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]> 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]> 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]> > 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 >> [email protected] >> 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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Libmesh-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/libmesh-users
