From 8bc5469b3d883be0ce088386e1ec794e448003ef Mon Sep 17 00:00:00 2001 From: Jesse Chan <1156048+jlchan@users.noreply.github.com> Date: Wed, 11 Oct 2023 06:22:49 -0500 Subject: [PATCH 1/2] fix bug in `apply_jacobian_parabolic!` for `P4estMesh` (#1668) * fix bug in parabolic jacobian computations * formatting * updating test results and removing duplicate test --------- Co-authored-by: Hendrik Ranocha --- src/solvers/dgsem_tree/dg_2d_parabolic.jl | 20 +++++++++++++++++++- src/solvers/dgsem_tree/dg_3d_parabolic.jl | 23 +++++++++++++++++++++-- test/test_parabolic_2d.jl | 16 ++++------------ 3 files changed, 44 insertions(+), 15 deletions(-) diff --git a/src/solvers/dgsem_tree/dg_2d_parabolic.jl b/src/solvers/dgsem_tree/dg_2d_parabolic.jl index 3dbc55412ad..1c32703c7c3 100644 --- a/src/solvers/dgsem_tree/dg_2d_parabolic.jl +++ b/src/solvers/dgsem_tree/dg_2d_parabolic.jl @@ -935,7 +935,7 @@ end # This is because the parabolic fluxes are assumed to be of the form # `du/dt + df/dx = dg/dx + source(x,t)`, # where f(u) is the inviscid flux and g(u) is the viscous flux. -function apply_jacobian_parabolic!(du, mesh::Union{TreeMesh{2}, P4estMesh{2}}, +function apply_jacobian_parabolic!(du, mesh::TreeMesh{2}, equations::AbstractEquationsParabolic, dg::DG, cache) @unpack inverse_jacobian = cache.elements @@ -951,4 +951,22 @@ function apply_jacobian_parabolic!(du, mesh::Union{TreeMesh{2}, P4estMesh{2}}, return nothing end + +function apply_jacobian_parabolic!(du, mesh::P4estMesh{2}, + equations::AbstractEquationsParabolic, + dg::DG, cache) + @unpack inverse_jacobian = cache.elements + + @threaded for element in eachelement(dg, cache) + for j in eachnode(dg), i in eachnode(dg) + factor = inverse_jacobian[i, j, element] + + for v in eachvariable(equations) + du[v, i, j, element] *= factor + end + end + end + + return nothing +end end # @muladd diff --git a/src/solvers/dgsem_tree/dg_3d_parabolic.jl b/src/solvers/dgsem_tree/dg_3d_parabolic.jl index 9817e0e5f0e..37492dbcb91 100644 --- a/src/solvers/dgsem_tree/dg_3d_parabolic.jl +++ b/src/solvers/dgsem_tree/dg_3d_parabolic.jl @@ -1125,8 +1125,9 @@ end # This is because the parabolic fluxes are assumed to be of the form # `du/dt + df/dx = dg/dx + source(x,t)`, # where f(u) is the inviscid flux and g(u) is the viscous flux. -function apply_jacobian_parabolic!(du, mesh::Union{TreeMesh{3}, P4estMesh{3}}, - equations::AbstractEquationsParabolic, dg::DG, cache) +function apply_jacobian_parabolic!(du, mesh::TreeMesh{3}, + equations::AbstractEquationsParabolic, + dg::DG, cache) @unpack inverse_jacobian = cache.elements @threaded for element in eachelement(dg, cache) @@ -1141,4 +1142,22 @@ function apply_jacobian_parabolic!(du, mesh::Union{TreeMesh{3}, P4estMesh{3}}, return nothing end + +function apply_jacobian_parabolic!(du, mesh::P4estMesh{3}, + equations::AbstractEquationsParabolic, + dg::DG, cache) + @unpack inverse_jacobian = cache.elements + + @threaded for element in eachelement(dg, cache) + for k in eachnode(dg), j in eachnode(dg), i in eachnode(dg) + factor = inverse_jacobian[i, j, k, element] + + for v in eachvariable(equations) + du[v, i, j, k, element] *= factor + end + end + end + + return nothing +end end # @muladd diff --git a/test/test_parabolic_2d.jl b/test/test_parabolic_2d.jl index 967aa1069a0..98aa337afb4 100644 --- a/test/test_parabolic_2d.jl +++ b/test/test_parabolic_2d.jl @@ -260,24 +260,16 @@ isdir(outdir) && rm(outdir, recursive=true) @trixi_testset "P4estMesh2D: elixir_advection_diffusion_periodic_curved.jl" begin @test_trixi_include(joinpath(examples_dir(), "p4est_2d_dgsem", "elixir_advection_diffusion_periodic_curved.jl"), trees_per_dimension = (1, 1), initial_refinement_level = 2, tspan=(0.0, 0.5), - l2 = [0.012380458938507371], - linf = [0.10860506906472567] - ) - end - - @trixi_testset "P4estMesh2D: elixir_advection_diffusion_periodic_curved.jl" begin - @test_trixi_include(joinpath(examples_dir(), "p4est_2d_dgsem", "elixir_advection_diffusion_periodic_curved.jl"), - trees_per_dimension = (1, 1), initial_refinement_level = 2, tspan=(0.0, 0.5), - l2 = [0.012380458938507371], - linf = [0.10860506906472567] + l2 = [0.006708147442490916], + linf = [0.04807038397976693] ) end @trixi_testset "P4estMesh2D: elixir_advection_diffusion_nonperiodic_curved.jl" begin @test_trixi_include(joinpath(examples_dir(), "p4est_2d_dgsem", "elixir_advection_diffusion_nonperiodic_curved.jl"), trees_per_dimension = (1, 1), initial_refinement_level = 2, tspan=(0.0, 0.5), - l2 = [0.04933902988507035], - linf = [0.2550261714590271] + l2 = [0.00919917034843865], + linf = [0.14186297438393505] ) end From 1727b072fa9f269bcde73b516bc7b00f13fc9c99 Mon Sep 17 00:00:00 2001 From: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Date: Wed, 11 Oct 2023 16:23:12 +0200 Subject: [PATCH 2/2] Show percentage of simulation progress (#1659) * show percentage of simulation progress * add notes about AnalysisCallback in docs * generalize for general initial time --------- Co-authored-by: Hendrik Ranocha --- docs/src/callbacks.md | 5 +++++ src/callbacks_step/alive.jl | 10 ++++++++-- src/callbacks_step/analysis.jl | 10 ++++++++-- 3 files changed, 21 insertions(+), 4 deletions(-) diff --git a/docs/src/callbacks.md b/docs/src/callbacks.md index 7f44dfd5925..f018bcf7c39 100644 --- a/docs/src/callbacks.md +++ b/docs/src/callbacks.md @@ -30,6 +30,11 @@ An example elixir using AMR can be found at [`examples/tree_2d_dgsem/elixir_adve The [`AnalysisCallback`](@ref) can be used to analyze the numerical solution, e.g. calculate errors or user-specified integrals, and print the results to the screen. The results can also be saved in a file. An example can be found at [`examples/tree_2d_dgsem/elixir_euler_vortex.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_vortex.jl). +Note that the errors (e.g. `L2 error` or `Linf error`) are computed with respect to the initial condition. +The percentage of the simulation time refers to the ratio of the current time and the final time, i.e. it does +not consider the maximal number of iterations. So the simulation could finish before 100% are reached. +Note that, e.g., due to AMR or smaller time step sizes, the simulation can actually take longer than +the percentage indicates. In [Performance metrics of the `AnalysisCallback`](@ref performance-metrics) you can find a detailed description of the different performance metrics the `AnalysisCallback` computes. diff --git a/src/callbacks_step/alive.jl b/src/callbacks_step/alive.jl index eeacd9681d8..9df7181521e 100644 --- a/src/callbacks_step/alive.jl +++ b/src/callbacks_step/alive.jl @@ -86,9 +86,15 @@ function (alive_callback::AliveCallback)(integrator) println("─"^100) println() elseif mpi_isroot() + t = integrator.t + t_initial = first(integrator.sol.prob.tspan) + t_final = last(integrator.sol.prob.tspan) + sim_time_percentage = (t - t_initial) / (t_final - t_initial) * 100 runtime_absolute = 1.0e-9 * (time_ns() - alive_callback.start_time) - @printf("#timesteps: %6d │ Δt: %.4e │ sim. time: %.4e │ run time: %.4e s\n", - integrator.stats.naccept, integrator.dt, integrator.t, runtime_absolute) + println(rpad(@sprintf("#timesteps: %6d │ Δt: %.4e │ sim. time: %.4e (%5.3f%%)", + integrator.stats.naccept, integrator.dt, t, + sim_time_percentage), 71) * + @sprintf("│ run time: %.4e s", runtime_absolute)) end # avoid re-evaluating possible FSAL stages diff --git a/src/callbacks_step/analysis.jl b/src/callbacks_step/analysis.jl index a3e49007fb6..e5b4a01a885 100644 --- a/src/callbacks_step/analysis.jl +++ b/src/callbacks_step/analysis.jl @@ -232,6 +232,12 @@ function (analysis_callback::AnalysisCallback)(u_ode, du_ode, integrator, semi) @unpack dt, t = integrator iter = integrator.stats.naccept + # Compute the percentage of the simulation that is done + t = integrator.t + t_initial = first(integrator.sol.prob.tspan) + t_final = last(integrator.sol.prob.tspan) + sim_time_percentage = (t - t_initial) / (t_final - t_initial) * 100 + # Record performance measurements and compute performance index (PID) runtime_since_last_analysis = 1.0e-9 * (time_ns() - analysis_callback.start_time_last_analysis) @@ -291,8 +297,8 @@ function (analysis_callback::AnalysisCallback)(u_ode, du_ode, integrator, semi) " " * " └── GC time: " * @sprintf("%10.8e s (%5.3f%%)", gc_time_absolute, gc_time_percentage)) - mpi_println(" sim. time: " * @sprintf("%10.8e", t) * - " " * + mpi_println(rpad(" sim. time: " * + @sprintf("%10.8e (%5.3f%%)", t, sim_time_percentage), 46) * " time/DOF/rhs!: " * @sprintf("%10.8e s", runtime_relative)) mpi_println(" " * " " * " " *