Read in capacity for parallel TreeMesh

examples/tree_2d_dgsem/elixir_advection_restart_amr.jl

@@ -0,0 +1,58 @@
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# Define time integration algorithm
+alg = CarpenterKennedy2N54(williamson_condition = false)
+# Create a restart file
+trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_extended.jl"), alg = alg,
+              tspan = (0.0, 3.0))
+
+###############################################################################
+# adapt the parameters that have changed compared to "elixir_advection_extended.jl"
+
+# Note: If you get a restart file from somewhere else, you need to provide
+# appropriate setups in the elixir loading a restart file
+
+restart_filename = joinpath("out", "restart_000040.h5")
+mesh = load_mesh(restart_filename)
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
+
+tspan = (load_time(restart_filename), 5.0)
+dt = load_dt(restart_filename)
+ode = semidiscretize(semi, tspan, restart_filename);
+
+# Do not overwrite the initial snapshot written by elixir_advection_extended.jl.
+save_solution.condition.save_initial_solution = false
+
+# Add AMR callback
+amr_controller = ControllerThreeLevel(semi, IndicatorMax(semi, variable = first),
+                                      base_level = 3,
+                                      med_level = 4, med_threshold = 0.8,
+                                      max_level = 5, max_threshold = 1.2)
+amr_callback = AMRCallback(semi, amr_controller,
+                           interval = 5,
+                           adapt_initial_condition = false,
+                           adapt_initial_condition_only_refine = true)
+callbacks_ext = CallbackSet(amr_callback, callbacks.discrete_callbacks...)
+
+integrator = init(ode, alg,
+                  dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
+                  callback = callbacks_ext, maxiters = 100_000; ode_default_options()...)
+
+# Load saved context for adaptive time integrator
+if integrator.opts.adaptive
+    load_adaptive_time_integrator!(integrator, restart_filename)
+end
+
+# Get the last time index and work with that.
+load_timestep!(integrator, restart_filename)
+
+###############################################################################
+# run the simulation
+
+sol = solve!(integrator)
+
+summary_callback() # print the timer summary

src/meshes/mesh_io.jl

@@ -370,17 +370,18 @@ function load_mesh_parallel(mesh_file::AbstractString; n_cells_max, RealT)
 
     if mesh_type == "TreeMesh"
         if mpi_isroot()
-            n_cells = h5open(mesh_file, "r") do file
-                read(attributes(file)["n_cells"])
+            n_cells, capacity = h5open(mesh_file, "r") do file
+                return read(attributes(file)["n_cells"]),
+                       read(attributes(file)["capacity"])
             end
-            MPI.Bcast!(Ref(ndims_), mpi_root(), mpi_comm())
             MPI.Bcast!(Ref(n_cells), mpi_root(), mpi_comm())
+            MPI.Bcast!(Ref(capacity), mpi_root(), mpi_comm())
         else
-            ndims_ = MPI.Bcast!(Ref(0), mpi_root(), mpi_comm())[]
             n_cells = MPI.Bcast!(Ref(0), mpi_root(), mpi_comm())[]
+            capacity = MPI.Bcast!(Ref(0), mpi_root(), mpi_comm())[]
         end
 
-        mesh = TreeMesh(ParallelTree{ndims_}, max(n_cells, n_cells_max))
+        mesh = TreeMesh(ParallelTree{ndims_}, max(n_cells, n_cells_max, capacity))
         load_mesh!(mesh, mesh_file)
     elseif mesh_type == "P4estMesh"
         if mpi_isroot()

test/test_mpi_tree.jl

@@ -70,6 +70,14 @@ CI_ON_WINDOWS = (get(ENV, "GITHUB_ACTIONS", false) == "true") && Sys.iswindows()
                             coverage_override=(maxiters = 6,))
     end
 
+    @trixi_testset "elixir_advection_restart_amr.jl" begin
+        @test_trixi_include(joinpath(EXAMPLES_DIR,
+                                     "elixir_advection_restart_amr.jl"),
+                            l2=[7.870371848717432e-5],
+                            linf=[0.0007374081713964475],
+                            coverage_override=(maxiters = 50,))
+    end
+
     # Linear scalar advection with AMR
     # These example files are only for testing purposes and have no practical use
     @trixi_testset "elixir_advection_amr_refine_twice.jl" begin