[petsc-users] DMPlex partition problem

Wed Apr 8 14:22:30 CDT 2020

Hi Matt,

Here is something pretty interesting. I modified ex1.c file with output of number of nodes and cells (as shown below) .  And I also changed the stencil size to 1.

    /* get coordinates and section */

    ierr = DMGetCoordinatesLocal(*dm,&gc);CHKERRQ(ierr);

    ierr = DMGetCoordinateDM(*dm,&cda);CHKERRQ(ierr);

    ierr = DMGetSection(cda,&cs);CHKERRQ(ierr);

    ierr = PetscSectionGetChart(cs,&istart,&iend);CHKERRQ(ierr);

    num_nodes = iend-istart;

    num_cells = istart;

    /* Output rank and processor information */

printf("rank %d: of nprcs: %d, num_nodes %d, num_cess %d\n", rank, size, num_nodes, num_cells);  

If I compile the code using ‘make ex1’ and then run the test using ‘mpiexec -n 2 ./ex1 -filename basin2layer.exo’, I get the same problem as the modified ex1f90 code I sent.

➜  tests mpiexec -n 2 ./ex1 -filename basin2layer.exo 

rank 1: of nprcs: 2, num_nodes 699, num_cess 824

rank 0: of nprcs: 2, num_nodes 699, num_cess 824

➜  tests mpiexec -n 4 ./ex1 -filename basin2layer.exo

rank 1: of nprcs: 4, num_nodes 432, num_cess 486

rank 0: of nprcs: 4, num_nodes 405, num_cess 448

rank 2: of nprcs: 4, num_nodes 411, num_cess 464

rank 3: of nprcs: 4, num_nodes 420, num_cess 466

However, if I compile and run the code using the script you shared, I get reasonable results.

➜  petsc-3.13.0 make -f ./gmakefile test globsearch="dm_impls_plex_tests-ex1_cylinder" EXTRA_OPTIONS="-filename ./basin2layer.exo -dm_view hdf5:$PWD/mesh.h5 -dm_partition_view" NP=2

#      > rank 0: of nprcs: 2, num_nodes 429, num_cess 484

#      > rank 1: of nprcs: 2, num_nodes 402, num_cess 446

➜  petsc-3.13.0 make -f ./gmakefile test globsearch="dm_impls_plex_tests-ex1_cylinder" EXTRA_OPTIONS="-filename ./basin2layer.exo -dm_view hdf5:$PWD/mesh.h5 -dm_partition_view" NP=4

#      > rank 1: of nprcs: 4, num_nodes 246, num_cess 260

#      > rank 2: of nprcs: 4, num_nodes 264, num_cess 274

#      > rank 3: of nprcs: 4, num_nodes 264, num_cess 280

#      > rank 0: of nprcs: 4, num_nodes 273, num_cess 284

Is there some difference in compiling or runtime options that cause the difference? Would you please check if you can reproduce the same problem using the modified ex1.c?

Thanks,

Danyang

From: Danyang Su <danyang.su at gmail.com>
Date: Wednesday, April 8, 2020 at 9:37 AM
To: Matthew Knepley <knepley at gmail.com>
Cc: PETSc <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] DMPlex partition problem

From: Matthew Knepley <knepley at gmail.com>
Date: Wednesday, April 8, 2020 at 9:20 AM
To: Danyang Su <danyang.su at gmail.com>
Cc: PETSc <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] DMPlex partition problem

On Wed, Apr 8, 2020 at 12:13 PM Danyang Su <danyang.su at gmail.com> wrote:

From: Matthew Knepley <knepley at gmail.com>
Date: Wednesday, April 8, 2020 at 6:45 AM
To: Danyang Su <danyang.su at gmail.com>
Cc: PETSc <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] DMPlex partition problem

On Wed, Apr 8, 2020 at 7:25 AM Matthew Knepley <knepley at gmail.com> wrote:

On Wed, Apr 8, 2020 at 12:48 AM Danyang Su <danyang.su at gmail.com> wrote:

Dear All,

Hope you are safe and healthy.

I have a question regarding pretty different partition results of prism mesh. The partition in PETSc generates much more ghost nodes/cells than the partition in Gmsh, even though both use metis as partitioner. Attached please find the prism mesh in both vtk and exo format, the test code modified based on ex1f90 example. Similar problem are observed for larger dataset with more layers.

I will figure this out by next week.

I have run your mesh and do not get those weird partitions. I am running in master. What are you using? Also, here is an easy way

to do this using a PETSc test:

cd $PETSC_DIR

make -f ./gmakefile test globsearch="dm_impls_plex_tests-ex1_cylinder" EXTRA_OPTIONS="-filename ${HOME}/Downloads/basin2layer.exo -dm_view hdf5:$PWD/mesh.h5 -dm_partition_view" NP=5 

./lib/petsc/bin/petsc_gen_xdmf.py mesh.h5

and then load mesh.xmf into Paraview. Here is what I see (attached). Is it possible for you to try the master branch?

Hi Matt,

Thanks for your quick response. If I use your script, the partition looks good, as shown in the attached figure. I am working on PETSc 3.13.0 release version on Mac OS. 

Does the above script use code /petsc/src/dm/label/tutorials/ex1c.c?

It uses $PETSC_DIR/src/dm/impls/plex/tests/ex1.c

I looked at your code and cannot see any difference. Also, no changes are in master that are not in 3.13. This is very strange.

I guess we will have to go one step at a time between the example and your code.

I will add mesh output to the ex1f90 example and check if the cell/vertex rank is exactly the same. I wrote the mesh output myself based on the partition but there should be no problem in that part. The number of ghost nodes and cells is pretty easy to check. Not sure if there is any difference between the C code and Fortran code that causes the problem. Anyway, I will keep you updated.

  Thanks,

    Matt

  Thanks,

    Matt

  Thanks,

     Matt

For example, in Gmsh, I get partition results using two processors and four processors as shown below, which are pretty reasonable.

However, in PETSc, the partition looks a bit weird. Looks like it takes layer partition first and then inside layer. If the number of nodes per layer is very large, this kind of partitioning results into much more ghost nodes/cells. 

Anybody know how to improve the partitioning in PETSc? I have tried parmetis and chaco. There is no big difference between them. 

Thanks,

Danyang

-- 

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/

-- 

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/

-- 

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/

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