[petsc-dev] Kokkos/Crusher perforance
Barry Smith
bsmith at petsc.dev
Wed Jan 26 13:51:48 CST 2022
I have added a mini-MR to print out the key so we can see if it is 0 or some crazy number. https://gitlab.com/petsc/petsc/-/merge_requests/4766
Note that the table data structure is not sent through MPI so if MPI is the culprit it is not just that MPI is putting incorrect (or no) information in the receive buffer; it is that MPI is seemingly messing up other data.
> On Jan 26, 2022, at 2:25 PM, Mark Adams <mfadams at lbl.gov> wrote:
>
> I have used valgrind here. I did not run it on this MPI error. I will.
>
> On Wed, Jan 26, 2022 at 10:56 AM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>
> Any way to run with valgrind (or a HIP variant of valgrind)? It looks like a memory corruption issue and tracking down exactly when the corruption begins is 3/4's of the way to finding the exact cause.
>
> Are the crashes reproducible in the same place with identical runs?
>
>
>> On Jan 26, 2022, at 10:46 AM, Mark Adams <mfadams at lbl.gov <mailto:mfadams at lbl.gov>> wrote:
>>
>> I think it is an MPI bug. It works with GPU aware MPI turned off.
>> I am sure Summit will be fine.
>> We have had users fix this error by switching thier MPI.
>>
>> On Wed, Jan 26, 2022 at 10:10 AM Junchao Zhang <junchao.zhang at gmail.com <mailto:junchao.zhang at gmail.com>> wrote:
>> 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 <mailto: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/ <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 <mailto: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 <mailto: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 <mailto: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 <mailto: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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