[petsc-users] Unstructured mesh

Tue Dec 14 01:42:07 CST 2021

I tried adding the -mat_block_size 3 but I still get the same error message.

Thanks,
Karthik.

From: Mark Adams <mfadams at lbl.gov>
Date: Monday, 13 December 2021 at 19:54
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk>
Cc: Matthew Knepley <knepley at gmail.com>, "petsc-users at mcs.anl.gov" <petsc-users at mcs.anl.gov>
Subject: Re: [petsc-users] Unstructured mesh

Try adding -mat_block_size 3

On Mon, Dec 13, 2021 at 11:57 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:

I tried to run the problem using -pc_type hypre but it errored out:

./ex56 -cells 4,4,2  -max_conv_its 1 -lx 1. -alpha .01 -petscspace_degree 1 -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8 -pc_type hypre -pc_hypre_type boomeramg  -snes_monitor -use_mat_nearnullspace true -snes_rtol 1.e-10 -ex56_dm_view -log_view -ex56_dm_vec_type cuda -ex56_dm_mat_type hypre  -options_left

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------

[0]PETSC ERROR: Petsc has generated inconsistent data

[0]PETSC ERROR: Blocksize of layout 1 must match that of mapping 3 (or the latter must be 1)

[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.

[0]PETSC ERROR: Petsc Development GIT revision: v3.16.1-353-g887dddf386  GIT Date: 2021-11-19 20:24:41 +0000

[0]PETSC ERROR: ./ex56 on a arch-linux2-c-opt named sqg2b13.bullx by kxc07-lxm25 Mon Dec 13 16:50:02 2021

[0]PETSC ERROR: Configure options --with-debugging=0 --with-blaslapack-dir=/lustre/scafellpike/local/apps/intel/intel_cs/2018.0.128/mkl --with-cuda=1 --with-cuda-arch=70 --download-hypre=yes --download-hypre-configure-arguments="--with-cuda=yes --enable-gpu-profiling=yes --enable-cusparse=yes --enable-cublas=yes --enable-curand=yes  --enable-unified-memory=yes HYPRE_CUDA_SM=70" --with-shared-libraries=1 --known-mpi-shared-libraries=1 --with-cc=mpicc --with-cxx=mpicxx -with-fc=mpif90

[0]PETSC ERROR: #1 PetscLayoutSetISLocalToGlobalMapping() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/vec/is/utils/pmap.c:371

[0]PETSC ERROR: #2 MatSetLocalToGlobalMapping() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/mat/interface/matrix.c:2089

[0]PETSC ERROR: #3 DMCreateMatrix_Plex() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/dm/impls/plex/plex.c:2460

[0]PETSC ERROR: #4 DMCreateMatrix() at /lustre/scafellpike/local/HT04048/lxm25/kxc07-lxm25/petsc-main/petsc/src/dm/interface/dm.c:1445

[0]PETSC ERROR: #5 main() at ex56.c:439

[0]PETSC ERROR: PETSc Option Table entries:

[0]PETSC ERROR: -alpha .01

[0]PETSC ERROR: -cells 4,4,2

[0]PETSC ERROR: -ex56_dm_mat_type hypre

[0]PETSC ERROR: -ex56_dm_vec_type cuda

[0]PETSC ERROR: -ex56_dm_view

[0]PETSC ERROR: -ksp_monitor

[0]PETSC ERROR: -ksp_rtol 1.e-8

[0]PETSC ERROR: -ksp_type cg

[0]PETSC ERROR: -log_view

[0]PETSC ERROR: -lx 1.

[0]PETSC ERROR: -max_conv_its 1

[0]PETSC ERROR: -options_left

[0]PETSC ERROR: -pc_hypre_type boomeramg

[0]PETSC ERROR: -pc_type hypre

[0]PETSC ERROR: -petscspace_degree 1

[0]PETSC ERROR: -snes_monitor

[0]PETSC ERROR: -snes_rtol 1.e-10

[0]PETSC ERROR: -use_gpu_aware_mpi 0

[0]PETSC ERROR: -use_mat_nearnullspace true

[0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov----------

--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 77.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------

From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
Date: Monday, 13 December 2021 at 13:58
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>, "petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Unstructured mesh

On Mon, Dec 13, 2021 at 8:35 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Thanks Matt. Couple of weeks back you mentioned
“There are many unstructured grid examples, e.g. SNES ex13, ex17, ex56. The solver can run on the GPU, but the vector/matrix FEM assembly does not. I am working on that now.”

I am able to run other examples in ksp/tutorials on gpus. I complied ex56 in snes/tutorials no differently. The only difference being I didn’t specify _dm_vec_type and _dm_vec_type (as you mentioned they are not assembled on gpus anyways plus I am working on an unstructured grid thought _dm is not right type for this problem). I was hoping to see gpu flops recorded for KSPSolve, which I didn’t.

Okay, I will wait for Mark to comment.

This (DM) example works like any other, with a prefix, as far as GPU: -ex56_dm_vec_type cuda and -ex56_dm_mat_type cusparse, or aijkokkos/kokkos, etc.
Run with -options_left to verify that these are used.

Kind regards,
Karthik.

From: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>
Date: Monday, 13 December 2021 at 13:17
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>, "petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Unstructured mesh

On Mon, Dec 13, 2021 at 7:15 AM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:

Thank you. I was able to confirm both the below options produced the same mesh

 ./ex56 -cells 2,2,1 -max_conv_its 2

./ex56 -cells 4,4,2 -max_conv_its 1
Good

But I didn’t get how is -cells i,j,k <1,1,1> is related to the number of MPI processes.
It is not. The number of processes is specified independently using 'mpiexec -n <p>' or when using the test system NP=<p>.

(i)     Say I start with -cells 1,1,1 -max_conv its 7; that would eventually leave all refinement on level 7 running on 1 MPI process?

(ii)    Say I start with -cells 2,2,1 -max_conv its n; is it recommended to run on 4 MPI processes?
No, those options do not influence the number of processes.

I am running ex56 on gpu; I am looking at KSPSolve (or any other event) but no gpu flops are recorded in the -log_view?

I do not think you are running on the GPU then. Mark can comment, but we usually specify GPU execution using the Vec and Mat types
through -dm_vec_type and -dm_mat_type.

  Thanks,

     Matt

For your reference I used the below flags:

./ex56 -cells 1,1,1 -max_conv_its 3 -lx 1. -alpha .01 -petscspace_degree 1 -ksp_type cg -ksp_monitor -ksp_rtol 1.e-8 -pc_type asm -snes_monitor -use_mat_nearnullspace true -snes_rtol 1.e-10 -ex56_dm_view -log_view

Kind regards,
Karthik.

From: Mark Adams <mfadams at lbl.gov<mailto:mfadams at lbl.gov>>
Date: Sunday, 12 December 2021 at 23:00
To: "Chockalingam, Karthikeyan (STFC,DL,HC)" <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>>
Cc: Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>>, "petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>" <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>>
Subject: Re: [petsc-users] Unstructured mesh

On Sun, Dec 12, 2021 at 3:19 PM Karthikeyan Chockalingam - STFC UKRI <karthikeyan.chockalingam at stfc.ac.uk<mailto:karthikeyan.chockalingam at stfc.ac.uk>> wrote:
Thank for your response that was helpful. I have a couple of questions:

(i)                  How can I control the level of refinement? I tried to pass the flag “-ex56_dm_refine 0” but that didn’t stop the refinement from 8 giving 32 cubes.

I answered this question recently but ex56 clobbers ex56_dm_refine in the convergence loop. I have an MR that prints a warning if you provide a ex56_dm_refine.

* snes/ex56 runs a convergence study and confusingly sets the options manually, thus erasing your -ex56_dm_refine.

* To refine, use -max_conv_its N <3>, this sets the number of steps of refinement. That is, the length of the convergence study

* You can adjust where it starts from with -cells i,j,k <1,1,1>
You do want to set this if you have multiple MPI processes so that the size of this mesh is the number of processes. That way it starts with one cell per process and refines from there.

(ii)                What does -cell 2,2,1 correspond to?

The initial mesh or mesh_0. The convergence test uniformly refines this mesh. So if you want to refine this twice you could use -cells 8,8,4

How can I determine the total number of dofs?
Unfortunately, that is not printed but you can calculate from the initial cell grid, the order of the element and the refinement in each iteration of the convergence tests.

So that I can perform a scaling study by changing the input of the flag -cells.

You can and the convergence test gives you data for a strong speedup study in one run. Each solve is put in its own "stage" of the output and you want to look at KSPSolve lines in the log_view output.

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