[petsc-users] Slow convergence while parallel computations.
Pierre Jolivet
pierre at joliv.et
Thu Sep 2 07:34:35 CDT 2021
> On 2 Sep 2021, at 2:31 PM, Pierre Jolivet <pierre at joliv.et> wrote:
>
>
>
>> On 2 Sep 2021, at 2:07 PM, Viktor Nazdrachev <numbersixvs at gmail.com <mailto:numbersixvs at gmail.com>> wrote:
>>
>> Hello, Pierre!
>>
>> Thank you for your response!
>> I attached log files (txt files with convergence behavior and RAM usage log in separate txt files) and resulting table with convergence investigation data(xls). Data for main non-regular grid with 500K cells and heterogeneous properties are in 500K folder, whereas data for simple uniform 125K cells grid with constant properties are in 125K folder.
>>
>> >Dear Viktor,
>> >
>> >> On 1 Sep 2021, at 10:42 AM, Наздрачёв Виктор <numbersixvs at gmail.com <https://lists.mcs.anl.gov/mailman/listinfo/petsc-users>> > <>wrote:
>> >>
>> >> Dear all,
>> >>
>> >> I have a 3D elasticity problem with heterogeneous properties. There is unstructured grid with aspect ratio varied from 4 to 25. Zero Dirichlet BCs are imposed on bottom face of mesh. Also, Neumann (traction) BCs are imposed on side faces. Gravity load is also accounted for. The grid I use consists of 500k cells (which is approximately 1.6M of DOFs).
>> >>
>> >> The best performance and memory usage for single MPI process was obtained with HPDDM(BFBCG) solver
>> >>
>> >Block Krylov solvers are (most often) only useful if you have multiple right-hand sides, e.g., in the context of elasticity, multiple loadings.
>> Is that really the case? If not, you may as well stick to “standard” CG instead of the breakdown-free block (BFB) variant.
>> >
>>
>> In that case only single right-hand side is utilized, so I switched to “standard” cg solver (-ksp_hpddm_type cg), but I noticed the interesting convergence behavior. For non-regular grid with 500K cells and heterogeneous properties CG solver converged with 1 iteration (log_hpddm(cg)_gamg_nearnullspace_1_mpi.txt), but for more simple uniform grid with 125K cells and homogeneous properties CG solves linear system successfully(log_hpddm(cg)_gamg_nearnullspace_1_mpi.txt).
>> BFBCG solver works properly for both grids.
>
> Just stick to -ksp_type cg or maybe -ksp_type gmres -ksp_gmres_modifiedgramschmidt (even if the problem is SPD).
> Sorry if I repeat myself, but KSPHPDDM methods are mostly useful for either blocking or recycling.
> If you use something as simple as CG, you’ll get better diagnostics and error handling if you use the native PETSc implementation (KSPCG) instead of the external implementation (-ksp_hpddm_type cg).
>
>>
>> >> and bjacobian + ICC (1) in subdomains as preconditioner, it took 1 m 45 s and RAM 5.0 GB. Parallel computation with 4 MPI processes took 2 m 46 s when using 5.6 GB of RAM. This because of number of iterations required to achieve the same tolerance is significantly increased.
>> >>
>> >> I`ve also tried PCGAMG (agg) preconditioner with ICС (1) sub-precondtioner. For single MPI process, the calculation took 10 min and 3.4 GB of RAM. To improve the convergence rate, the nullspace was attached using MatNullSpaceCreateRigidBody and MatSetNearNullSpace subroutines. This has reduced calculation time to 3 m 58 s when using 4.3 GB of RAM. Also, there is peak memory usage with 14.1 GB, which appears just before the start of the iterations. Parallel computation with 4 MPI processes took 2 m 53 s when using 8.4 GB of RAM. In that case the peak memory usage is about 22 GB.
>> >>
>> >I’m surprised that GAMG is converging so slowly. What do you mean by "ICC(1) sub-preconditioner"? Do you use that as a smoother or as a coarse level solver?
>> >
>>
>> Sorry for misleading, ICC is used only for BJACOBI preconditioner, no ICC for GAMG.
>>
>> >How many iterations are required to reach convergence?
>> >Could you please maybe run the solver with -ksp_view -log_view and send us the output?
>> >
>>
>> For case with 4 MPI processes and attached nullspace it is required 177 iterations to reach convergence (you may see detailed log in log_hpddm(bfbcg)_gamg_nearnullspace_4_mpi.txt and memory usage log in RAM_log_hpddm(bfbcg)_gamg_nearnullspace_4_mpi.txt). For comparison, 90 iterations are required for sequential run(log_hpddm(bfbcg)_gamg_nearnullspace_1_mpi.txt).
>>
>>
>> >Most of the default parameters of GAMG should be good enough for 3D elasticity, provided that your MatNullSpace is correct.
>> >
>>
>> How can I be sure that nullspace is attached correctly? Is there any way for self-checking (Well perhaps calculate some parameters using matrix and solution vector)?
>>
>> >One parameter that may need some adjustments though is the aggregation threshold -pc_gamg_threshold (you could try values in the [0.01; 0.1] range, that’s what I always use for elasticity problems).
>> >
>>
>> Tried to find optimal value of this option, set -pc_gamg_threshold 0.01 and -pc_gamg_threshold_scale 2, but I didn't notice any significant changes (Need more time for experiments )
>>
> I don’t see anything too crazy in your logs at first sight. In addition to maybe trying GMRES with a more robust orthogonalization scheme, here is what I would do:
> 1) MatSetBlockSize(Pmat, 6), it seems to be missing right now, cf.
Sorry for the noise, but this should read 3, not 6…
Thanks,
Pierre
> linear system matrix = precond matrix:
> Mat Object: 4 MPI processes
> type: mpiaij
> rows=1600200, cols=1600200
> total: nonzeros=124439742, allocated nonzeros=259232400
> total number of mallocs used during MatSetValues calls=0
> has attached near null space
> 2) -mg_coarse_pc_type redundant -mg_coarse_redundant_pc_type lu
> 3) more playing around with the threshold, this can be critical for hard problems
> If you can share your matrix/nullspace/RHS, we could have a crack at it as well.
>
> Thanks,
> Pierre
>
>> Kind regards,
>>
>> Viktor Nazdrachev
>>
>> R&D senior researcher
>>
>> Geosteering Technologies LLC
>>
>>
>> ср, 1 сент. 2021 г. в 12:01, Pierre Jolivet <pierre at joliv.et <mailto:pierre at joliv.et>>:
>> Dear Viktor,
>>
>>> On 1 Sep 2021, at 10:42 AM, Наздрачёв Виктор <numbersixvs at gmail.com <mailto:numbersixvs at gmail.com>> wrote:
>>>
>>> Dear all,
>>>
>>> I have a 3D elasticity problem with heterogeneous properties. There is unstructured grid with aspect ratio varied from 4 to 25. Zero Dirichlet BCs are imposed on bottom face of mesh. Also, Neumann (traction) BCs are imposed on side faces. Gravity load is also accounted for. The grid I use consists of 500k cells (which is approximately 1.6M of DOFs).
>>>
>>> The best performance and memory usage for single MPI process was obtained with HPDDM(BFBCG) solver
>>>
>> Block Krylov solvers are (most often) only useful if you have multiple right-hand sides, e.g., in the context of elasticity, multiple loadings.
>> Is that really the case? If not, you may as well stick to “standard” CG instead of the breakdown-free block (BFB) variant.
>>
>>> and bjacobian + ICC (1) in subdomains as preconditioner, it took 1 m 45 s and RAM 5.0 GB. Parallel computation with 4 MPI processes took 2 m 46 s when using 5.6 GB of RAM. This because of number of iterations required to achieve the same tolerance is significantly increased.
>>>
>>> I`ve also tried PCGAMG (agg) preconditioner with ICС (1) sub-precondtioner. For single MPI process, the calculation took 10 min and 3.4 GB of RAM. To improve the convergence rate, the nullspace was attached using MatNullSpaceCreateRigidBody and MatSetNearNullSpace subroutines. This has reduced calculation time to 3 m 58 s when using 4.3 GB of RAM. Also, there is peak memory usage with 14.1 GB, which appears just before the start of the iterations. Parallel computation with 4 MPI processes took 2 m 53 s when using 8.4 GB of RAM. In that case the peak memory usage is about 22 GB.
>>>
>> I’m surprised that GAMG is converging so slowly. What do you mean by "ICC(1) sub-preconditioner"? Do you use that as a smoother or as a coarse level solver?
>> How many iterations are required to reach convergence?
>> Could you please maybe run the solver with -ksp_view -log_view and send us the output?
>> Most of the default parameters of GAMG should be good enough for 3D elasticity, provided that your MatNullSpace is correct.
>> One parameter that may need some adjustments though is the aggregation threshold -pc_gamg_threshold (you could try values in the [0.01; 0.1] range, that’s what I always use for elasticity problems).
>>
>> Thanks,
>> Pierre
>>
>>> Are there ways to avoid decreasing of the convergence rate for bjacobi precondtioner in parallel mode? Does it make sense to use hierarchical or nested krylov methods with a local gmres solver (sub_pc_type gmres) and some sub-precondtioner (for example, sub_pc_type bjacobi)?
>>>
>>>
>>> Is this peak memory usage expected for gamg preconditioner? is there any way to reduce it?
>>>
>>>
>>> What advice would you give to improve the convergence rate with multiple MPI processes, but keep memory consumption reasonable?
>>>
>>>
>>> Kind regards,
>>>
>>> Viktor Nazdrachev
>>>
>>> R&D senior researcher
>>>
>>> Geosteering Technologies LLC
>>>
>>
>> <logs.rar>
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