[petsc-users] dmplex extruded layers

Wed Nov 24 11:59:36 CST 2021

On Wed, Nov 24, 2021 at 12:27 PM Bhargav Subramanya <
bhargav.subramanya at kaust.edu.sa> wrote:

> Dear Matt and Mark,
>
> Thank you very much for your reply. Your inputs are very useful to me.
>
> On Mon, Nov 22, 2021 at 9:38 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Mon, Nov 22, 2021 at 12:10 PM Bhargav Subramanya <
>> bhargav.subramanya at kaust.edu.sa> wrote:
>>
>>> Dear All,
>>>
>>> I have a prismatic mesh generated by extruding a base icosahedron
>>> spherical surface mesh. The mesh is distributed on 2 processes after
>>> extrusion. The dof for my problem are defined only on the simplices of the
>>> spherical layers.
>>>
>>> 1. For a given spherical layer, I want to get points, which are
>>> basically simplices, lying on that layer only. DMPlexGetHeightStratum
>>> returns the points on all the spherical Layers. I can probably use
>>> DMPlexFindVertices (based on the radius of the spherical layer) and
>>> DMPlexGetSimplexOrBoxCells. Could you suggest if there is a better way to
>>> retrieve the points (which are simplices) on a given spherical layer in the
>>> extruded mesh?
>>>
>>
>> DMPlexGetHeightStratum() refers to height in the Hasse Diagram, which is
>> a DAG, not in the mesh. For example, height 0 points are the cells, height
>> 1 are the faces, etc.
>>
>> I believe the default numbering for extrusion (in the main branch), is
>> that all vertices produced from a given vertex be in order. This would mean
>> that if v were the vertex point number, then
>>
>>   (v - vStart) % Nl == l
>>
>> where Nl is the number of layers and l is the layer of that vertex. It is
>> also the same for triangles. So if you want to segregate each shell, after
>> extrusion, make a label that gives triangles this marker, and then use
>> DMPlexLabelComplete(). Then after refinement you will still have the shells
>> labeled correctly.
>>
>> I would be happy to help you make an example that does this. It seems
>> cool.
>>
>
> ----- Sure, I am interested to make an example of it. And, I really
> appreciate your help.
>
>>
>>
>>> 2. I am able to visualize the entire mesh using dm_view. Is there a way
>>> to get the mesh file for the local dm from a specific process?
>>>
>>
>> You can use -dm_partition_view which outputs a field with the process
>> number. Then use Clip inside Paraview and clip to the process number you
>> want,
>> or just view that field so each process has a different color.
>>
>>
>>> 3. One of my previous emails might have got lost as I mistakenly
>>> attached a large mesh file and sent it. So I am repeating the question
>>> here. DMPlexExtrude gives the following error after distributing the base
>>> 2D spherical mesh. Both refinement or/and extrusion after dm distribution
>>> does not work for me. In fact, I tried
>>> with src/dm/impls/plex/tutorials/ex10.c also. Although the mesh is
>>> distributed after the extrusion in ex10.c (which is working fine for me), I
>>> tried to distribute before extrusion, and I get the following error. Could
>>> you please suggest where I might be making a mistake?
>>>
>>
>> So you want to distribute the mesh before extruding. For that small
>> example (using the main branch), I run
>>
>>   mpiexec -n 3 ./meshtest -dm_plex_shape sphere -dm_refine_pre 2
>> -dm_distribute -dm_partition_view -dm_view hdf5:mesh.h5 -dm_extrude 3
>>
>
> ----- I pulled the code from the main branch and configured my petsc
> again. I am now finally able to reproduce the mesh that you have attached.
> I am able to do parallel mesh refinement, followed by extrusion, and use
> the following code to check that. However, I still have one problem.
> Attached are the extruded mesh files.
>
> 1. Mesh doesn't seem to be refined properly near interfaces between the
> processes. I then used -init_dm_distribute_overlap of 1 and that fixed the
> problem. I hope this is the way to do that.
>

Hmm, something is wrong here. We should track this down and fix it. I do
not see this. Could you tell me how to reproduce the problem?

> 2. The parallel mesh refinement doesn't seem to take care of the spherical
> geometry (shown in the attached mesh file). Could you please suggest how to
> fix it?
>

Okay, this is more subtle. Let me explain how things work inside.

1) When you refine, it inserts new cells/faces/edges/vertices. When we
insert a new vertex, we ask what the coordinates should be. If no special
information is there, we
     just average the surrounding vertices.

2) Then we allow a second step that processed all coordinates in the mesh
after refinement

For the sphere, we use 2) to make all points stick to the implicit surface
(radius R). We cannot do this for the extruded mesh, so we turn it off.
What makes the most sense to me is to do

1) Serial mesh refinement to get enough cells to distribute evenly

2) Mesh distribution

3) Mesh refinement

4) Extrusion

This should preserve the geometry and scale well. Does that sound right?

  Thanks,

     Matt

> command line options:
> -init_dm_plex_shape sphere -init_dm_plex_sphere_radius 1.0
> -init_dm_refine_pre 2 -init_dm_distribute -dm_refine 2 -dm_partition_view
> -dm_view hdf5:mesh.h5 -dm_extrude 3
>
>  ierr = DMCreate(PETSC_COMM_WORLD, &dm);CHKERRQ(ierr);
> ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
> ierr = PetscObjectSetOptionsPrefix((PetscObject) dm,
> "init_");CHKERRQ(ierr);
> ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
>
> ierr = DMPlexIsDistributed(dm, &distributed);
> ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "%d \n", distributed);
> CHKERRQ(ierr);
> ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
>
> ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, NULL);CHKERRQ(ierr);
> ierr = DMSetFromOptions(dm);CHKERRQ(ierr);
> ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
>
>
>> and I get the attached picture.
>>
>>   Thanks,
>>
>>     Matt
>>
>>
>>> [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> [0]PETSC ERROR: Object is in wrong state
>>> [0]PETSC ERROR: This DMPlex is distributed but its PointSF has no graph
>>> set
>>> [0]PETSC ERROR: See https://petsc.org/release/faq/
>>> <https://urldefense.com/v3/__https://petsc.org/release/faq/__;!!Nmw4Hv0!hb2EaePjZqAA4Ns2bFzuHqtjvdZrySmfJcO-7YL5Twmqdh_n0Ym4CneeBI7x1Z5UiaOW2dk_COg$>
>>> for trouble shooting.
>>> [0]PETSC ERROR: Petsc Release Version 3.16.1, unknown
>>> [0]PETSC ERROR: ./cavity_flow.out on a arch-darwin-c-debug named
>>> kl-21859 by subrambm Mon Nov 22 19:47:14 2021
>>> [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>>> --with-fc=gfortran --download-mpich --download-fblaslapack
>>> --download-superlu_dist --download-hypre --download-fiat
>>> --download-generator --download-triangle --download-tetgen --download-chaco
>>> --download-make -download-boost --download-cmake --download-ml
>>> --download-mumps=https://bitbucket.org/petsc/pkg-mumps.git
>>> <https://urldefense.com/v3/__https://bitbucket.org/petsc/pkg-mumps.git__;!!Nmw4Hv0!hb2EaePjZqAA4Ns2bFzuHqtjvdZrySmfJcO-7YL5Twmqdh_n0Ym4CneeBI7x1Z5UiaOW414fjd0$>
>>> --download-mumps-commit=v5.4.1-p1 --download-scalapack --download-ptscotch
>>> --download-hdf5 --force
>>> [0]PETSC ERROR: #1 DMPlexCheckPointSF() at
>>> /Users/subrambm/petsc/src/dm/impls/plex/plex.c:8554
>>> [0]PETSC ERROR: #2 DMPlexOrientInterface_Internal() at
>>> /Users/subrambm/petsc/src/dm/impls/plex/plexinterpolate.c:595
>>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>>> /Users/subrambm/petsc/src/dm/impls/plex/plexinterpolate.c:1357
>>> [0]PETSC ERROR: #4 DMPlexExtrude() at
>>> /Users/subrambm/petsc/src/dm/impls/plex/plexcreate.c:1543
>>> [0]PETSC ERROR: #5 CreateMesh() at ex10.c:161
>>> [0]PETSC ERROR: #6 main() at ex10.c:180
>>> [0]PETSC ERROR: PETSc Option Table entries:
>>> [0]PETSC ERROR: -dm_plex_extrude_layers 3
>>> [0]PETSC ERROR: -dm_view vtk:mesh.vtk
>>> [0]PETSC ERROR: -init_dm_plex_dim 2
>>> [0]PETSC ERROR: -petscpartitioner_type simple
>>> [0]PETSC ERROR: -srf_dm_distribute
>>> [0]PETSC ERROR: -srf_dm_refine 0
>>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>>> error message to petsc-maint at mcs.anl.gov----------
>>>
>>> Thanks,
>>> Bhargav
>>>
>>>
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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
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!Nmw4Hv0!hb2EaePjZqAA4Ns2bFzuHqtjvdZrySmfJcO-7YL5Twmqdh_n0Ym4CneeBI7x1Z5UiaOWdEg9at8$>
>>
>
> ------------------------------
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
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> distribution is prohibited. Please consider the environment before printing
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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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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