[petsc-users] MG on GPU: Benchmarking and avoiding vector host->device copy

Tue Feb 7 05:40:24 CST 2023

On Tue, Feb 7, 2023 at 6:23 AM Mark Adams <mfadams at lbl.gov> wrote:

> I do one complete solve to get everything setup, to be safe.
>
> src/ts/tutorials/ex13.c does this and runs multiple solves, if you like
> but one solve is probably fine.
>

I think that is SNES ex13

  Matt

> This was designed as a benchmark and is nice because it can do any order
> FE solve of Poisson (uses DM/PetscFE, slow).
> src/ksp/ksp/tutorials/ex56.c is old school, hardwired for elasticity but
> is simpler and the setup is faster if you are doing large problems per MPI
> process.
>
> Mark
>
> On Mon, Feb 6, 2023 at 2:06 PM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>>  It should not crash, take a look at the test cases at the bottom of the
>> file. You are likely correct if the code, unfortunately, does use
>> DMCreateMatrix() it will not work out of the box for geometric multigrid.
>> So it might be the wrong example for you.
>>
>>   I don't know what you mean about clever. If you simply set the solution
>> to zero at the beginning of the loop then it will just do the same solve
>> multiple times. The setup should not do much of anything after the first
>> solver.  Thought usually solves are big enough that one need not run solves
>> multiple times to get a good understanding of their performance.
>>
>>
>>
>>
>>
>>
>> On Feb 6, 2023, at 12:44 PM, Paul Grosse-Bley <
>> paul.grosse-bley at ziti.uni-heidelberg.de> wrote:
>>
>> Hi Barry,
>>
>> src/ksp/ksp/tutorials/bench_kspsolve.c is certainly the better starting
>> point, thank you! Sadly I get a segfault when executing that example with
>> PCMG and more than one level, i.e. with the minimal args:
>>
>> $ mpiexec -c 1 ./bench_kspsolve -split_ksp -pc_type mg -pc_mg_levels 2
>> ===========================================
>> Test: KSP performance - Poisson
>>     Input matrix: 27-pt finite difference stencil
>>     -n 100
>>     DoFs = 1000000
>>     Number of nonzeros = 26463592
>>
>> Step1  - creating Vecs and Mat...
>> Step2a - running PCSetUp()...
>> [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>> [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and
>> https://petsc.org/release/faq/
>> [0]PETSC ERROR: or try
>> https://docs.nvidia.com/cuda/cuda-memcheck/index.html on NVIDIA CUDA
>> systems to find memory corruption errors
>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> [0]PETSC ERROR: to get more information on the crash.
>> [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is
>> causing the crash.
>> --------------------------------------------------------------------------
>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>> with errorcode 59.
>>
>> 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.
>> --------------------------------------------------------------------------
>>
>> As the matrix is not created using DMDACreate3d I expected it to fail due
>> to the missing geometric information, but I expected it to fail more
>> gracefully than with a segfault.
>> I will try to combine bench_kspsolve.c with ex45.c to get easy MG
>> preconditioning, especially since I am interested in the 7pt stencil for
>> now.
>>
>> Concerning my benchmarking loop from before: Is it generally discouraged
>> to do this for KSPSolve due to PETSc cleverly/lazily skipping some of the
>> work when doing the same solve multiple times or are the solves not
>> iterated in bench_kspsolve.c (while the MatMuls are with -matmult) just to
>> keep the runtime short?
>>
>> Thanks,
>> Paul
>>
>> On Monday, February 06, 2023 17:04 CET, Barry Smith <bsmith at petsc.dev>
>> wrote:
>>
>>
>>
>>
>>
>>   Paul,
>>
>>    I think src/ksp/ksp/tutorials/benchmark_ksp.c is the code intended to
>> be used for simple benchmarking.
>>
>>    You can use VecCudaGetArray() to access the GPU memory of the vector
>> and then call a CUDA kernel to compute the right hand side vector directly
>> on the GPU.
>>
>>   Barry
>>
>>
>>
>> On Feb 6, 2023, at 10:57 AM, Paul Grosse-Bley <
>> paul.grosse-bley at ziti.uni-heidelberg.de> wrote:
>>
>> Hi,
>>
>> I want to compare different implementations of multigrid solvers for
>> Nvidia GPUs using the poisson problem (starting from ksp tutorial example
>> ex45.c).
>> Therefore I am trying to get runtime results comparable to hpgmg-cuda
>> <https://bitbucket.org/nsakharnykh/hpgmg-cuda/src/master/>
>> (finite-volume), i.e. using multiple warmup and measurement solves and
>> avoiding measuring setup time.
>> For now I am using -log_view with added stages:
>>
>> PetscLogStageRegister("Solve Bench", &solve_bench_stage);
>>   for (int i = 0; i < BENCH_SOLVES; i++) {
>>     PetscCall(KSPSetComputeInitialGuess(ksp, ComputeInitialGuess, NULL));
>> // reset x
>>     PetscCall(KSPSetUp(ksp)); // try to avoid setup overhead during solve
>>     PetscCall(PetscDeviceContextSynchronize(dctx)); // make sure that
>> everything is done
>>
>>     PetscLogStagePush(solve_bench_stage);
>>     PetscCall(KSPSolve(ksp, NULL, NULL));
>>     PetscLogStagePop();
>>   }
>>
>> This snippet is preceded by a similar loop for warmup.
>>
>> When profiling this using Nsight Systems, I see that the very first solve
>> is much slower which mostly correspods to H2D (host to device) copies and
>> e.g. cuBLAS setup (maybe also paging overheads as mentioned in the docs
>> <https://petsc.org/release/docs/manual/profiling/#accurate-profiling-and-paging-overheads>,
>> but probably insignificant in this case). The following solves have some
>> overhead at the start from a H2D copy of a vector (the RHS I guess, as the
>> copy is preceeded by a matrix-vector product) in the first MatResidual call
>> (callchain:
>> KSPSolve->MatResidual->VecAYPX->VecCUDACopyTo->cudaMemcpyAsync). My
>> interpretation of the profiling results (i.e. cuBLAS calls) is that that
>> vector is overwritten with the residual in Daxpy and therefore has to be
>> copied again for the next iteration.
>>
>> Is there an elegant way of avoiding that H2D copy? I have seen some
>> examples on constructing matrices directly on the GPU, but nothing about
>> vectors. Any further tips for benchmarking (vs profiling) PETSc solvers? At
>> the moment I am using jacobi as smoother, but I would like to have a CUDA
>> implementation of SOR instead. Is there a good way of achieving that, e.g.
>> using PCHYPREs boomeramg with a single level and "SOR/Jacobi"-smoother  as
>> smoother in PCMG? Or is the overhead from constantly switching between
>> PETSc and hypre too big?
>>
>> Thanks,
>> Paul
>>
>>
>>

-- 
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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