[petsc-dev] Using PETSC with GPUs
Mark Adams
mfadams at lbl.gov
Fri Jan 14 17:18:07 CST 2022
If you do a warm up you can probably warm it up with another method (like
MatTransposeMult) to keep your timing separe. It's not clear to me what you
mean by "warm up" exactly.
OK, I see you got the GPUs working.
On Fri, Jan 14, 2022 at 4:59 PM Rohan Yadav <rohany at alumni.cmu.edu> wrote:
> A log_view is attached at the end of the mail.
>
> I am running on a large problem size (639 million nonzeros).
>
> > * I assume you are assembling the matrix on the CPU. The copy of data to
> the GPU takes time and you really should be creating the matrix on the GPU
>
> How do I do this? I'm loading the matrix in from a file, but I'm running
> the computation several times (and with a warmup), so I would expect that
> the data is copied onto the GPU the first time. My (cpu) code to do this is
> here:
> https://github.com/rohany/taco/blob/5c0a4f4419ba392838590ce24e0043f632409e7b/petsc/benchmark.cpp#L68
> .
>
> Log view:
>
> ---------------------------------------------- PETSc Performance Summary:
> ----------------------------------------------
>
> ./bin/benchmark on a named lassen75 with 2 processors, by yadav2 Fri Jan
> 14 13:54:09 2022
> Using Petsc Release Version 3.16.3, unknown
>
> Max Max/Min Avg Total
> Time (sec): 1.026e+02 1.000 1.026e+02
> Objects: 1.200e+01 1.000 1.200e+01
> Flop: 1.156e+10 1.009 1.151e+10 2.303e+10
> Flop/sec: 1.127e+08 1.009 1.122e+08 2.245e+08
> MPI Messages: 3.500e+01 1.000 3.500e+01 7.000e+01
> MPI Message Lengths: 2.210e+10 1.000 6.313e+08 4.419e+10
> MPI Reductions: 4.100e+01 1.000
>
> Flop counting convention: 1 flop = 1 real number operation of type
> (multiply/divide/add/subtract)
> e.g., VecAXPY() for real vectors of length N
> --> 2N flop
> and VecAXPY() for complex vectors of length N
> --> 8N flop
>
> Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages
> --- -- Message Lengths -- -- Reductions --
> Avg %Total Avg %Total Count
> %Total Avg %Total Count %Total
> 0: Main Stage: 1.0257e+02 100.0% 2.3025e+10 100.0% 7.000e+01
> 100.0% 6.313e+08 100.0% 2.300e+01 56.1%
>
>
> ------------------------------------------------------------------------------------------------------------------------
> See the 'Profiling' chapter of the users' manual for details on
> interpreting output.
> Phase summary info:
> Count: number of times phase was executed
> Time and Flop: Max - maximum over all processors
> Ratio - ratio of maximum to minimum over all processors
> Mess: number of messages sent
> AvgLen: average message length (bytes)
> Reduct: number of global reductions
> Global: entire computation
> Stage: stages of a computation. Set stages with PetscLogStagePush() and
> PetscLogStagePop().
> %T - percent time in this phase %F - percent flop in this
> phase
> %M - percent messages in this phase %L - percent message lengths
> in this phase
> %R - percent reductions in this phase
> Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over
> all processors)
> GPU Mflop/s: 10e-6 * (sum of flop on GPU over all processors)/(max GPU
> time over all processors)
> CpuToGpu Count: total number of CPU to GPU copies per processor
> CpuToGpu Size (Mbytes): 10e-6 * (total size of CPU to GPU copies per
> processor)
> GpuToCpu Count: total number of GPU to CPU copies per processor
> GpuToCpu Size (Mbytes): 10e-6 * (total size of GPU to CPU copies per
> processor)
> GPU %F: percent flops on GPU in this event
>
> ------------------------------------------------------------------------------------------------------------------------
> Event Count Time (sec) Flop
> --- Global --- --- Stage ---- Total GPU - CpuToGpu - -
> GpuToCpu - GPU
> Max Ratio Max Ratio Max Ratio Mess AvgLen
> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s Mflop/s Count Size
> Count Size %F
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> --- Event Stage 0: Main Stage
>
> BuildTwoSided 1 1.0 1.8650e-013467.8 0.00e+00 0.0 2.0e+00 4.0e+00
> 1.0e+00 0 0 3 0 2 0 0 3 0 4 0 0 0 0.00e+00 0
> 0.00e+00 0
> MatMult 30 1.0 6.6642e+01 1.0 1.16e+10 1.0 6.4e+01 6.4e+08
> 1.0e+00 65100 91 93 2 65100 91 93 4 346 0 0 0.00e+00 31
> 2.65e+04 0
> MatAssemblyBegin 1 1.0 3.1100e-07 1.1 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
> MatAssemblyEnd 1 1.0 1.9798e+01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 4.0e+00 19 0 0 0 10 19 0 0 0 17 0 0 0 0.00e+00 0
> 0.00e+00 0
> MatLoad 1 1.0 3.5519e+01 1.0 0.00e+00 0.0 6.0e+00 5.4e+08
> 1.6e+01 35 0 9 7 39 35 0 9 7 70 0 0 0 0.00e+00 0
> 0.00e+00 0
> VecSet 5 1.0 5.8959e-02 1.1 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
> VecScatterBegin 30 1.0 5.4085e+00 1.0 0.00e+00 0.0 6.4e+01 6.4e+08
> 1.0e+00 5 0 91 93 2 5 0 91 93 4 0 0 0 0.00e+00 0
> 0.00e+00 0
> VecScatterEnd 30 1.0 9.2544e+00 2.5 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 6 0 0 0 0 6 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
> VecCUDACopyFrom 31 1.0 4.0174e-01 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 31
> 2.65e+04 0
> SFSetGraph 1 1.0 4.4912e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
> SFSetUp 1 1.0 5.2595e+00 1.0 0.00e+00 0.0 4.0e+00 1.7e+08
> 1.0e+00 5 0 6 2 2 5 0 6 2 4 0 0 0 0.00e+00 0
> 0.00e+00 0
> SFPack 30 1.0 3.4021e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
> SFUnpack 30 1.0 1.9222e-05 1.5 0.00e+00 0.0 0.0e+00 0.0e+00
> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0
> 0.00e+00 0
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> Memory usage is given in bytes:
>
> Object Type Creations Destructions Memory Descendants' Mem.
> Reports information only for process 0.
>
> --- Event Stage 0: Main Stage
>
> Matrix 3 0 0 0.
> Viewer 2 0 0 0.
> Vector 4 1 1792 0.
> Index Set 2 2 335250404 0.
> Star Forest Graph 1 0 0 0.
>
> ========================================================================================================================
> Average time to get PetscTime(): 3.77e-08
> Average time for MPI_Barrier(): 8.754e-07
> Average time for zero size MPI_Send(): 2.6755e-06
> #PETSc Option Table entries:
> -log_view
> -mat_type aijcusparse
> -matrix /p/gpfs1/yadav2/tensors//petsc/kmer_V1r.petsc
> -n 20
> -vec_type cuda
> -warmup 10
> #End of PETSc Option Table entries
> Compiled without FORTRAN kernels
> Compiled with full precision matrices (default)
> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8
> sizeof(PetscScalar) 8 sizeof(PetscInt) 4
> Configure options: --download-c2html=0 --download-hwloc=0
> --download-sowing=0 --prefix=./petsc-install/ --with-64-bit-indices=0
> --with-blaslapack-lib="/usr/tcetmp/packages/lapack/lapack-3.9.0-gcc-7.3.1/lib/liblapack.so
> /usr/tcetmp/packages/lapack/lapack-3.9.0-gcc-7.3.1/lib/libblas.so"
> --with-cc=/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigcc
> --with-clanguage=C --with-cxx-dialect=C++17
> --with-cxx=/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpig++
> --with-cuda=1 --with-debugging=0
> --with-fc=/usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigfortran
> --with-fftw=0
> --with-hdf5-dir=/usr/tcetmp/packages/petsc/build/3.13.0/spack/opt/spack/linux-rhel7-power9le/xl_r-16.1/hdf5-1.10.6-e7e7urb5k7va3ib7j4uro56grvzmcmd4
> --with-hdf5=1 --with-mumps=0 --with-precision=double --with-scalapack=0
> --with-scalar-type=real --with-shared-libraries=1 --with-ssl=0
> --with-suitesparse=0 --with-trilinos=0 --with-valgrind=0 --with-x=0
> --with-zlib-include=/usr/include --with-zlib-lib=/usr/lib64/libz.so
> --with-zlib=1 CFLAGS="-g -DNoChange" COPTFLAGS="-O3" CXXFLAGS="-O3"
> CXXOPTFLAGS="-O3" FFLAGS=-g CUDAFLAGS=-std=c++17 FOPTFLAGS=
> PETSC_ARCH=arch-linux-c-opt
> -----------------------------------------
> Libraries compiled on 2022-01-14 20:56:04 on lassen99
> Machine characteristics:
> Linux-4.14.0-115.21.2.1chaos.ch6a.ppc64le-ppc64le-with-redhat-7.6-Maipo
> Using PETSc directory: /g/g15/yadav2/taco/petsc/petsc/petsc-install
> Using PETSc arch:
> -----------------------------------------
>
> Using C compiler:
> /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigcc
> -g -DNoChange -fPIC "-O3"
> Using Fortran compiler:
> /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigfortran
> -g -fPIC
> -----------------------------------------
>
> Using include paths:
> -I/g/g15/yadav2/taco/petsc/petsc/petsc-install/include
> -I/usr/tcetmp/packages/petsc/build/3.13.0/spack/opt/spack/linux-rhel7-power9le/xl_r-16.1/hdf5-1.10.6-e7e7urb5k7va3ib7j4uro56grvzmcmd4/include
> -I/usr/include -I/usr/tce/packages/cuda/cuda-11.1.0/include
> -----------------------------------------
>
> Using C linker:
> /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigcc
> Using Fortran linker:
> /usr/tce/packages/spectrum-mpi/spectrum-mpi-rolling-release-gcc-8.3.1/bin/mpigfortran
> Using libraries:
> -Wl,-rpath,/g/g15/yadav2/taco/petsc/petsc/petsc-install/lib
> -L/g/g15/yadav2/taco/petsc/petsc/petsc-install/lib -lpetsc
> -Wl,-rpath,/usr/tcetmp/packages/lapack/lapack-3.9.0-gcc-7.3.1/lib
> -L/usr/tcetmp/packages/lapack/lapack-3.9.0-gcc-7.3.1/lib
> -Wl,-rpath,/usr/tcetmp/packages/petsc/build/3.13.0/spack/opt/spack/linux-rhel7-power9le/xl_r-16.1/hdf5-1.10.6-e7e7urb5k7va3ib7j4uro56grvzmcmd4/lib
> -L/usr/tcetmp/packages/petsc/build/3.13.0/spack/opt/spack/linux-rhel7-power9le/xl_r-16.1/hdf5-1.10.6-e7e7urb5k7va3ib7j4uro56grvzmcmd4/lib
> -Wl,-rpath,/usr/tce/packages/cuda/cuda-11.1.0/lib64
> -L/usr/tce/packages/cuda/cuda-11.1.0/lib64
> -Wl,-rpath,/usr/tce/packages/spectrum-mpi/ibm/spectrum-mpi-rolling-release/lib
> -L/usr/tce/packages/spectrum-mpi/ibm/spectrum-mpi-rolling-release/lib
> -Wl,-rpath,/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib/gcc/ppc64le-redhat-linux/8
> -L/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib/gcc/ppc64le-redhat-linux/8
> -Wl,-rpath,/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib/gcc
> -L/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib/gcc
> -Wl,-rpath,/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib64
> -L/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib64
> -Wl,-rpath,/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib
> -L/usr/tce/packages/gcc/gcc-8.3.1/rh/usr/lib -llapack -lblas -lhdf5_hl
> -lhdf5 -lm /usr/lib64/libz.so -lcuda -lcudart -lcufft -lcublas -lcusparse
> -lcusolver -lcurand -lstdc++ -ldl -lmpiprofilesupport -lmpi_ibm_usempi
> -lmpi_ibm_mpifh -lmpi_ibm -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
> -lpthread -lquadmath -lstdc++ -ldl
> -----------------------------------------
>
> On Fri, Jan 14, 2022 at 1:43 PM Mark Adams <mfadams at lbl.gov> wrote:
>
>> There are a few things:
>> * GPU have higher latencies and so you basically need a large
>> enough problem to get GPU speedup
>> * I assume you are assembling the matrix on the CPU. The copy of data to
>> the GPU takes time and you really should be creating the matrix on the GPU
>> * I agree with Barry, Roughly 1M / GPU is around where you start seeing a
>> win but this depends on a lot of things.
>> * There are startup costs, like the CPU-GPU copy. It is best to run one
>> mat-vec, or whatever, push a new stage and then run the benchmark. The
>> timing for this new stage will be separate in the log view data. Look at
>> that.
>> - You can fake this by running your benchmark many times to amortize any
>> setup costs.
>>
>> On Fri, Jan 14, 2022 at 4:27 PM Rohan Yadav <rohany at alumni.cmu.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> I'm looking to use PETSc with GPUs to do some linear algebra operations,
>>> like SpMV, SPMM etc. Building PETSc with `--with-cuda=1` and running with
>>> `-mat_type aijcusparse -vec_type cuda` gives me a large slowdown from the
>>> same code running on the CPU. This is not entirely unexpected, as things
>>> like data transfer costs across the PCIE might erroneously be included in
>>> my timing. Are there some examples of benchmarking GPU computations with
>>> PETSc, or just the proper way to write code in PETSc that will work for
>>> CPUs and GPUs?
>>>
>>> Rohan
>>>
>>
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