[petsc-dev] Kokkos/Crusher perforance

Wed Jan 26 13:28:45 CST 2022

On Wed, 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> 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> 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>
>> 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> 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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