From: Rossi, S. <sr...@em...> - 2017-04-27 20:02:15
|
Ok, I ran again the tests with different max_h_levels with the perflog enabled. Let me know if you see anything here. Thanks, Simone NO AMR ----------------------------------------------------------------------------------------------------------------- | libMesh Performance: Alive time=77.5482, Active time=40.2976 | ----------------------------------------------------------------------------------------------------------------- | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |-----------------------------------------------------------------------------------------------------------------| | | | | | DefaultCoupling | | operator() 98306 0.1609 0.000002 0.1609 0.000002 0.40 0.40 | | | | DofMap | | add_neighbors_to_send_list() 1 0.0959 0.095930 0.3744 0.374369 0.24 0.93 | | build_sparsity() 1 0.4701 0.470055 1.1433 1.143297 1.17 2.84 | | create_dof_constraints() 1 0.0137 0.013673 0.0137 0.013673 0.03 0.03 | | distribute_dofs() 1 0.0126 0.012578 0.4376 0.437647 0.03 1.09 | | dof_indices() 11010048 9.9728 0.000001 9.9728 0.000001 24.75 24.75 | | prepare_send_list() 2 0.0000 0.000002 0.0000 0.000002 0.00 0.00 | | reinit() 1 0.0507 0.050692 0.0507 0.050692 0.13 0.13 | | | | EquationSystems | | build_parallel_solution_vector() 5 1.4241 0.284811 2.4934 0.498673 3.53 6.19 | | build_solution_vector() 5 0.0002 0.000050 2.4936 0.498724 0.00 6.19 | | | | ExodusII_IO | | write_nodal_data() 3 0.0774 0.025816 0.0774 0.025816 0.19 0.19 | | | | FE | | compute_shape_functions() 10027008 11.7027 0.000001 11.7027 0.000001 29.04 29.04 | | init_shape_functions() 102 0.0007 0.000007 0.0007 0.000007 0.00 0.00 | | | | FEMap | | compute_affine_map() 10027008 9.9328 0.000001 9.9328 0.000001 24.65 24.65 | | init_reference_to_physical_map() 102 0.0008 0.000008 0.0008 0.000008 0.00 0.00 | | | | GMVIO | | write_nodal_data() 2 0.2260 0.113020 0.2260 0.113020 0.56 0.56 | | | | GenericProjector | | operator() 1 0.8425 0.842529 2.0842 2.084232 2.09 5.17 | | project_edges 98304 0.0765 0.000001 0.0765 0.000001 0.19 0.19 | | project_interior 98304 0.0765 0.000001 0.0765 0.000001 0.19 0.19 | | project_nodes 98304 0.0865 0.000001 0.0865 0.000001 0.21 0.21 | | project_sides 98304 0.0763 0.000001 0.0763 0.000001 0.19 0.19 | | | | Mesh | | find_neighbors() 1 0.1105 0.110532 0.1105 0.110532 0.27 0.27 | | renumber_nodes_and_elem() 2 0.0063 0.003125 0.0063 0.003125 0.02 0.02 | | | | MeshOutput | | write_equation_systems() 5 0.0001 0.000021 2.7972 0.559445 0.00 6.94 | | | | MeshTools::Generation | | build_cube() 1 0.0280 0.027995 0.0280 0.027995 0.07 0.07 | | | | Parallel | | allgather() 1 0.0000 0.000003 0.0000 0.000003 0.00 0.00 | | | | Partitioner | | single_partition() 1 0.0028 0.002767 0.0028 0.002767 0.01 0.01 | | | | PetscLinearSolver | | solve() 101 4.8469 0.047989 4.8469 0.047989 12.03 12.03 | | | | System | | project_fem_vector() 1 0.0034 0.003364 2.0876 2.087598 0.01 5.18 | | project_vector(FunctionBase) 1 0.0000 0.000011 2.0876 2.087610 0.00 5.18 | ----------------------------------------------------------------------------------------------------------------- | Totals: 3.156e+07 40.2976 100.00 | ----------------------------------------------------------------------------------------------------------------- AMR: 1 refinement ----------------------------------------------------------------------------------------------------------------- | libMesh Performance: Alive time=395.981, Active time=261.811 | ----------------------------------------------------------------------------------------------------------------- | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |-----------------------------------------------------------------------------------------------------------------| | | | | | DefaultCoupling | | operator() 1336320 2.0806 0.000002 2.0806 0.000002 0.79 0.79 | | | | DofMap | | add_neighbors_to_send_list() 102 1.2626 0.012378 4.8311 0.047363 0.48 1.85 | | build_sparsity() 102 6.5962 0.064669 15.1863 0.148885 2.52 5.80 | | create_dof_constraints() 102 0.1384 0.001356 0.2351 0.002305 0.05 0.09 | | distribute_dofs() 102 0.1489 0.001459 5.6797 0.055684 0.06 2.17 | | dof_indices() 22510266 19.3897 0.000001 19.3897 0.000001 7.41 7.41 | | enforce_constraints_exactly() 303 0.1463 0.000483 0.1463 0.000483 0.06 0.06 | | old_dof_indices() 11914452 11.0468 0.000001 11.0468 0.000001 4.22 4.22 | | prepare_send_list() 103 0.0001 0.000001 0.0001 0.000001 0.00 0.00 | | reinit() 102 0.6993 0.006856 0.6993 0.006856 0.27 0.27 | | | | EquationSystems | | build_parallel_solution_vector() 5 0.1832 0.036644 0.3127 0.062538 0.07 0.12 | | build_solution_vector() 5 0.0001 0.000018 0.3128 0.062557 0.00 0.12 | | | | ExodusII_IO | | write_nodal_data() 3 0.0094 0.003131 0.0094 0.003131 0.00 0.00 | | | | FE | | compute_shape_functions() 12975978 16.6602 0.000001 16.6602 0.000001 6.36 6.36 | | init_shape_functions() 10329700 16.6365 0.000002 16.6365 0.000002 6.35 6.35 | | inverse_map() 10386411 11.3644 0.000001 11.3644 0.000001 4.34 4.34 | | | | FEMap | | compute_affine_map() 12975978 13.4041 0.000001 13.4041 0.000001 5.12 5.12 | | compute_face_map() 7691859 8.9240 0.000001 8.9240 0.000001 3.41 3.41 | | init_face_shape_functions() 101 0.0004 0.000004 0.0004 0.000004 0.00 0.00 | | init_reference_to_physical_map() 10329700 11.4379 0.000001 11.4379 0.000001 4.37 4.37 | | | | GMVIO | | write_nodal_data() 2 0.0979 0.048947 0.0979 0.048947 0.04 0.04 | | | | GenericProjector | | copy_dofs 3917556 15.7713 0.000004 59.2081 0.000015 6.02 22.61 | | operator() 304 11.6914 0.038458 95.5809 0.314411 4.47 36.51 | | project_edges 66216 0.0489 0.000001 0.0489 0.000001 0.02 0.02 | | project_interior 66216 0.0493 0.000001 0.0493 0.000001 0.02 0.02 | | project_nodes 66216 0.2561 0.000004 3.4858 0.000053 0.10 1.33 | | project_sides 66216 0.0498 0.000001 0.0498 0.000001 0.02 0.02 | | | | JumpErrorEstimator | | estimate_error() 101 73.8216 0.730907 231.1510 2.288624 28.20 88.29 | | | | Mesh | | contract() 101 0.0296 0.000293 0.0581 0.000575 0.01 0.02 | | find_neighbors() 101 1.4534 0.014391 1.4534 0.014391 0.56 0.56 | | renumber_nodes_and_elem() 303 0.0847 0.000280 0.0847 0.000280 0.03 0.03 | | | | MeshOutput | | write_equation_systems() 5 0.0001 0.000017 0.4202 0.084033 0.00 0.16 | | | | MeshRefinement | | _coarsen_elements() 202 0.0812 0.000402 0.0812 0.000402 0.03 0.03 | | _refine_elements() 202 0.1485 0.000735 0.2795 0.001383 0.06 0.11 | | add_node() 64512 0.0546 0.000001 0.0546 0.000001 0.02 0.02 | | make_coarsening_compatible() 204 0.3018 0.001479 0.3018 0.001479 0.12 0.12 | | make_flags_parallel_consistent() 303 0.2300 0.000759 0.2300 0.000759 0.09 0.09 | | make_refinement_compatible() 204 0.0242 0.000119 0.0242 0.000119 0.01 0.01 | | | | MeshTools::Generation | | build_cube() 1 0.0039 0.003937 0.0039 0.003937 0.00 0.00 | | | | OldSolutionValue | | Number eval_at_node() 215712 0.2301 0.000001 2.9735 0.000014 0.09 1.14 | | check_old_context(c) 3917556 10.9141 0.000003 27.5061 0.000007 4.17 10.51 | | check_old_context(c,p) 68724 0.1726 0.000003 0.4012 0.000006 0.07 0.15 | | eval_at_point() 68724 0.8513 0.000012 2.6627 0.000039 0.33 1.02 | | eval_old_dofs() 3917556 6.6409 0.000002 38.7818 0.000010 2.54 14.81 | | | | Parallel | | allgather() 102 0.0001 0.000001 0.0001 0.000001 0.00 0.00 | | | | Partitioner | | single_partition() 101 0.0341 0.000338 0.0341 0.000338 0.01 0.01 | | | | PetscLinearSolver | | solve() 202 1.6660 0.008248 1.6660 0.008248 0.64 0.64 | | | | StatisticsVector | | maximum() 101 0.0018 0.000017 0.0018 0.000017 0.00 0.00 | | | | System | | assemble() 202 11.5849 0.057351 28.7372 0.142263 4.42 10.98 | | project_fem_vector() 1 0.0004 0.000417 0.2583 0.258341 0.00 0.10 | | project_vector(FunctionBase) 1 0.0000 0.000008 0.2584 0.258351 0.00 0.10 | | project_vector(old,new) 303 5.2799 0.017425 109.1696 0.360296 2.02 41.70 | | | | TopologyMap | | init() 202 0.1071 0.000530 0.1071 0.000530 0.04 0.04 | ----------------------------------------------------------------------------------------------------------------- | Totals: 1.129e+08 261.8108 100.00 | ----------------------------------------------------------------------------------------------------------------- AMR 2 refinements ----------------------------------------------------------------------------------------------------------------- | libMesh Performance: Alive time=156.79, Active time=103.985 | ----------------------------------------------------------------------------------------------------------------- | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |-----------------------------------------------------------------------------------------------------------------| | | | | | DefaultCoupling | | operator() 487585 0.7671 0.000002 0.7671 0.000002 0.74 0.74 | | | | DofMap | | add_neighbors_to_send_list() 203 0.4861 0.002394 1.8338 0.009034 0.47 1.76 | | build_sparsity() 203 2.8815 0.014194 6.2119 0.030601 2.77 5.97 | | create_dof_constraints() 203 0.2105 0.001037 0.4801 0.002365 0.20 0.46 | | distribute_dofs() 203 0.0596 0.000294 2.1454 0.010569 0.06 2.06 | | dof_indices() 8055927 7.4875 0.000001 7.4875 0.000001 7.20 7.20 | | enforce_constraints_exactly() 606 0.3674 0.000606 0.3674 0.000606 0.35 0.35 | | old_dof_indices() 4358601 4.2132 0.000001 4.2132 0.000001 4.05 4.05 | | prepare_send_list() 204 0.0002 0.000001 0.0002 0.000001 0.00 0.00 | | reinit() 203 0.2510 0.001237 0.2510 0.001237 0.24 0.24 | | | | EquationSystems | | build_parallel_solution_vector() 5 0.0316 0.006312 0.0543 0.010852 0.03 0.05 | | build_solution_vector() 5 0.0001 0.000014 0.0543 0.010868 0.00 0.05 | | | | ExodusII_IO | | write_nodal_data() 3 0.0024 0.000816 0.0024 0.000816 0.00 0.00 | | | | FE | | compute_shape_functions() 4507581 6.1953 0.000001 6.1953 0.000001 5.96 5.96 | | init_shape_functions() 3783756 6.6310 0.000002 6.6310 0.000002 6.38 6.38 | | inverse_map() 3875385 4.5491 0.000001 4.5491 0.000001 4.37 4.37 | | | | FEMap | | compute_affine_map() 4507581 5.2201 0.000001 5.2201 0.000001 5.02 5.02 | | compute_face_map() 2763882 3.5520 0.000001 3.5520 0.000001 3.42 3.42 | | init_face_shape_functions() 202 0.0007 0.000004 0.0007 0.000004 0.00 0.00 | | init_reference_to_physical_map() 3783756 4.6286 0.000001 4.6286 0.000001 4.45 4.45 | | | | GMVIO | | write_nodal_data() 2 0.1665 0.083237 0.1665 0.083237 0.16 0.16 | | | | GenericProjector | | copy_dofs 1361385 5.6580 0.000004 21.6490 0.000016 5.44 20.82 | | operator() 607 5.0012 0.008239 40.4516 0.066642 4.81 38.90 | | project_edges 97080 0.0766 0.000001 0.0766 0.000001 0.07 0.07 | | project_interior 97080 0.0751 0.000001 0.0751 0.000001 0.07 0.07 | | project_nodes 97080 0.4693 0.000005 5.0553 0.000052 0.45 4.86 | | project_sides 97080 0.0770 0.000001 0.0770 0.000001 0.07 0.07 | | | | JumpErrorEstimator | | estimate_error() 202 28.7106 0.142132 89.7093 0.444106 27.61 86.27 | | | | Mesh | | contract() 202 0.0160 0.000079 0.0280 0.000139 0.02 0.03 | | find_neighbors() 203 0.5978 0.002945 0.5978 0.002945 0.57 0.57 | | renumber_nodes_and_elem() 608 0.0350 0.000058 0.0350 0.000058 0.03 0.03 | | | | MeshOutput | | write_equation_systems() 5 0.0001 0.000013 0.2233 0.044669 0.00 0.21 | | | | MeshRefinement | | _coarsen_elements() 404 0.0378 0.000094 0.0378 0.000094 0.04 0.04 | | _refine_elements() 404 0.1563 0.000387 0.4010 0.000993 0.15 0.39 | | add_node() 113664 0.1007 0.000001 0.1007 0.000001 0.10 0.10 | | make_coarsening_compatible() 407 0.1988 0.000489 0.1988 0.000489 0.19 0.19 | | make_flags_parallel_consistent() 606 0.0937 0.000155 0.0937 0.000155 0.09 0.09 | | make_refinement_compatible() 407 0.0102 0.000025 0.0102 0.000025 0.01 0.01 | | | | MeshTools::Generation | | build_cube() 1 0.0007 0.000677 0.0007 0.000677 0.00 0.00 | | | | OldSolutionValue | | Number eval_at_node() 382176 0.3948 0.000001 4.1027 0.000011 0.38 3.95 | | check_old_context(c) 1361385 4.0214 0.000003 10.1149 0.000007 3.87 9.73 | | check_old_context(c,p) 85266 0.2420 0.000003 0.5679 0.000007 0.23 0.55 | | eval_at_point() 85266 1.1648 0.000014 3.5999 0.000042 1.12 3.46 | | eval_old_dofs() 1361385 2.4347 0.000002 14.2695 0.000010 2.34 13.72 | | | | Parallel | | allgather() 203 0.0002 0.000001 0.0002 0.000001 0.00 0.00 | | | | Partitioner | | single_partition() 203 0.0140 0.000069 0.0140 0.000069 0.01 0.01 | | | | PetscLinearSolver | | solve() 303 0.7612 0.002512 0.7612 0.002512 0.73 0.73 | | | | StatisticsVector | | maximum() 202 0.0008 0.000004 0.0008 0.000004 0.00 0.00 | | | | System | | assemble() 303 3.4738 0.011465 8.5615 0.028256 3.34 8.23 | | project_fem_vector() 1 0.0001 0.000142 0.0331 0.033134 0.00 0.03 | | project_vector(FunctionBase) 1 0.0000 0.000009 0.0331 0.033144 0.00 0.03 | | project_vector(old,new) 606 2.3051 0.003804 46.4861 0.076710 2.22 44.70 | | | | TopologyMap | | init() 404 0.1561 0.000386 0.1561 0.000386 0.15 0.15 | ----------------------------------------------------------------------------------------------------------------- | Totals: 4.127e+07 103.9851 100.00 | ----------------------------------------------------------------------------------------------------------------- AMR 3 refinements ----------------------------------------------------------------------------------------------------------------- | libMesh Performance: Alive time=455.466, Active time=308.123 | ----------------------------------------------------------------------------------------------------------------- | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |-----------------------------------------------------------------------------------------------------------------| | | | | | DefaultCoupling | | operator() 1153034 1.9001 0.000002 1.9001 0.000002 0.62 0.62 | | | | DofMap | | add_neighbors_to_send_list() 304 1.1509 0.003786 4.4251 0.014556 0.37 1.44 | | build_sparsity() 304 8.8682 0.029172 16.6976 0.054926 2.88 5.42 | | create_dof_constraints() 304 1.6469 0.005417 3.9951 0.013142 0.53 1.30 | | distribute_dofs() 304 0.2173 0.000715 5.4146 0.017811 0.07 1.76 | | dof_indices() 19916934 18.6126 0.000001 18.6126 0.000001 6.04 6.04 | | enforce_constraints_exactly() 909 2.8034 0.003084 2.8034 0.003084 0.91 0.91 | | old_dof_indices() 10268793 10.0124 0.000001 10.0124 0.000001 3.25 3.25 | | prepare_send_list() 305 0.0003 0.000001 0.0003 0.000001 0.00 0.00 | | reinit() 304 0.7707 0.002535 0.7707 0.002535 0.25 0.25 | | | | EquationSystems | | build_parallel_solution_vector() 5 0.0498 0.009954 0.0849 0.016974 0.02 0.03 | | build_solution_vector() 5 0.0001 0.000015 0.0850 0.016991 0.00 0.03 | | | | ExodusII_IO | | write_nodal_data() 3 0.0016 0.000526 0.0016 0.000526 0.00 0.00 | | | | FE | | compute_shape_functions() 12087258 16.7562 0.000001 16.7562 0.000001 5.44 5.44 | | init_shape_functions() 10555340 23.3502 0.000002 23.3502 0.000002 7.58 7.58 | | inverse_map() 11670851 13.6081 0.000001 13.6081 0.000001 4.42 4.42 | | | | FEMap | | compute_affine_map() 12087258 15.1613 0.000001 15.1613 0.000001 4.92 4.92 | | compute_face_map() 6822171 8.8288 0.000001 8.8288 0.000001 2.87 2.87 | | init_face_shape_functions() 303 0.0011 0.000004 0.0011 0.000004 0.00 0.00 | | init_reference_to_physical_map() 10555340 14.9343 0.000001 14.9343 0.000001 4.85 4.85 | | | | GMVIO | | write_nodal_data() 2 0.0676 0.033816 0.0676 0.033816 0.02 0.02 | | | | GenericProjector | | copy_dofs 2157561 8.8513 0.000004 33.9505 0.000016 2.87 11.02 | | operator() 910 18.4194 0.020241 155.7304 0.171132 5.98 50.54 | | project_edges 1299333 1.0235 0.000001 1.0235 0.000001 0.33 0.33 | | project_interior 1299333 1.0026 0.000001 1.0026 0.000001 0.33 0.33 | | project_nodes 1299333 6.3258 0.000005 76.0383 0.000059 2.05 24.68 | | project_sides 1299333 1.0258 0.000001 1.0258 0.000001 0.33 0.33 | | | | JumpErrorEstimator | | estimate_error() 303 71.4588 0.235838 222.8668 0.735534 23.19 72.33 | | | | Mesh | | contract() 303 0.0998 0.000329 0.1462 0.000483 0.03 0.05 | | find_neighbors() 304 2.2488 0.007397 2.2488 0.007397 0.73 0.73 | | renumber_nodes_and_elem() 911 0.1348 0.000148 0.1348 0.000148 0.04 0.04 | | | | MeshOutput | | write_equation_systems() 5 0.0001 0.000013 0.1542 0.030848 0.00 0.05 | | | | MeshRefinement | | _coarsen_elements() 606 0.1621 0.000268 0.1621 0.000268 0.05 0.05 | | _refine_elements() 606 1.6498 0.002722 4.9647 0.008193 0.54 1.61 | | add_node() 1542432 1.3647 0.000001 1.3647 0.000001 0.44 0.44 | | make_coarsening_compatible() 809 1.4420 0.001782 1.4420 0.001782 0.47 0.47 | | make_flags_parallel_consistent() 909 0.2881 0.000317 0.2881 0.000317 0.09 0.09 | | make_refinement_compatible() 809 0.0552 0.000068 0.0552 0.000068 0.02 0.02 | | | | MeshTools::Generation | | build_cube() 1 0.0002 0.000230 0.0002 0.000230 0.00 0.00 | | | | OldSolutionValue | | Number eval_at_node() 5196564 5.4931 0.000001 63.1554 0.000012 1.78 20.50 | | check_old_context(c) 2157561 6.2716 0.000003 15.8724 0.000007 2.04 5.15 | | check_old_context(c,p) 1343484 3.6784 0.000003 8.6255 0.000006 1.19 2.80 | | eval_at_point() 1343484 18.1202 0.000013 55.9662 0.000042 5.88 18.16 | | eval_old_dofs() 2157561 3.8284 0.000002 22.3994 0.000010 1.24 7.27 | | | | Parallel | | allgather() 304 0.0003 0.000001 0.0003 0.000001 0.00 0.00 | | | | Partitioner | | single_partition() 304 0.0450 0.000148 0.0450 0.000148 0.01 0.01 | | | | PetscLinearSolver | | solve() 404 1.5022 0.003718 1.5022 0.003718 0.49 0.49 | | | | StatisticsVector | | maximum() 303 0.0019 0.000006 0.0019 0.000006 0.00 0.00 | | | | System | | assemble() 404 7.4765 0.018506 18.1484 0.044922 2.43 5.89 | | project_fem_vector() 1 0.0001 0.000109 0.0045 0.004474 0.00 0.00 | | project_vector(FunctionBase) 1 0.0000 0.000010 0.0045 0.004485 0.00 0.00 | | project_vector(old,new) 909 6.4352 0.007079 174.8106 0.192311 2.09 56.73 | | | | TopologyMap | | init() 606 0.9755 0.001610 0.9755 0.001610 0.32 0.32 | ----------------------------------------------------------------------------------------------------------------- | Totals: 1.162e+08 308.1230 100.00 | ----------------------------------------------------------------------------------------------------------------- On Apr 27, 2017, at 12:14, Vikram Garg <vik...@gm...<mailto:vik...@gm...>> wrote: Rossi, yes compiling with perflog should give you all the details as in the example. On Thu, Apr 27, 2017 at 10:54 AM, Rossi, Simone <sr...@em...<mailto:sr...@em...>> wrote: Dear Vikram, as in the examples, I am using the libmesh::KellyErrorEstimator. I’m compiling libmesh with the --enable-perflog option. Does it automatically give all the details you have listed in the example? For the time being, I am attaching two perfLogs I had saved with only “coarse scale” data for 2 levels of refinements. It looks like that most of the time is spent in the AMR step, probably in the call to reinit(). Thanks, Simone NO AMR: ------------------------------------------------------------------------------------------------------------ | perf_log Performance: Alive time=18.0494, Active time=18.0426 | ------------------------------------------------------------------------------------------------------------ | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |------------------------------------------------------------------------------------------------------------| | no amr matrix assembly 1 0.1545 0.154465 0.1545 0.154465 0.86 0.86 | | no amr linear solve 101 4.8069 0.047593 4.8069 0.047593 26.64 26.64 | | no amr rhs assembly 101 12.0348 0.119156 12.0348 0.119156 66.70 66.70 | | time loop 1 1.0464 1.046422 17.8884 17.888405 5.80 99.15 | ------------------------------------------------------------------------------------------------------------ | Totals: 204 18.0426 100.00 | ------------------------------------------------------------------------------------------------------------ AMR: ------------------------------------------------------------------------------------------------------------ | perf_log Performance: Alive time=209.305, Active time=209.298 | ------------------------------------------------------------------------------------------------------------ | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |------------------------------------------------------------------------------------------------------------| | | | amr 303 195.1102 0.643928 195.1102 0.643928 93.22 93.22 | | amr solve 303 13.9907 0.046174 13.9907 0.046174 6.68 6.68 | | time loop 1 0.1974 0.197370 209.2990 209.299042 0.09 100.00 | ------------------------------------------------------------------------------------------------------------ | Totals: 607 209.2983 100.00 | ------------------------------------------------------------------------------------------------------------ On Apr 27, 2017, at 11:02, Vikram Garg <vik...@gm...<mailto:vik...@gm...>> wrote: Hello Rossi, Two questions: 1) Which error estimator/indicator are you using to mark elements for refinement ? 2) Can you send the perfLog output from libMesh ? You might need to recompile libMesh with the option --enable-perflog. Looks something like this: ----------------------------------------------------------------------------------------------------------------- | libMesh Performance: Alive time=0.013423, Active time=0.007095 | ----------------------------------------------------------------------------------------------------------------- | Event nCalls Total Time Avg Time Total Time Avg Time % of Active Time | | w/o Sub w/o Sub With Sub With Sub w/o S With S | |-----------------------------------------------------------------------------------------------------------------| | | | | | DofMap | | add_neighbors_to_send_list() 6 0.0001 0.000012 0.0001 0.000012 1.01 1.01 | | build_sparsity() 6 0.0002 0.000033 0.0011 0.000187 2.78 15.84 | | create_dof_constraints() 6 0.0000 0.000001 0.0000 0.000001 0.07 0.07 | | distribute_dofs() 6 0.0001 0.000025 0.0004 0.000066 2.09 5.57 | | dof_indices() 688 0.0010 0.000001 0.0010 0.000001 14.36 14.36 | | old_dof_indices() 300 0.0001 0.000000 0.0001 0.000000 0.96 0.96 | | prepare_send_list() 7 0.0000 0.000000 0.0000 0.000000 0.01 0.01 | | reinit() 6 0.0002 0.000041 0.0002 0.000041 3.48 3.48 | | | | EquationSystems | | build_solution_vector() 1 0.0001 0.000056 0.0001 0.000064 0.79 0.90 | Thanks. On Wed, Apr 26, 2017 at 10:09 PM, Rossi, Simone <sr...@em...<mailto:sr...@em...>> wrote: Dear Roy, dear Paul, dear all, I am testing AMR in libmesh using simple linear elements. My test case is a propagating front described by a reaction-diffusion equation with a cubic bistable reaction term. I followed the adaptivity examples to create this test case. The run times for 100 timesteps using AMR can be more than 10 times slower than when using a fine uniform grid. For example, with a 16 x 16 x 16 uniform grid, 100 iterations take about 18 seconds with a single processor. With AMR, using a 2 x 2 x 2 grid and 3 levels of refinement, 100 iterations take about 800 seconds. I’m attaching the code I’m using. Without AMR, I build the matrix ( mass + dt * stiffness ) once and I update the rhs at every timestep. Conversely, with AMR I am building the matrix and the rhs at every timestep for all the refinement levels. Do you have any suggestions? Thanks a lot for your help, All the best, Simone ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://slashdot.org/>! http://sdm.link/slashdot _______________________________________________ Libmesh-users mailing list Lib...@li...<mailto:Lib...@li...> https://lists.sourceforge.net/lists/listinfo/libmesh-users -- Vikram Garg Postdoctoral Associate The University of Texas at Austin http://vikramvgarg.wordpress.com/ http://www.runforindia.org/runners/vikramg -- Vikram Garg Postdoctoral Associate The University of Texas at Austin http://vikramvgarg.wordpress.com/ http://www.runforindia.org/runners/vikramg |