[petsc-dev] Kokkos/Crusher perforance
Junchao Zhang
junchao.zhang at gmail.com
Wed Jan 26 09:10:34 CST 2022
I don't know if this is due to bugs in petsc/kokkos backend. See if you
can run 6 nodes (48 mpi ranks). If it fails, then run the same problem on
Summit with 8 nodes to see if it still fails. If yes, it is likely a bug of
our own.
--Junchao Zhang
On Wed, Jan 26, 2022 at 8:44 AM Mark Adams <mfadams at lbl.gov> wrote:
> I am not able to reproduce this with a small problem. 2 nodes or less
> refinement works. This is from the 8 node test, the -dm_refine 5 version.
> I see that it comes from PtAP.
> This is on the fine grid. (I was thinking it could be on a reduced grid
> with idle processors, but no)
>
> [15]PETSC ERROR: Argument out of range
> [15]PETSC ERROR: Key <= 0
> [15]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [15]PETSC ERROR: Petsc Development GIT revision: v3.16.3-696-g46640c56cb
> GIT Date: 2022-01-25 09:20:51 -0500
> [15]PETSC ERROR:
> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tests/data/../ex13 on a
> arch-olcf-crusher named crusher020 by adams Wed Jan 26 08:35:47 2022
> [15]PETSC ERROR: Configure options --with-cc=cc --with-cxx=CC
> --with-fc=ftn --with-fortran-bindings=0
> LIBS="-L/opt/cray/pe/mpich/8.1.12/gtl/lib -lmpi_gtl_hsa" --with-debugging=0
> --COPTFLAGS="-g -O" --CXXOPTFLAGS="-g -O" --FOPTFLAGS=-g
> --with-mpiexec="srun -p batch -N 1 -A csc314_crusher -t 00:10:00"
> --with-hip --with-hipc=hipcc --download-hypre --with-hip-arch=gfx90a
> --download-kokkos --download-kokkos-kernels --with-kokkos-kernels-tpl=0
> --download-p4est=1
> --with-zlib-dir=/sw/crusher/spack-envs/base/opt/cray-sles15-zen3/cce-13.0.0/zlib-1.2.11-qx5p4iereg4sjvfi5uwk6jn56o6se2q4
> PETSC_ARCH=arch-olcf-crusher
> [15]PETSC ERROR: #1 PetscTableFind() at
> /gpfs/alpine/csc314/scratch/adams/petsc/include/petscctable.h:131
> [15]PETSC ERROR: #2 MatSetUpMultiply_MPIAIJ() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/mmaij.c:35
> [15]PETSC ERROR: #3 MatAssemblyEnd_MPIAIJ() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/mpiaij.c:735
> [15]PETSC ERROR: #4 MatAssemblyEnd_MPIAIJKokkos() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx:14
> [15]PETSC ERROR: #5 MatAssemblyEnd() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/interface/matrix.c:5678
> [15]PETSC ERROR: #6 MatSetMPIAIJKokkosWithSplitSeqAIJKokkosMatrices() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx:267
> [15]PETSC ERROR: #7 MatSetMPIAIJKokkosWithGlobalCSRMatrix() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx:825
> [15]PETSC ERROR: #8 MatProductSymbolic_MPIAIJKokkos() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/impls/aij/mpi/kokkos/mpiaijkok.kokkos.cxx:1167
> [15]PETSC ERROR: #9 MatProductSymbolic() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/interface/matproduct.c:825
> [15]PETSC ERROR: #10 MatPtAP() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/mat/interface/matrix.c:9656
> [15]PETSC ERROR: #11 PCGAMGCreateLevel_GAMG() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/pc/impls/gamg/gamg.c:87
> [15]PETSC ERROR: #12 PCSetUp_GAMG() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/pc/impls/gamg/gamg.c:663
> [15]PETSC ERROR: #13 PCSetUp() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/pc/interface/precon.c:1017
> [15]PETSC ERROR: #14 KSPSetUp() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/ksp/interface/itfunc.c:417
> [15]PETSC ERROR: #15 KSPSolve_Private() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/ksp/interface/itfunc.c:863
> [15]PETSC ERROR: #16 KSPSolve() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/ksp/ksp/interface/itfunc.c:1103
> [15]PETSC ERROR: #17 SNESSolve_KSPONLY() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/impls/ksponly/ksponly.c:51
> [15]PETSC ERROR: #18 SNESSolve() at
> /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/interface/snes.c:4810
> [15]PETSC ERROR: #19 main() at ex13.c:169
> [15]PETSC ERROR: PETSc Option Table entries:
> [15]PETSC ERROR: -benchmark_it 10
>
> On Wed, Jan 26, 2022 at 7:26 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>> The GPU aware MPI is dying going 1 to 8 nodes, 8 processes per node.
>> I will make a minimum reproducer. start with 2 nodes, one process on each
>> node.
>>
>>
>> On Tue, Jan 25, 2022 at 10:19 PM Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>> So the MPI is killing you in going from 8 to 64. (The GPU flop rate
>>> scales almost perfectly, but the overall flop rate is only half of what it
>>> should be at 64).
>>>
>>> On Jan 25, 2022, at 9:24 PM, Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>> It looks like we have our instrumentation and job configuration in
>>> decent shape so on to scaling with AMG.
>>> In using multiple nodes I got errors with table entries not found, which
>>> can be caused by a buggy MPI, and the problem does go away when I turn GPU
>>> aware MPI off.
>>> Jed's analysis, if I have this right, is that at *0.7T* flops we are at
>>> about 35% of theoretical peal wrt memory bandwidth.
>>> I run out of memory with the next step in this study (7 levels of
>>> refinement), with 2M equations per GPU. This seems low to me and we will
>>> see if we can fix this.
>>> So this 0.7Tflops is with only 1/4 M equations so 35% is not terrible.
>>> Here are the solve times with 001, 008 and 064 nodes, and 5 or 6 levels
>>> of refinement.
>>>
>>> out_001_kokkos_Crusher_5_1.txt:KSPSolve 10 1.0 1.2933e+00
>>> 1.0 4.13e+10 1.1 1.8e+05 8.4e+03 5.8e+02 3 87 86 78 48 100100100100100
>>> 248792 423857 6840 3.85e+02 6792 3.85e+02 100
>>> out_001_kokkos_Crusher_6_1.txt:KSPSolve 10 1.0 5.3667e+00
>>> 1.0 3.89e+11 1.0 2.1e+05 3.3e+04 6.7e+02 2 87 86 79 48 100100100100100
>>> 571572 *700002* 7920 1.74e+03 7920 1.74e+03 100
>>> out_008_kokkos_Crusher_5_1.txt:KSPSolve 10 1.0 1.9407e+00
>>> 1.0 4.94e+10 1.1 3.5e+06 6.2e+03 6.7e+02 5 87 86 79 47 100100100100100
>>> 1581096 3034723 7920 6.88e+02 7920 6.88e+02 100
>>> out_008_kokkos_Crusher_6_1.txt:KSPSolve 10 1.0 7.4478e+00
>>> 1.0 4.49e+11 1.0 4.1e+06 2.3e+04 7.6e+02 2 88 87 80 49 100100100100100
>>> 3798162 5557106 9367 3.02e+03 9359 3.02e+03 100
>>> out_064_kokkos_Crusher_5_1.txt:KSPSolve 10 1.0 2.4551e+00
>>> 1.0 5.40e+10 1.1 4.2e+07 5.4e+03 7.3e+02 5 88 87 80 47 100100100100100
>>> 11065887 23792978 8684 8.90e+02 8683 8.90e+02 100
>>> out_064_kokkos_Crusher_6_1.txt:KSPSolve 10 1.0 1.1335e+01
>>> 1.0 5.38e+11 1.0 5.4e+07 2.0e+04 9.1e+02 4 88 88 82 49 100100100100100
>>> 24130606 43326249 11249 4.26e+03 11249 4.26e+03 100
>>>
>>> On Tue, Jan 25, 2022 at 1:49 PM Mark Adams <mfadams at lbl.gov> wrote:
>>>
>>>>
>>>>> Note that Mark's logs have been switching back and forth between
>>>>> -use_gpu_aware_mpi and changing number of ranks -- we won't have that
>>>>> information if we do manual timing hacks. This is going to be a routine
>>>>> thing we'll need on the mailing list and we need the provenance to go with
>>>>> it.
>>>>>
>>>>
>>>> GPU aware MPI crashes sometimes so to be safe, while debugging, I had
>>>> it off. It works fine here so it has been on in the last tests.
>>>> Here is a comparison.
>>>>
>>>>
>>> <tt.tar>
>>>
>>>
>>>
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