[petsc-users] SuperLU + GPUs
Xiaoye S. Li
xsli at lbl.gov
Sat Apr 18 10:45:35 CDT 2020
When you install "-download-superlu_dist", that is from 'master' branch?
In the error trace, I recognized this:
> [h50n09:102287] [ 9] /ccs/home/adams/petsc/arch-
summit-opt-gnu-cuda-omp/lib/libsuperlu_dist.so.6(dDestroy_
LU+0xc4)[0x20000195aff4]
This is to free the L and U data structures at the end of the program.
Sherry
On Sat, Apr 18, 2020 at 7:24 AM Mark Adams <mfadams at lbl.gov> wrote:
> Back to SuperLU + GPUs (adding Sherry)
>
> I get this error (appended) running 'check', as I said before. It looks
> like ex19 is *failing* with CUDA but it is not clear it has anything to
> do with SuperLU. I can not find these diagnostics that got printed after
> the error in PETSc or SuperLU.
>
> So this is a problem, but moving on to my code (plex/ex11 in
> mark/feature-xgc-interface-rebase-v2, configure script appended). It runs.
> I use superlu and GPUs, but they do not seem to be used in SuperLU:
>
>
> ------------------------------------------------------------------------------------------------------------------------
> 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
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> ....
> MatLUFactorNum 12 1.0 *2.3416e+01* 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00 31 0 0 0 0 31 0 0 0 0 0 0 *0
> 0.00e+00 0 0.00e+00 0*
>
> No CUDA version. The times are the same and no GPU communication above. So
> SuperLU does not seem to be using GPUs.
>
>
> ------------------------------------------------------------------------------------------------------------------------
> Event Count Time (sec) Flop
> --- Global --- --- Stage ---- Total
> Max Ratio Max Ratio Max Ratio Mess AvgLen
> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s
>
> ------------------------------------------------------------------------------------------------------------------------
> ....
> MatLUFactorNum 12 1.0 *2.3421e+01* 1.0 0.00e+00 0.0 0.0e+00
> 0.0e+00 0.0e+00 5 0 0 0 0 5 0 0 0 0 0
>
> There are some differences: ex19 use DMDA and I use DMPlex, 'check' is run
> in my home directory, where files can not be written, and I run my code in
> the project areas.
>
> The timings are different without superlu so I think superlu is being
> used. THis is how I run this (w and w/o -mat_superlu_equil -dm_mat_type
> sell)
>
> jsrun -n 1 -a 1 -c 2 -g 1 ./ex113d_no_cuda -dim 3 -dm_view hdf5:re33d.h5
> -vec_view hdf5:re33d.h5::append -test_type spitzer -Ez 0 -petscspace_degree
> 2 -mass_petscspace_degree 2 -petscspace_poly_tensor 1
> -mass_petscspace_poly_tensor 1 -dm_type p8est -ion_masses 4 -ion_charges 2
> -thermal_temps 4,4 -n 1,.5 -n_0 1e20 -ts_monitor -ts_adapt_monitor
> -snes_rtol 1.e-6 -snes_stol 1.e-9 -snes_monitor -snes_converged_reason
> -snes_max_it 15 -ts_type arkimex -ts_exact_final_time stepover
> -ts_arkimex_type 1bee -ts_max_snes_failures -1 -ts_rtol 1e-3 -ts_dt 1e-1
> -ts_adapt_clip .25,1.05 -ts_adapt_dt_max 10 -ts_adapt_dt_min 2e-2
> -ts_max_time 3200 -ts_max_steps 1 -ts_adapt_scale_solve_failed 0.75
> -ts_adapt_time_step_increase_delay 5 -pc_type lu -ksp_type preonly
> -amr_levels_max 11 -amr_re_levels 0 -amr_z_refine1 0 -amr_z_refine2 0
> -amr_post_refine 0 -domain_radius -.95 -re_radius 4 -z_radius1 8 -z_radius2
> .1 -plot_dt .10 -impurity_source_type pulse -pulse_start_time 2600
> -pulse_width_time 100 -pulse_rate 1e+0 -t_cold .005 -info :dm,tsadapt:
> -sub_thread_block_size 4 -options_left -log_view -pc_factor_mat_solver_type
> superlu -mat_superlu_equil -dm_mat_type sell
>
> So there is a bug in ex19 on SUMMIT and I am not getting GPUs turned on in
> SuperLU.
> Thoughts?
>
> Thanks,
> Mark
>
> 09:28 mark/feature-xgc-interface-rebase-v2 *= ~/petsc$ make
> PETSC_DIR=/ccs/home/adams/petsc PETSC_ARCH=arch-summit-opt-gnu-cuda-omp
> check
> Running check examples to verify correct installation
> Using PETSC_DIR=/ccs/home/adams/petsc and
> PETSC_ARCH=arch-summit-opt-gnu-cuda-omp
> C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
> C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes
> 2c2,39
> < Number of SNES iterations = 2
> ---
>
> *> ex19: cudahook.cc:762: CUresult host_free_callback(void*): Assertion
> `cacheNode != __null' failed.*> [h50n09:102287] *** Process received
> signal ***
> > CUDA version: v 10010
> > CUDA Devices:
> >
> > 0 : Tesla V100-SXM2-16GB 7 0
> > Global memory: 16128 mb
> > Shared memory: 48 kb
> > Constant memory: 64 kb
> > Block registers: 65536
> >
> > [h50n09:102287] Signal: Aborted (6)
> > [h50n09:102287] Associated errno: Unknown error 1072693248 (1072693248)
> > [h50n09:102287] Signal code: User function (kill, sigsend, abort, etc.)
> (0)
> > [h50n09:102287] [ 0] [0x2000000504d8]
> > [h50n09:102287] [ 1] /lib64/libc.so.6(abort+0x2b4)[0x200021bf2094]
> > [h50n09:102287] [ 2] /lib64/libc.so.6(+0x356d4)[0x200021be56d4]
> > [h50n09:102287] [ 3] /lib64/libc.so.6(__assert_fail+0x64)[0x200021be57c4]
> > [h50n09:102287] [ 4]
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/container/../lib/libpami_cudahook.so(_Z18host_free_callbackPv+0x2d8)[0x2000000cd2c8]
> > [h50n09:102287] [ 5]
> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/container/../lib/libpami_cudahook.so(cuMemFreeHost+0xb0)[0x2000000c3cc0]
> > [h50n09:102287] [ 6]
> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(+0x42f50)[0x20000ed02f50]
> > [h50n09:102287] [ 7]
> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(+0x11db8)[0x20000ecd1db8]
> > [h50n09:102287] [ 8]
> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(cudaFreeHost+0x74)[0x20000ed12ea4]
> > [h50n09:102287] [ 9]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libsuperlu_dist.so.6(dDestroy_LU+0xc4)[0x20000195aff4]
> > [h50n09:102287] [10]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(+0x7cdb70)[0x2000008bdb70]
> > [h50n09:102287] [11]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(MatLUFactorNumeric+0x1ec)[0x2000005f1a8c]
> > [h50n09:102287] [12]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(+0xbf8270)[0x200000ce8270]
> > [h50n09:102287] [13]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(PCSetUp+0x1a4)[0x200000d8d5a4]
> > [h50n09:102287] [14]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(KSPSetUp+0x40c)[0x200000dc498c]
> > [h50n09:102287] [15]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(+0xcd56fc)[0x200000dc56fc]
> > [h50n09:102287] [16]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(KSPSolve+0x20)[0x200000dc8260]
> > [h50n09:102287] [17]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(+0xe0a170)[0x200000efa170]
> > [h50n09:102287] [18]
> /ccs/home/adams/petsc/arch-summit-opt-gnu-cuda-omp/lib/libpetsc.so.3.013(SNESSolve+0x814)[0x200000ebd394]
> > [h50n09:102287] [19] ./ex19[0x10001a6c]
> > [h50n09:102287] [20] /lib64/libc.so.6(+0x25200)[0x200021bd5200]
> > [h50n09:102287] [21]
> /lib64/libc.so.6(__libc_start_main+0xc4)[0x200021bd53f4]
> > [h50n09:102287] *** End of error message ***
> > ERROR: One or more process (first noticed rank 0) terminated with
> signal 6
> /ccs/home/adams/petsc/src/snes/tutorials
> Possible problem with ex19 running with superlu_dist, diffs above
>
>
>
>
> #!/usr/bin/env python
> if __name__ == '__main__':
> import sys
> import os
> sys.path.insert(0, os.path.abspath('config'))
> import configure
> configure_options = [
> '--with-fc=0',
> '--COPTFLAGS=-g -O2 -fPIC -fopenmp',
> '--CXXOPTFLAGS=-g -O2 -fPIC -fopenmp',
> '--FOPTFLAGS=-g -O2 -fPIC -fopenmp',
> '--CUDAOPTFLAGS=-O2 -g',
> '--with-ssl=0',
> '--with-batch=0',
> '--with-cxx=mpicxx',
> '--with-mpiexec=jsrun -g1',
> '--with-cuda=1',
> '--with-cudac=nvcc',
> '--download-p4est=1',
> '--download-zlib',
> '--download-hdf5=1',
> '--download-metis',
> '--download-superlu',
> '--download-superlu_dist',
> '--with-make-np=16',
> # '--with-hwloc=0',
> '--download-parmetis',
> # '--download-hypre',
> '--download-triangle',
> # '--download-amgx',
> # '--download-fblaslapack',
> '--with-blaslapack-lib=-L' + os.environ['OLCF_NETLIB_LAPACK_ROOT'] +
> '/lib64 -lblas -llapack',
> '--with-cc=mpicc',
> # '--with-fc=mpif90',
> '--with-shared-libraries=1',
> # '--known-mpi-shared-libraries=1',
> '--with-x=0',
> '--with-64-bit-indices=0',
> '--with-debugging=0',
> 'PETSC_ARCH=arch-summit-opt-gnu-cuda-omp',
> '--with-openmp=1',
> '--with-threadsaftey=1',
> '--with-log=1'
> ]
> configure.petsc_configure(configure_options)
>
>
>
> On Wed, Apr 15, 2020 at 9:58 PM Satish Balay <balay at mcs.anl.gov> wrote:
>
>> The crash is inside Superlu_DIST - so don't know what to suggest.
>>
>> Might have to debug this via debugger and check with Sherry.
>>
>> Satish
>>
>> On Wed, 15 Apr 2020, Mark Adams wrote:
>>
>> > Ah, OK 'check' will test SuperLU. Semi worked:
>> >
>> > s20:13 mark/feature-xgc-interface-rebase *= ~/petsc$ make
>> > PETSC_DIR=/ccs/home/adams/petsc PETSC_ARCH=arch-summit-dbg-gnu-cuda-omp
>> > check
>> > Running check examples to verify correct installation
>> > Using PETSC_DIR=/ccs/home/adams/petsc and
>> > PETSC_ARCH=arch-summit-dbg-gnu-cuda-omp
>> > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI
>> process
>> > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
>> processes
>> > 2c2,38
>> > < Number of SNES iterations = 2
>> > ---
>> > > CUDA version: v 10010
>> > > CUDA Devices:
>> > >
>> > > 0 : Tesla V100-SXM2-16GB 7 0
>> > > Global memory: 16128 mb
>> > > Shared memory: 48 kb
>> > > Constant memory: 64 kb
>> > > Block registers: 65536
>> > >
>> > > ex19: cudahook.cc:762: CUresult host_free_callback(void*): Assertion
>> > `cacheNode != __null' failed.
>> > > [h16n07:78357] *** Process received signal ***
>> > > [h16n07:78357] Signal: Aborted (6)
>> > > [h16n07:78357] Signal code: (1704218624)
>> > > [h16n07:78357] [ 0] [0x2000000504d8]
>> > > [h16n07:78357] [ 1] /lib64/libc.so.6(abort+0x2b4)[0x200023992094]
>> > > [h16n07:78357] [ 2] /lib64/libc.so.6(+0x356d4)[0x2000239856d4]
>> > > [h16n07:78357] [ 3]
>> /lib64/libc.so.6(__assert_fail+0x64)[0x2000239857c4]
>> > > [h16n07:78357] [ 4]
>> >
>> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/container/../lib/libpami_cudahook.so(_Z18host_free_callbackPv+0x2d8)[0x2000000cd2c8]
>> > > [h16n07:78357] [ 5]
>> >
>> /autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/spectrum-mpi-10.3.1.2-20200121-awz2q5brde7wgdqqw4ugalrkukeub4eb/container/../lib/libpami_cudahook.so(cuMemFreeHost+0xb0)[0x2000000c3cc0]
>> > > [h16n07:78357] [ 6]
>> >
>> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(+0x42f50)[0x200010aa2f50]
>> > > [h16n07:78357] [ 7]
>> >
>> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(+0x11db8)[0x200010a71db8]
>> > > [h16n07:78357] [ 8]
>> >
>> /sw/summit/cuda/10.1.243/lib64/libcudart.so.10.1(cudaFreeHost+0x74)[0x200010ab2ea4]
>> > > [h16n07:78357] [ 9]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libsuperlu_dist.so.6(dDestroy_LU+0x150)[0x200003188058]
>> > > [h16n07:78357] [10]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(+0x12ebc6c)[0x2000013dbc6c]
>> > > [h16n07:78357] [11]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(MatLUFactorNumeric+0x934)[0x200000d2fae4]
>> > > [h16n07:78357] [12]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(+0x1cca7a4)[0x200001dba7a4]
>> > > [h16n07:78357] [13]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(PCSetUp+0xde0)[0x200001f3f990]
>> > > [h16n07:78357] [14]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(KSPSetUp+0x1848)[0x200001fc5594]
>> > > [h16n07:78357] [15]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(+0x1ed9908)[0x200001fc9908]
>> > > [h16n07:78357] [16]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(KSPSolve+0x5d0)[0x200001fcc690]
>> > > [h16n07:78357] [17]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(+0x21e16ac)[0x2000022d16ac]
>> > > [h16n07:78357] [18]
>> >
>> /ccs/home/adams/petsc/arch-summit-dbg-gnu-cuda-omp/lib/libpetsc.so.3.013(SNESSolve+0x23f4)[0x2000022255c0]
>> > > [h16n07:78357] [19] ./ex19[0x10002ac8]
>> > > [h16n07:78357] [20] /lib64/libc.so.6(+0x25200)[0x200023975200]
>> > > [h16n07:78357] [21]
>> > /lib64/libc.so.6(__libc_start_main+0xc4)[0x2000239753f4]
>> > > [h16n07:78357] *** End of error message ***
>> > > ERROR: One or more process (first noticed rank 0) terminated with
>> signal
>> > 6
>> > /ccs/home/adams/petsc/src/snes/tutorials
>> > Possible problem with ex19 running with superlu_dist, diffs above
>> > =========================================
>> >
>> > On Wed, Apr 15, 2020 at 5:58 PM Satish Balay <balay at mcs.anl.gov> wrote:
>> >
>> > > Please send configure.log
>> > >
>> > > This is what I get on my linux build:
>> > >
>> > > [balay at p1 petsc]$ ./configure
>> > > --with-mpi-dir=/home/petsc/soft/openmpi-4.0.2-cuda --with-cuda=1
>> > > --with-openmp=1 --download-superlu-dist=1 && make && make check
>> > > <snip>
>> > > Running check examples to verify correct installation
>> > > Using PETSC_DIR=/home/balay/petsc and PETSC_ARCH=arch-linux-c-debug
>> > > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI
>> process
>> > > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
>> processes
>> > > 1a2,19
>> > > > CUDA version: v 10020
>> > > > CUDA Devices:
>> > > >
>> > > > 0 : Quadro T2000 7 5
>> > > > Global memory: 3911 mb
>> > > > Shared memory: 48 kb
>> > > > Constant memory: 64 kb
>> > > > Block registers: 65536
>> > > >
>> > > > CUDA version: v 10020
>> > > > CUDA Devices:
>> > > >
>> > > > 0 : Quadro T2000 7 5
>> > > > Global memory: 3911 mb
>> > > > Shared memory: 48 kb
>> > > > Constant memory: 64 kb
>> > > > Block registers: 65536
>> > > >
>> > > /home/balay/petsc/src/snes/tutorials
>> > > Possible problem with ex19 running with superlu_dist, diffs above
>> > > =========================================
>> > > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI
>> process
>> > > Completed test examples
>> > >
>> > >
>> > > On Wed, 15 Apr 2020, Mark Adams wrote:
>> > >
>> > > > On Wed, Apr 15, 2020 at 5:17 PM Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> > > >
>> > > > > The build should work. It should give some verbose info [at
>> runtime]
>> > > > > regarding GPUs - from the following code.
>> > > > >
>> > > > >
>> > > > I don't see that and I am running GPUs in my code and have gotten
>> > > cusparse
>> > > > LU to run. Should I use '-info :sys:' ?
>> > > >
>> > > >
>> > > > > >>>>> SRC/cublas_utils.c >>>>>>>>>>>
>> > > > > void DisplayHeader()
>> > > > > {
>> > > > > const int kb = 1024;
>> > > > > const int mb = kb * kb;
>> > > > > // cout << "NBody.GPU" << endl << "=========" << endl << endl;
>> > > > >
>> > > > > printf("CUDA version: v %d\n",CUDART_VERSION);
>> > > > > //cout << "Thrust version: v" << THRUST_MAJOR_VERSION << "."
>> <<
>> > > > > THRUST_MINOR_VERSION << endl << endl;
>> > > > >
>> > > > > int devCount;
>> > > > > cudaGetDeviceCount(&devCount);
>> > > > > printf( "CUDA Devices: \n \n");
>> > > > > <snip>
>> > > > > <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
>> > > > >
>> > > > > Satish
>> > > > >
>> > > > > On Wed, 15 Apr 2020, Junchao Zhang wrote:
>> > > > >
>> > > > > > I remember Barry said superlu gpu support is broken.
>> > > > > > --Junchao Zhang
>> > > > > >
>> > > > > >
>> > > > > > On Wed, Apr 15, 2020 at 3:47 PM Mark Adams <mfadams at lbl.gov>
>> wrote:
>> > > > > >
>> > > > > > > How does one use SuperLU with GPUs. I don't seem to get any
>> GPU
>> > > > > > > performance data so I assume GPUs are not getting turned on.
>> Am I
>> > > wrong
>> > > > > > > about that?
>> > > > > > >
>> > > > > > > I configure with:
>> > > > > > > configure options: --with-fc=0 --COPTFLAGS="-g -O2 -fPIC
>> -fopenmp"
>> > > > > > > --CXXOPTFLAGS="-g -O2 -fPIC -fopenmp" --FOPTFLAGS="-g -O2
>> -fPIC
>> > > > > -fopenmp"
>> > > > > > > --CUDAOPTFLAGS="-O2 -g" --with-ssl=0 --with-batch=0
>> > > --with-cxx=mpicxx
>> > > > > > > --with-mpiexec="jsrun -g1" --with-cuda=1 --with-cudac=nvcc
>> > > > > > > --download-p4est=1 --download-zlib --download-hdf5=1
>> > > --download-metis
>> > > > > > > --download-superlu --download-superlu_dist --with-make-np=16
>> > > > > > > --download-parmetis --download-triangle
>> > > > > > >
>> > > > >
>> > >
>> --with-blaslapack-lib="-L/autofs/nccs-svm1_sw/summit/.swci/1-compute/opt/spack/20180914/linux-rhel7-ppc64le/gcc-6.4.0/netlib-lapack-3.8.0-wcabdyqhdi5rooxbkqa6x5d7hxyxwdkm/lib64
>> > > > > > > -lblas -llapack" --with-cc=mpicc --with-shared-libraries=1
>> > > --with-x=0
>> > > > > > > --with-64-bit-indices=0 --with-debugging=0
>> > > > > > > PETSC_ARCH=arch-summit-opt-gnu-cuda-omp --with-openmp=1
>> > > > > > > --with-threadsaftey=1 --with-log=1
>> > > > > > >
>> > > > > > > Thanks,
>> > > > > > > Mark
>> > > > > > >
>> > > > > >
>> > > > >
>> > > > >
>> > > >
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