a lot for the reply. I am now able to generate the prismatic mesh
properly.

In the case of mpiexec -n 2 ./meshtest -dm_plex_shape sphere -dm_refine_pre
3 -dm_distribute -dm_refine 2 and DMExtrude(), where I am ordering the
extruded cells on the layers first; Is the mesh extruded in parallel for
this case?

The first time I distributed the mesh, it was only the spherical surface
mesh. After dmplex extrude, the mesh changes. Do I need to redistribute the
mesh again?

Thanks,
Bhargav

On Wed, Nov 10, 2021 at 12:56 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Nov 9, 2021 at 9:54 AM Bhargav Subramanya <
> bhargav.subramanya at kaust.edu.sa> wrote:
>
>> Dear All,
>>
>> I want to generate a prismatic mesh from a base spherical surface mesh. I
>> first refine the base icosahedron sequential mesh to some extent,
>> distribute the mesh, continue the refinement in parallel, project the mesh
>> to a unit sphere, and then finally extrude the mesh. The following is the
>> code I am using. As the extrusion is performed in parallel, the extruded
>> mesh seems to be broken as shown in the attached figure. May I know how to
>> get an intact extruded mesh in parallel? Also, is it possible to make mesh
>> refinement respect the spherical surface geometry, without having to
>> project it using a function as shown below?
>>
>
> I think you can do most of what you want from the command line. Here is a
> simple code:
>
> #include <petsc.h>
>
> int main(int argc, char **argv)
> {
>   DM             dm;
>   PetscErrorCode ierr;
>
>   ierr = PetscInitialize(&argc, &argv, NULL, NULL);if (ierr) return ierr;
>   ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
>   ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
>   ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
>   ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
>   ierr = DMDestroy(&dm);CHKERRQ(ierr);
>   ierr = PetscFinalize();
>   return ierr;
> }
>
> that I run using
>
>   mpiexec -n 2 ./meshtest -dm_plex_shape sphere -dm_refine_pre 3
> -dm_extrude 5 -dm_plex_transform_extrude_thickness 0.1 -dm_distribute
> -dm_view hdf5:mesh.h5
>
> and get the attached picture. I am refining before distribution only here,
> since the after distribution refinement would refine the extrude thing,
> which is not what you want.
> If you want refinement after distribution, you could use this code to do
>
>   mpiexec -n 2 ./meshtest -dm_plex_shape sphere -dm_refine_pre
> 3 -dm_distribute -dm_refine 2
>
> and then call DMExtrude() by hand after that. Alternatively, I could make
> a pre-extrusion refinement option.
>
>   Thanks,
>
>      Matt
>
>
>> Thanks,
>> Bhargav
>>
>> /* refine the sequential mesh first */
>> for (int r = 0; r < numRefinePre; ++r) {
>> DM rdm = NULL;
>> DMRefine(dm, MPI_COMM_WORLD, &rdm);
>> DMDestroy(&dm);
>> dm = rdm;
>>  }
>>
>> /* project to a unit sphere */
>> ierr = ProjectToUnitSphere(dm); CHKERRQ(ierr);
>>
>> /* create and distribute DM */
>> ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
>> if (dmDist) {
>> DMDestroy(&dm);
>> dm   = dmDist;
>> }
>>
>> /* refine the mesh in parallel */
>> for (int r = 0; r < numRefine; ++r) {
>> DM rdm = NULL;
>> DMRefine(dm, MPI_COMM_WORLD, &rdm);
>> DMDestroy(&dm);
>> dm = rdm;
>>  }
>>
>> /* project to a unit sphere */
>> ierr = ProjectToUnitSphere(dm); CHKERRQ(ierr);
>>
>> ierr = DMPlexExtrude(dm, numLayers-1, radialThickness, PETSC_FALSE, NULL,
>> PETSC_TRUE, &dm3D);CHKERRQ(ierr);
>>
>> if (dm3D) {
>> DMDestroy(&dm);
>> dm = dm3D;
>> }
>>
>>
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>
>
>
> --
> 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
>
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