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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> 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
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Vikram Garg
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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
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