[petsc-users] overlap cpu and gpu?
nicola varini
nicola.varini at gmail.com
Thu Aug 13 10:28:37 CDT 2020
Dear Barry, you are right. The Cray argument checking is incorrect. It does
work with download-fblaslapack.
However it does fail to converge. Is there anything obviously wrong with my
petscrc?
Anything else am I missing?
Thanks
Il giorno gio 13 ago 2020 alle ore 03:17 Barry Smith <bsmith at petsc.dev> ha
scritto:
>
> The QR is always done on the CPU, we don't have generic calls to
> blas/lapack go to the GPU currently.
>
> The error message is:
>
> On entry to __cray_mgm_dgeqrf, parameter 7 had an illegal value (info =
> -7)
>
> argument 7 is &LWORK which is defined by
>
> PetscBLASInt LWORK=N*bs;
>
> and
>
> N=nSAvec is the column block size of new P.
>
> Presumably this is a huge run with many processes so using the debugger
> is not practical?
>
> We need to see what these variables are
>
> N, bs, nSAvec
>
> perhaps nSAvec is zero which could easily upset LAPACK.
>
> Crudest thing would be to just put a print statement in the code
> before the LAPACK call of if they are called many times add an error check
> like that
> generates an error if any of these three values are 0 (or negative).
>
> Barry
>
>
> It is not impossible that the Cray argument checking is incorrect and
> the value passed in is fine. You can check this by using
> --download-fblaslapack and see if the same or some other error comes up.
>
>
>
>
>
>
>
>
> On Aug 12, 2020, at 7:19 PM, Mark Adams <mfadams at lbl.gov> wrote:
>
> Can you reproduce this on the CPU?
> The QR factorization seems to be failing. That could be from bad data or a
> bad GPU QR.
>
> On Wed, Aug 12, 2020 at 4:19 AM nicola varini <nicola.varini at gmail.com>
> wrote:
>
>> Dear all, following the suggestions I did resubmit the simulation with
>> the petscrc below.
>> However I do get the following error:
>> ========
>> 7362 [592]PETSC ERROR: #1 formProl0() line 748 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/agg.c
>> 7363 [339]PETSC ERROR: Petsc has generated inconsistent data
>> 7364 [339]PETSC ERROR: xGEQRF error
>> 7365 [339]PETSC ERROR: See
>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>> shooting.
>> 7366 [339]PETSC ERROR: Petsc Release Version 3.13.3, Jul 01, 2020
>> 7367 [339]PETSC ERROR:
>> /users/nvarini/gbs_test_nicola/bin/gbs_daint_gpu_gnu on a named nid05083
>> by nvarini Wed Aug 12 10:06:15 2020
>> 7368 [339]PETSC ERROR: Configure options --with-cc=cc --with-fc=ftn
>> --known-mpi-shared-libraries=1 --known-mpi-c-double-complex=1
>> --known-mpi-int64_t=1 --known-mpi-long-double=1 --with-batch=1
>> --known-64-bit-blas-indices=0 --LIBS=-lstdc++ --with-cxxlib-autodetect=0
>> --with-scalapa ck=1 --with-cxx=CC --with-debugging=0
>> --with-hypre-dir=/opt/cray/pe/tpsl/19.06.1/GNU/8.2/haswell
>> --prefix=/scratch/snx3000/nvarini/petsc3.13.3-gpu --with-cuda=1
>> --with-cuda-c=nvcc --with-cxxlib-autodetect=0
>> --COPTFLAGS=-I/opt/cray/pe/mpt/7.7.10/gni/mpich-intel/16.0/include -
>> -with-cxx=CC
>> --CXXOPTFLAGS=-I/opt/cray/pe/mpt/7.7.10/gni/mpich-intel/16.0/include
>> 7369 [592]PETSC ERROR: #2 PCGAMGProlongator_AGG() line 1063 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/agg.c
>> 7370 [592]PETSC ERROR: #3 PCSetUp_GAMG() line 548 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/gamg.c
>> 7371 [592]PETSC ERROR: #4 PCSetUp() line 898 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/interface/precon.c
>> 7372 [592]PETSC ERROR: #5 KSPSetUp() line 376 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7373 [592]PETSC ERROR: #6 KSPSolve_Private() line 633 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7374 [316]PETSC ERROR: #3 PCSetUp_GAMG() line 548 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/gamg.c
>> 7375 [339]PETSC ERROR: #1 formProl0() line 748 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/agg.c
>> 7376 [339]PETSC ERROR: #2 PCGAMGProlongator_AGG() line 1063 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/agg.c
>> 7377 [339]PETSC ERROR: #3 PCSetUp_GAMG() line 548 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/gamg.c
>> 7378 [339]PETSC ERROR: #4 PCSetUp() line 898 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/interface/precon.c
>> 7379 [339]PETSC ERROR: #5 KSPSetUp() line 376 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7380 [592]PETSC ERROR: #7 KSPSolve() line 853 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7381 [339]PETSC ERROR: #6 KSPSolve_Private() line 633 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7382 [339]PETSC ERROR: #7 KSPSolve() line 853 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/ksp/interface/itfunc.c
>> 7383 On entry to __cray_mgm_dgeqrf, parameter 7 had an illegal value
>> (info = -7)
>> 7384 [160]PETSC ERROR: #3 PCSetUp_GAMG() line 548 in
>> /scratch/snx3000/nvarini/petsc-3.13.3/src/ksp/pc/impls/gamg/gamg.c
>> ========
>>
>> I did try other pc_gamg_type but they fails as well.
>>
>>
>> #PETSc Option Table entries:
>> -ampere_dm_mat_type aijcusparse
>> -ampere_dm_vec_type cuda
>> -ampere_ksp_atol 1e-15
>> -ampere_ksp_initial_guess_nonzero yes
>> -ampere_ksp_reuse_preconditioner yes
>> -ampere_ksp_rtol 1e-7
>> -ampere_ksp_type dgmres
>> -ampere_mg_levels_esteig_ksp_max_it 10
>> -ampere_mg_levels_esteig_ksp_type cg
>> -ampere_mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05
>> -ampere_mg_levels_ksp_type chebyshev
>> -ampere_mg_levels_pc_type jacobi
>> -ampere_pc_gamg_agg_nsmooths 1
>> -ampere_pc_gamg_coarse_eq_limit 10
>> -ampere_pc_gamg_reuse_interpolation true
>> -ampere_pc_gamg_square_graph 1
>> -ampere_pc_gamg_threshold 0.05
>> -ampere_pc_gamg_threshold_scale .0
>> -ampere_pc_gamg_type agg
>> -ampere_pc_type gamg
>> -dm_mat_type aijcusparse
>> -dm_vec_type cuda
>> -log_view
>> -poisson_dm_mat_type aijcusparse
>> -poisson_dm_vec_type cuda
>> -poisson_ksp_atol 1e-15
>> -poisson_ksp_initial_guess_nonzero yes
>> -poisson_ksp_reuse_preconditioner yes
>> -poisson_ksp_rtol 1e-7
>> -poisson_ksp_type dgmres
>> -poisson_log_view
>> -poisson_mg_levels_esteig_ksp_max_it 10
>> -poisson_mg_levels_esteig_ksp_type cg
>> -poisson_mg_levels_ksp_chebyshev_esteig 0,0.05,0,1.05
>> -poisson_mg_levels_ksp_max_it 1
>> -poisson_mg_levels_ksp_type chebyshev
>> -poisson_mg_levels_pc_type jacobi
>> -poisson_pc_gamg_agg_nsmooths 1
>> -poisson_pc_gamg_coarse_eq_limit 10
>> -poisson_pc_gamg_reuse_interpolation true
>> -poisson_pc_gamg_square_graph 1
>> -poisson_pc_gamg_threshold 0.05
>> -poisson_pc_gamg_threshold_scale .0
>> -poisson_pc_gamg_type agg
>> -poisson_pc_type gamg
>> -use_mat_nearnullspace true
>> #End of PETSc Option Table entries
>>
>> Regards,
>>
>> Nicola
>>
>> Il giorno mar 4 ago 2020 alle ore 17:57 Mark Adams <mfadams at lbl.gov> ha
>> scritto:
>>
>>>
>>>
>>> On Tue, Aug 4, 2020 at 6:35 AM Stefano Zampini <
>>> stefano.zampini at gmail.com> wrote:
>>>
>>>> Nicola,
>>>>
>>>> You are actually not using the GPU properly, since you use HYPRE
>>>> preconditioning, which is CPU only. One of your solvers is actually slower
>>>> on “GPU”.
>>>> For a full AMG GPU, you can use PCGAMG, with cheby smoothers and with
>>>> Jacobi preconditioning. Mark can help you out with the specific command
>>>> line options.
>>>> When it works properly, everything related to PC application is
>>>> offloaded to the GPU, and you should expect to get the well-known and
>>>> branded 10x (maybe more) speedup one is expecting from GPUs during KSPSolve
>>>>
>>>>
>>> The speedup depends on the machine, but on SUMMIT, using enough CPUs to
>>> saturate the memory bus vs all 6 GPUs the speedup is a function of problem
>>> subdomain size. I saw 10x at about 100K equations/process.
>>>
>>>
>>>> Doing what you want to do is one of the last optimization steps of an
>>>> already optimized code before entering production. Yours is not even
>>>> optimized for proper GPU usage yet.
>>>> Also, any specific reason why you are using dgmres and fgmres?
>>>>
>>>> PETSc has not been designed with multi-threading in mind. You can
>>>> achieve “overlap” of the two solves by splitting the communicator. But then
>>>> you need communications to let the two solutions talk to each other.
>>>>
>>>> Thanks
>>>> Stefano
>>>>
>>>>
>>>> On Aug 4, 2020, at 12:04 PM, nicola varini <nicola.varini at gmail.com>
>>>> wrote:
>>>>
>>>> Dear all, thanks for your replies. The reason why I've asked if it is
>>>> possible to overlap poisson and ampere is because they roughly
>>>> take the same amount of time. Please find in attachment the profiling
>>>> logs for only CPU and only GPU.
>>>> Of course it is possible to split the MPI communicator and run each
>>>> solver on different subcommunicator, however this would involve more
>>>> communication.
>>>> Did anyone ever tried to run 2 solvers with hyperthreading?
>>>> Thanks
>>>>
>>>>
>>>> Il giorno dom 2 ago 2020 alle ore 14:09 Mark Adams <mfadams at lbl.gov>
>>>> ha scritto:
>>>>
>>>>> I suspect that the Poisson and Ampere's law solve are not coupled. You
>>>>> might be able to duplicate the communicator and use two threads. You would
>>>>> want to configure PETSc with threadsafty and threads and I think it
>>>>> could/should work, but this mode is never used by anyone.
>>>>>
>>>>> That said, I would not recommend doing this unless you feel like
>>>>> playing in computer science, as opposed to doing application science. The
>>>>> best case scenario you get a speedup of 2x. That is a strict upper bound,
>>>>> but you will never come close to it. Your hardware has some balance of CPU
>>>>> to GPU processing rate. Your application has a balance of volume of work
>>>>> for your two solves. They have to be the same to get close to 2x speedup
>>>>> and that ratio(s) has to be 1:1. To be concrete, from what little I can
>>>>> guess about your applications let's assume that the cost of each of these
>>>>> two solves is about the same (eg, Laplacians on your domain and the best
>>>>> case scenario). But, GPU machines are configured to have roughly 1-10% of
>>>>> capacity in the GPUs, these days, that gives you an upper bound of about
>>>>> 10% speedup. That is noise. Upshot, unless you configure your hardware to
>>>>> match this problem, and the two solves have the same cost, you will not see
>>>>> close to 2x speedup. Your time is better spent elsewhere.
>>>>>
>>>>> Mark
>>>>>
>>>>> On Sat, Aug 1, 2020 at 3:24 PM Jed Brown <jed at jedbrown.org> wrote:
>>>>>
>>>>>> You can use MPI and split the communicator so n-1 ranks create a DMDA
>>>>>> for one part of your system and the other rank drives the GPU in the other
>>>>>> part. They can all be part of the same coupled system on the full
>>>>>> communicator, but PETSc doesn't currently support some ranks having their
>>>>>> Vec arrays on GPU and others on host, so you'd be paying host-device
>>>>>> transfer costs on each iteration (and that might swamp any performance
>>>>>> benefit you would have gotten).
>>>>>>
>>>>>> In any case, be sure to think about the execution time of each part.
>>>>>> Load balancing with matching time-to-solution for each part can be really
>>>>>> hard.
>>>>>>
>>>>>>
>>>>>> Barry Smith <bsmith at petsc.dev> writes:
>>>>>>
>>>>>> > Nicola,
>>>>>> >
>>>>>> > This is really viable or practical at this time with PETSc. It
>>>>>> is not impossible but requires careful coding with threads, another
>>>>>> possibility is to use one half of the virtual GPUs for each solve, this is
>>>>>> also not trivial. I would recommend first seeing what kind of performance
>>>>>> you can get on the GPU for each type of solve and revist this idea in the
>>>>>> future.
>>>>>> >
>>>>>> > Barry
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >
>>>>>> >> On Jul 31, 2020, at 9:23 AM, nicola varini <
>>>>>> nicola.varini at gmail.com> wrote:
>>>>>> >>
>>>>>> >> Hello, I would like to know if it is possible to overlap CPU and
>>>>>> GPU with DMDA.
>>>>>> >> I've a machine where each node has 1P100+1Haswell.
>>>>>> >> I've to resolve Poisson and Ampere equation for each time step.
>>>>>> >> I'm using 2D DMDA for each of them. Would be possible to compute
>>>>>> poisson
>>>>>> >> and ampere equation at the same time? One on CPU and the other on
>>>>>> GPU?
>>>>>> >>
>>>>>> >> Thanks
>>>>>>
>>>>> <out_gpu><out_nogpu>
>>>>
>>>>
>>>>
>
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