[petsc-users] overlap cpu and gpu?

nicola varini nicola.varini at gmail.com
Fri Aug 14 04:01:03 CDT 2020 

Dear Barry, yes it gives the same problems.

Il giorno gio 13 ago 2020 alle ore 23:22 Barry Smith <bsmith at petsc.dev> ha
scritto:

>
>    Does the same thing work (with GAMG) if you run on the same problem on
> the same machine same number of MPI ranks but make a new PETSC_ARCH that
> does NOT use the GPUs?
>
>    Barry
>
>    Ideally one gets almost identical convergence with CPUs or GPUs (same
> problem, same machine) but a bug or numerically change "might" affect this.
>
> On Aug 13, 2020, at 10:28 AM, nicola varini <nicola.varini at gmail.com>
> wrote:
>
> 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>
>>>>>
>>>>>
>>>>>
>> <out_miniapp_f_poisson>
>
>
>
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