Yes, you should use your system_matrix. AdditionalData can be used to modify the parameters used by ILU. The interface of PreconditionILU should work very similarly to BlockJacobi see https://dealii.org/current/doxygen/deal.II/step_17.html#ElasticProblemsolve There are several tutorials that use petsc: steps 17, 18, 40, 50, and 55. We also have test that use PreconditionILU https://github.com/dealii/dealii/blob/master/tests/petsc/solver_03_precondition_ilu.cc
Bruno Le jeu. 10 mars 2022 à 10:19, Hermes Sampedro <hermesampe...@gmail.com> a écrit : > Dear Bruno, > > Thank you very much, I will try this. > The last question if it is not too much to ask is about In the > PreconditionILU matrix: > > PETScWrappers::PreconditionILU::PreconditionILU > (const MatrixBase > <https://dealii.org/current/doxygen/deal.II/classPETScWrappers_1_1MatrixBase.html> > & > matrix, const AdditionalData > <https://dealii.org/current/doxygen/deal.II/structPETScWrappers_1_1PreconditionILU_1_1AdditionalData.html> > & > additional_data = AdditionalData > <https://dealii.org/current/doxygen/deal.II/structPETScWrappers_1_1PreconditionILU_1_1AdditionalData.html> > () ) > > Is it correct in this case to use my system_matrix? Is there any example > in the tutorials about this? I can not find any. > > Thank you very much > Regards, > H. > > El jueves, 10 de marzo de 2022 a las 15:29:59 UTC+1, bruno.t...@gmail.com > escribió: > >> If your matrix is symmetric definite positive, you use CG >> <https://dealii.org/current/doxygen/deal.II/classPETScWrappers_1_1SolverCG.html>. >> Otherwise, you use GMRES >> <https://dealii.org/current/doxygen/deal.II/classPETScWrappers_1_1SolverGMRES.html>. >> Here is the page for ILU >> <https://dealii.org/current/doxygen/deal.II/classPETScWrappers_1_1PreconditionILU.html> >> >> Bruno >> >> Le jeu. 10 mars 2022 à 09:18, Hermes Sampedro <hermes...@gmail.com> a >> écrit : >> > >> > Thank you for your suggestions. Could you please suggest me what >> function can work well for using a Krylov solver? I can no see examples. >> > My actual code is implemented using PETS (for sparsematrix, solver, >> etc). I can see that SLEPcWrappers::SolverKrylovSchur allows PETS matrices. >> > >> > >> > Thank you again >> > >> > El jueves, 10 de marzo de 2022 a las 15:12:19 UTC+1, >> bruno.t...@gmail.com escribió: >> >> >> >> Hermes, >> >> >> >> I think Cuthill-McKee only works on symmetric matrices, is your matrix >> >> symmetric? Also, the goal of Cuthill-McKee is to help with the fill in >> >> of the matrix.There is no guarantee that it helps with the >> >> performance. If you don't know which preconditioner to use, you can >> >> use ILU (Incomplete LU decomposition). Basically, you use a direct >> >> solver but you drop all the "small" entries in the matrix. It's not >> >> the best preconditioner but you can control how much time you spend in >> >> the "direct solver". The problem with direct solvers is that there is >> >> not much you can do to speed them up. In practice, everybody uses >> >> Krylov solvers because of the problems you are encountering now. >> >> >> >> Best, >> >> >> >> Bruno >> >> >> >> Le jeu. 10 mars 2022 à 09:00, Hermes Sampedro >> >> <hermes...@gmail.com> a écrit : >> >> > >> >> > Hi Bruno, >> >> > >> >> > Yes, for now, I have to use a direct solver due to the >> preconditioner. >> >> > I am experiencing long computational times with the solver function. >> I am trying to use DoFRenumbering::Cuthill_McKee(dof_handler), >> DoFRenumbering::boost::Cuthill_McKee(dof_handler,false,false) >> >> > but I get even higher computational times. Am I doing something >> wrong? >> >> > >> >> > In the setup_system() function I do: >> >> > dof_handler.distribute_dofs(fe); >> >> > DoFRenumbering::Cuthill_McKee(dof_handler); >> >> > >> >> > Then thee solver is >> >> > void LaplaceProblem<dim>::solve() >> >> > { >> >> > PETScWrappers::MPI::Vector >> completely_distributed_solution(locally_owned_dofs,mpi_communicator); >> >> > SolverControl cn; >> >> > PETScWrappers::SparseDirectMUMPS solver(cn, mpi_communicator); >> >> > solver.solve(system_matrix, completely_distributed_solution, >> system_rhs); >> >> > constraints.distribute(completely_distributed_solution); >> >> > locally_relevant_solution = completely_distributed_solution; >> >> > } >> >> > >> >> > Thank you >> >> > Regards, >> >> > H >> >> > >> >> > El jueves, 10 de marzo de 2022 a las 14:54:13 UTC+1, >> bruno.t...@gmail.com escribió: >> >> >> >> >> >> Hermes, >> >> >> >> >> >> For large systems, Krylov solvers are faster and require less memory >> >> >> than direct solvers. Direct solvers scale poorly, in terms of memory >> >> >> and performance, with the number of unknowns. The only problem with >> >> >> Krylov solvers is that you need to use a good preconditioner. The >> >> >> choice of the preconditioner depends on the system that you want to >> >> >> solve. >> >> >> >> >> >> Best, >> >> >> >> >> >> Bruno >> >> >> >> >> >> Le jeu. 10 mars 2022 à 02:51, Hermes Sampedro >> >> >> <hermes...@gmail.com> a écrit : >> >> >> > >> >> >> > Dear Bruno, >> >> >> > >> >> >> > Thank you again for your answer. >> >> >> > >> >> >> > I managed to solve now a system of 3.5 million DOF using the same >> solver as I posted above, SparseDirectMUMPS. Now, in release mode, the >> assembling takes a few minutes instead of hours, however, the solver >> function takes approximately 1.5h (per frequency iteration) using 40 >> processes in parallel (similar to step-40). >> >> >> > >> >> >> > I was expecting to get faster performance when running in >> parallel with 40 processes, especially because I need to run for several >> frequencies. I would like to ask if you also would expect faster >> performance. Would that be solved using the solver that you suggested >> (Krylov)? >> >> >> > >> >> >> > >> >> >> > Thank you >> >> >> > >> >> >> > Regards, >> >> >> > >> >> >> > H >> >> >> > >> >> >> > >> >> >> > El lunes, 7 de marzo de 2022 a las 15:04:19 UTC+1, >> bruno.t...@gmail.com escribió: >> >> >> >> >> >> >> >> Hermes, >> >> >> >> >> >> >> >> The problem is that you are using a direct solver. Direct solvers >> >> >> >> require a lot of memory because the inverse of a sparse matrix is >> >> >> >> generally not sparse. If you use a LU decomposition, which I >> think >> >> >> >> MUMPS does, you need a dense matrix to store the LU >> decomposition. >> >> >> >> That's a lot of memory! You will need to use a Krylov to solve a >> >> >> >> problem of this size. >> >> >> >> >> >> >> >> Best, >> >> >> >> >> >> >> >> Bruno >> >> >> >> >> >> >> >> Le dim. 6 mars 2022 à 07:19, Hermes Sampedro < >> hermes...@gmail.com> a écrit : >> >> >> >> > >> >> >> >> > Dear Bruno, >> >> >> >> > >> >> >> >> > Thank you very much for the comments. The problem was that I >> was running in Debug mode without knowing. Now, after changing to Release >> the assembling time is considerably reduced. >> >> >> >> > >> >> >> >> > Moreover, I am experiencing another issue that I would like to >> ask. My mesh is done with hyper_cube() in 3D and 5 refinements. The dof is >> around 3 million. When running, I always get a memory issue and the program >> stops. I realized that the problem is in the line that executes >> solver.solve(system_matrix, completely_distributed_solution, system_rhs); >> >> >> >> > I am using SparseMatrix and I do not fully understand where >> the problem could come from. The matrices are initialized beforehand, what >> reason do you think It could produce a memory issue in the solver? >> >> >> >> > >> >> >> >> > Below is the full solver function: >> >> >> >> > >> >> >> >> > template <int dim> >> >> >> >> > void LaplaceProblem<dim>::solve() >> >> >> >> > { >> >> >> >> > PETScWrappers::MPI::Vector >> completely_distributed_solution(locally_owned_dofs,mpi_communicator); >> >> >> >> > SolverControl cn; >> >> >> >> > PETScWrappers::SparseDirectMUMPS solver(cn, mpi_communicator); >> >> >> >> > solver.solve(system_matrix, completely_distributed_solution, >> system_rhs); >> >> >> >> > constraints.distribute(completely_distributed_solution); >> >> >> >> > locally_relevant_solution = completely_distributed_solution; >> >> >> >> > } >> >> >> >> > >> >> >> >> > >> >> >> >> > Thank you again for your help >> >> >> >> > Regards >> >> >> >> > H. >> >> >> >> > >> >> >> >> > El jueves, 3 de marzo de 2022 a las 15:13:30 UTC+1, >> bruno.t...@gmail.com escribió: >> >> >> >> >> >> >> >> >> >> Hermes, >> >> >> >> >> >> >> >> >> >> There is a couple of things that you could do but it probably >> won't give you a significant speed up. Are you sure that you are running in >> Release mode and not in Debug? Do you evaluate complicated functions in the >> assembly? >> >> >> >> >> A couple changes that could help: >> >> >> >> >> - don't use fe.system_to_component_index(i).first and >> fe.system_to_component_index(j).first everywhere. Just define const k = ... >> and const m = ... and use k and m. That might help the compiler with some >> optimizations >> >> >> >> >> - move the two if for the cell assembly outside the for loop >> on the quadrature point, similar to what you did for the boundaries. This >> could potentially help quite a bit if the cpu often gets the branch >> prediction wrong >> >> >> >> >> >> >> >> >> >> Best, >> >> >> >> >> >> >> >> >> >> Bruno >> >> >> >> >> >> >> >> >> >> On Thursday, March 3, 2022 at 4:31:04 AM UTC-5 >> hermes...@gmail.com wrote: >> >> >> >> >>> >> >> >> >> >>> Dear all, >> >> >> >> >>> >> >> >> >> >>> I am experiencing long times when computing the assembling >> and I would like to ask if this is common or there is something wrong with >> my implementation. >> >> >> >> >>> >> >> >> >> >>> My model is built in a similar way as step-29 and step-40 >> (using complex values ad solving with a direct solver using distributed >> parallel implementation). >> >> >> >> >>> Now I am running larger systems with 3.5million dof and the >> assembling took 16h, while the solver function took much less. >> >> >> >> >>> >> >> >> >> >>> I can show the structure of my assembly_system() function to >> ask if there is something that can be done in order to speed up the process: >> >> >> >> >>> >> >> >> >> >>> void Problem<dim>::assemble_system() >> >> >> >> >>> { >> >> >> >> >>> for (unsigned int i = 0; i < dofs_per_cell; ++i) { >> >> >> >> >>> for (unsigned int j = 0; j < dofs_per_cell; ++j) >> >> >> >> >>> { >> >> >> >> >>> for (unsigned int q_point = 0; q_point < n_q_points; >> ++q_point) >> >> >> >> >>> { >> >> >> >> >>> if (fe.system_to_component_index(i).first == >> fe.system_to_component_index(j).first) >> >> >> >> >>> { >> >> >> >> >>> cell_matrix(i, j) += .... >> >> >> >> >>> } >> >> >> >> >>> if (fe.system_to_component_index(i).first != >> fe.system_to_component_index(j).first) >> >> >> >> >>> { >> >> >> >> >>> cell_matrix(i, j) += .... >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> >> >> >> >> >>> // Boundaries >> >> >> >> >>> if (fe.system_to_component_index(i).first == >> fe.system_to_component_index(j).first) >> >> >> >> >>> { >> >> >> >> >>> for (unsigned int face_no : >> GeometryInfo<dim>::face_indices()) >> >> >> >> >>> if (cell->face(face_no)->at_boundary() && >> (cell->face(face_no)->boundary_id() == 0)) >> >> >> >> >>> { >> >> >> >> >>> fe_face_values.reinit(cell, face_no); >> >> >> >> >>> for (unsigned int q_point = 0; q_point < n_face_q_points; >> ++q_point) >> >> >> >> >>> cell_matrix(i, j) += .... >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> if (fe.system_to_component_index(i).first != >> fe.system_to_component_index(j).first) >> >> >> >> >>> { >> >> >> >> >>> for (unsigned int face_no : >> GeometryInfo<dim>::face_indices()) >> >> >> >> >>> { >> >> >> >> >>> if (cell->face(face_no)->at_boundary() && >> (cell->face(face_no)->boundary_id() == 0)) >> >> >> >> >>> { >> >> >> >> >>> fe_face_values.reinit(cell, face_no); >> >> >> >> >>> for (unsigned int q_point = 0; q_point < >> n_face_q_points;++q_point) >> >> >> >> >>> cell_matrix(i, j) += .... >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> } >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> Thank you very much. >> >> >> >> >>> Regards, >> >> >> >> >>> Hermes >> >> >> >> > >> >> >> >> > -- >> >> >> >> > The deal.II project is located at http://www.dealii.org/ >> >> >> >> > For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> >> >> >> > --- >> >> >> >> > You received this message because you are subscribed to a >> topic in the Google Groups "deal.II User Group" group. >> >> >> >> > To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/KQGIxkJZL6w/unsubscribe. >> >> >> >> > To unsubscribe from this group and all its topics, send an >> email to dealii+un...@googlegroups.com. >> >> >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/d80cbd1c-7d1f-4042-a9e8-e8382a721790n%40googlegroups.com >> . >> >> >> > >> >> >> > -- >> >> >> > The deal.II project is located at http://www.dealii.org/ >> >> >> > For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> >> >> > --- >> >> >> > You received this message because you are subscribed to a topic >> in the Google Groups "deal.II User Group" group. >> >> >> > To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/KQGIxkJZL6w/unsubscribe. >> >> >> > To unsubscribe from this group and all its topics, send an email >> to dealii+un...@googlegroups.com. >> >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/0438f349-0ecd-4503-944c-6a5068599ccfn%40googlegroups.com >> . >> >> > >> >> > -- >> >> > The deal.II project is located at http://www.dealii.org/ >> >> > For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> >> > --- >> >> > You received this message because you are subscribed to a topic in >> the Google Groups "deal.II User Group" group. >> >> > To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/KQGIxkJZL6w/unsubscribe. >> >> > To unsubscribe from this group and all its topics, send an email to >> dealii+un...@googlegroups.com. >> >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/cb8066c4-d160-4ebb-977b-d96ca07a93e5n%40googlegroups.com >> . >> > >> > -- >> > The deal.II project is located at http://www.dealii.org/ >> > For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> > --- >> > You received this message because you are subscribed to a topic in the >> Google Groups "deal.II User Group" group. >> > To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/dealii/KQGIxkJZL6w/unsubscribe. >> > To unsubscribe from this group and all its topics, send an email to >> dealii+un...@googlegroups.com. >> > To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/bea0a976-3413-4e85-aade-a05934440648n%40googlegroups.com >> . >> > -- > The deal.II project is located at http://www.dealii.org/ > For mailing list/forum options, see > https://groups.google.com/d/forum/dealii?hl=en > --- > You received this message because you are subscribed to a topic in the > Google Groups "deal.II User Group" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/dealii/KQGIxkJZL6w/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > dealii+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/dealii/b78563e3-8746-4107-b1d3-95f4ff8289c9n%40googlegroups.com > <https://groups.google.com/d/msgid/dealii/b78563e3-8746-4107-b1d3-95f4ff8289c9n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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