Merge branch 'main' into tm/autodiff_metrics

Author: tristanmontoya

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/[email protected].1
+        uses: crate-ci/[email protected].2

Project.toml

@@ -33,5 +33,5 @@ Static = "0.8, 1"
 StaticArrayInterface = "1.5.1"
 StaticArrays = "1"
 StrideArrays = "0.1.28"
-Trixi = "0.9.9, 0.10, 0.11"
+Trixi = "0.9.9, 0.10, 0.11, 0.12"
 julia = "1.9"

docs/make.jl

@@ -10,8 +10,8 @@ end
 using TrixiAtmo
 
 # Provide external links to the Trixi.jl docs (project root and inventory file)
-links = InterLinks("Trixi" => ("https://trixi-framework.github.io/Trixi.jl/stable/",
-                               "https://trixi-framework.github.io/Trixi.jl/stable/objects.inv"))
+links = InterLinks("Trixi" => ("https://trixi-framework.github.io/TrixiDocumentation/stable/",
+                               "https://trixi-framework.github.io/TrixiDocumentation/stable/objects.inv"))
 
 DocMeta.setdocmeta!(TrixiAtmo, :DocTestSetup, :(using TrixiAtmo);
                     recursive = true)

src/equations/shallow_water_3d.jl

@@ -37,7 +37,7 @@ This affects the implementation and use of these equations in various ways:
 * The flux values corresponding to the bottom topography must be zero.
 * The bottom topography values must be included when defining initial conditions, boundary conditions or
   source terms.
-* [`AnalysisCallback`](https://trixi-framework.github.io/Trixi.jl/stable/reference-trixi/#Trixi.AnalysisCallback) analyzes this variable.
+* [`AnalysisCallback`](https://trixi-framework.github.io/TrixiDocumentation/stable/reference-trixi/#Trixi.AnalysisCallback) analyzes this variable.
 * Trixi.jl's visualization tools will visualize the bottom topography by default.
 
 References:
@@ -115,8 +115,9 @@ end
 end
 
 """
-    flux_wintermeyer_etal(u_ll, u_rr, orientation_or_normal_direction,
-                          equations::ShallowWaterEquations2D)
+    flux_wintermeyer_etal(u_ll, u_rr,
+                          normal_direction::AbstractVector,
+                          equations::ShallowWaterEquations3D)
 
 Total energy conservative (mathematical entropy for shallow water equations) split form.
 When the bottom topography is nonzero this scheme will be well-balanced when used as a `volume_flux`.
@@ -160,8 +161,9 @@ Further details are available in Theorem 1 of the paper:
 end
 
 """
-    flux_fjordholm_etal(u_ll, u_rr, orientation,
-                        equations::ShallowWaterEquations1D)
+    flux_fjordholm_etal(u_ll, u_rr,
+                        normal_direction::AbstractVector,
+                        equations::ShallowWaterEquations3D)
 
 Total energy conservative (mathematical entropy for shallow water equations). When the bottom topography
 is nonzero this should only be used as a surface flux otherwise the scheme will not be well-balanced.

test/Project.toml

@@ -5,11 +5,13 @@ OrdinaryDiffEqLowStorageRK = "b0944070-b475-4768-8dec-fb6eb410534d"
 OrdinaryDiffEqSSPRK = "669c94d9-1f4b-4b64-b377-1aa079aa2388"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
+TrixiTest = "0a316866-cbd0-4425-8bcb-08103b2c1f26"
 
 [compat]
 NLsolve = "4.5.1"
 OrdinaryDiffEq = "6.91"
 OrdinaryDiffEqLowStorageRK = "1.2"
 OrdinaryDiffEqSSPRK = "1.2"
 Test = "1"
-Trixi = "0.9.9, 0.10, 0.11"
+Trixi = "0.9.9, 0.10, 0.11, 0.12"
+TrixiTest = "0.1"

test/runtests.jl

@@ -4,28 +4,41 @@ using Test
 # variable to determine the subset of tests to execute.
 #
 # We could do the same once we have a lot of tests
-const TRIXIATMO_TEST = get(ENV, "TRIXIATMO_TEST", "all")
-const TRIXIATMO_MPI_NPROCS = clamp(Sys.CPU_THREADS, 2, 3)
-const TRIXIATMO_NTHREADS = clamp(Sys.CPU_THREADS, 2, 3)
+const TRIXI_TEST = get(ENV, "TRIXI_TEST", "all")
+const TRIXI_MPI_NPROCS = clamp(Sys.CPU_THREADS, 2, 3)
+const TRIXI_NTHREADS = clamp(Sys.CPU_THREADS, 2, 3)
 
 @time @testset verbose=true showtiming=true "TrixiAtmo.jl tests" begin
-    @time if TRIXIATMO_TEST == "all" || TRIXIATMO_TEST == "trixi_consistency"
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "trixi_consistency"
         include("test_trixi_consistency.jl")
     end
 
-    @time if TRIXIATMO_TEST == "all" || TRIXIATMO_TEST == "moist_euler"
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "moist_euler"
         include("test_2d_moist_euler.jl")
     end
 
-    @time if TRIXIATMO_TEST == "all" || TRIXIATMO_TEST == "spherical_advection"
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "spherical_advection"
         include("test_spherical_advection.jl")
     end
 
-    @time if TRIXIATMO_TEST == "all" || TRIXIATMO_TEST == "shallow_water_3d"
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "shallow_water_3d"
         include("test_3d_shallow_water.jl")
     end
 
-    @time if TRIXIATMO_TEST == "all" || TRIXIATMO_TEST == "shallow_water_2d_covariant"
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "shallow_water_2d_covariant"
         include("test_2d_shallow_water_covariant.jl")
     end
+
+    @time if TRIXI_TEST == "all" || TRIXI_TEST == "threaded"
+        # Do a dummy `@test true`:
+        # If the process errors out the testset would error out as well,
+        # cf. https://github.com/JuliaParallel/MPI.jl/pull/391
+        @test true
+
+        run(`$(Base.julia_cmd()) --threads=$TRIXI_NTHREADS --check-bounds=yes --code-coverage=none $(abspath("test_threaded.jl"))`)
+    end
+
+    @time if TRIXI_TEST == "upstream"
+        include("test_trixi_consistency.jl")
+    end
 end

test/test_threaded.jl

@@ -0,0 +1,44 @@
+module TestThreaded
+
+using Test
+using TrixiAtmo
+
+include("test_trixiatmo.jl") # TODO - This is a repetition from Trixi.jl
+
+EXAMPLES_DIR = pkgdir(TrixiAtmo, "examples")
+
+@testset "Threaded tests" begin
+#! format: noindent
+
+@trixiatmo_testset "elixir_moist_euler_moist_bubble" begin
+    @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_moist_euler_moist_bubble.jl"),
+                        l2=[
+                            7.351043427240923e-6,
+                            1.1070342432069074e-7,
+                            0.0006974588377288118,
+                            1.715668353329522,
+                            8.831269143134121e-7,
+                            1.025579538944668e-6
+                        ],
+                        linf=[
+                            8.055695643149896e-5,
+                            1.1985203677080201e-6,
+                            0.005897639251024437,
+                            19.24776030163048,
+                            1.0043133039065386e-5,
+                            1.1439046776775402e-5
+                        ],
+                        polydeg=3,
+                        cells_per_dimension=(16, 8),
+                        tspan=(0.0, 0.1))
+    # Ensure that we do not have excessive memory allocations
+    # (e.g., from type instabilities)
+    let
+        t = sol.t[end]
+        u_ode = sol.u[end]
+        du_ode = similar(u_ode)
+        @test (@allocated TrixiAtmo.Trixi.rhs!(du_ode, u_ode, semi, t)) < 2000
+    end
+end
+end
+end # module

test/test_trixiatmo.jl

@@ -1,4 +1,5 @@
 using Test: @test
+using TrixiTest: @trixi_test_nowarn
 using Trixi: Trixi, examples_dir, trixi_include
 import TrixiAtmo
 
@@ -125,55 +126,16 @@ end
 
 # Modified version of `@test_nowarn` that prints the content of `stderr` when
 # it is not empty and ignores module replacements.
-macro test_nowarn_mod(expr, additional_ignore_content = String[])
+macro test_nowarn_mod(expr, additional_ignore_content = [])
     quote
-        let fname = tempname()
-            try
-                ret = open(fname, "w") do f
-                    redirect_stderr(f) do
-                        $(esc(expr))
-                    end
-                end
-                stderr_content = read(fname, String)
-                if !isempty(stderr_content)
-                    println("Content of `stderr`:\n", stderr_content)
-                end
-
-                # Patterns matching the following ones will be ignored. Additional patterns
-                # passed as arguments can also be regular expressions, so we just use the
-                # type `Any` for `ignore_content`.
-                ignore_content = Any[
-                                     # We need to ignore steady state information reported by our callbacks
-                                     r"┌ Info:   Steady state tolerance reached\n│   steady_state_callback .+\n└   t = .+\n",
-                                     # We also ignore our own compilation messages
-                                     "[ Info: You just called `trixi_include`. Julia may now compile the code, please be patient.\n",
-                                     # TODO: Upstream (PlotUtils). This should be removed again once the
-                                     #       deprecated stuff is fixed upstream.
-                                     "WARNING: importing deprecated binding Colors.RGB1 into Plots.\n",
-                                     "WARNING: importing deprecated binding Colors.RGB4 into Plots.\n",
-                                     r"┌ Warning: Keyword argument letter not supported with Plots.+\n└ @ Plots.+\n",
-                                     r"┌ Warning: `parse\(::Type, ::Coloarant\)` is deprecated.+\n│.+\n│.+\n└ @ Plots.+\n",
-                                     # TODO: Silence warning introduced by Flux v0.13.13. Should be properly fixed.
-                                     r"┌ Warning: Layer with Float32 parameters got Float64 input.+\n│.+\n│.+\n│.+\n└ @ Flux.+\n",
-                                     # NOTE: These warnings arose from Julia 1.10 onwards
-                                     r"WARNING: Method definition .* in module .* at .* overwritten .*.\n",
-                                     # Warnings from third party packages
-                                     r"┌ Warning: Problem status ALMOST_INFEASIBLE; solution may be inaccurate.\n└ @ Convex ~/.julia/packages/Convex/.*\n",
-                                     r"┌ Warning: Problem status ALMOST_OPTIMAL; solution may be inaccurate.\n└ @ Convex ~/.julia/packages/Convex/.*\n"]
-                append!(ignore_content, $additional_ignore_content)
-                for pattern in ignore_content
-                    stderr_content = replace(stderr_content, pattern => "")
-                end
-
-                # We also ignore simple module redefinitions for convenience. Thus, we
-                # check whether every line of `stderr_content` is of the form of a
-                # module replacement warning.
-                @test occursin(r"^(WARNING: replacing module .+\.\n)*$", stderr_content)
-                ret
-            finally
-                rm(fname, force = true)
-            end
-        end
+        add_to_additional_ignore_content = [
+            # We need to ignore steady state information reported by our callbacks
+            r"┌ Info:   Steady state tolerance reached\n│   steady_state_callback .+\n└   t = .+\n",
+            # NOTE: These warnings arose from Julia 1.10 onwards
+            r"WARNING: Method definition .* in module .* at .* overwritten .*.\n"
+        ]
+        append!($additional_ignore_content, add_to_additional_ignore_content)
+        @trixi_test_nowarn $(esc(expr)) $additional_ignore_content
     end
 end