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 <mfad...@lbl.gov> ha scritto: > > > On Tue, Aug 4, 2020 at 6:35 AM Stefano Zampini <stefano.zamp...@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.var...@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 <mfad...@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 <j...@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 <bsm...@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.var...@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> >> >> >>
