[petsc-users] Unstructured mesh

Tue Dec 14 12:57:56 CST 2021

I was able to get hypre to work on ex56 (snes) with -ex56_dm_mat_type
aijcusparse -ex56_dm_vec_type cuda (not hypre matrix).
This should copy the cusparse matrix to a hypre matrix before the solve. So
not optimal but the actual solve should be the same.
Hypre is not yet supported on this example so you might not want to spend
too much time on it.
In particular, we do not have an example that uses DMPlex and hypre on a
GPU.

src/ksp/ksp/tutotials/ex56 is old and does not use DMPLex, but it is
missing a call like ksp ex4 for hypre like this:
#if defined(PETSC_HAVE_HYPRE)
  ierr = MatHYPRESetPreallocation(A,5,NULL,5,NULL);CHKERRQ(ierr);
#endif
If you add that it might work, but again this is all pretty fragile at this
point.

Mark

Mark

On Tue, Dec 14, 2021 at 2:42 AM Karthikeyan Chockalingam - STFC UKRI <
karthikeyan.chockalingam at stfc.ac.uk> wrote:

> 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> 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>
> *Date: *Monday, 13 December 2021 at 13:58
> *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
>
>
>
>
>
>
>
> On Mon, Dec 13, 2021 at 8:35 AM Karthikeyan Chockalingam - STFC UKRI <
> 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>
> *Date: *Monday, 13 December 2021 at 13:17
> *To: *"Chockalingam, Karthikeyan (STFC,DL,HC)" <
> karthikeyan.chockalingam at stfc.ac.uk>
> *Cc: *Mark Adams <mfadams at lbl.gov>, "petsc-users at mcs.anl.gov" <
> 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> 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>
> *Date: *Sunday, 12 December 2021 at 23:00
> *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
>
>
>
>
>
>
>
> On Sun, Dec 12, 2021 at 3:19 PM Karthikeyan Chockalingam - STFC UKRI <
> 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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> --
>
> 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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