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Use VectorOfArray in wrap_array for DGMulti solvers (#2150)
* update bound on RecursiveArrayTools to have access to 3.27.3 d * comment out broken precompile statements * adding VoA for DGMulti * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * run `Trixi.rhs!` twice to try to avoid excessive allocations * bump lower compat of RecursiveArrayTools * run Trixi.rhs! twice to reduce allocation count * update l2, linf errors * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update test/test_dgmulti_2d.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Update test/test_dgmulti_2d.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Apply suggestions from code review Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * bump LinearAlgebra lower compat for Downgrade CI * fixing one precompile statement * Revert "fixing one precompile statement" This reverts commit 1b700bc. * change mu::Float64 to mu::Function in elixir * update CI * Formatting suggestions Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix threaded CI test values * bump LinearAlgebra compat to fix threaded_legacy tests * Update test/test_threaded.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * unwrap VoA for jacobian computations * unwrap VoA for PlotData1D/PlotData2D * Update src/semidiscretization/semidiscretization.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update src/visualization/types.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Unpack VoA for visualization test * bump Julia compat and ci.yml to v1.10 * Update test/test_visualization.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * fix VoA in test_visualization * Update test/test_dgmulti_3d.jl * Update test/test_dgmulti_3d.jl * uncommenting precompile statement * Auto stash before merge of "jc/wrap_VectorOfArray" and "origin/jc/wrap_VectorOfArray" * removing IfElse.jl from Project.toml (why did I add this?) * mark allocation tests as broken for now * mark allocation tests as broken for now mark all 1D allocated tests as broken for now * update dgmulti tests * remove @test_broken for passing tests * update DGMulti FDSBP 3D CI values * update parabolic dispatch * update parabolic dispatch update parabolic dispatch * Apply suggestions from code review Formatting Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Remove additional Trixi.rhs! call in tests * Reduce number of allowed allocations * remove additional Trixi.rhs! calls and reduce number of allowed allocations * remove more Trixi.rhs! calls * format * clean up parabolic rhs test * Update test/test_parabolic_2d.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * Update test/test_dgmulti_1d.jl Co-authored-by: Joshua Lampert <[email protected]> * use CFL based time stepping to fix positivity issue * format * fix docs * fix test values (use the ones I get locally) * Keep mu as a constant instead of a function * try to fix precompiling of summary callback * fix precompile * try compat "1" for LinearAlgebra * revert precompile stuff * remove #= FIXME comments * Update test/test_parabolic_3d.jl Co-authored-by: Joshua Lampert <[email protected]> * Update test/test_parabolic_3d.jl Co-authored-by: Joshua Lampert <[email protected]> * add news and bump dev version --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Joshua Lampert <[email protected]>
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‎NEWS.md‎

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@@ -4,6 +4,23 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
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used in the Julia ecosystem. Notable changes will be documented in this file
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for human readability.
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## Changes when updating to v0.10 from v0.9.x
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#### Added
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#### Changed
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- The numerical solution is wrapped in a `VectorOfArrays` from
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[RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl)
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for `DGMulti` solvers ([#2150]). You can use `Base.parent` to unwrap
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the original data.
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#### Deprecated
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#### Removed
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## Changes in the v0.9 lifecycle
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#### Added
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- The required Julia version is updated to v1.10.
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## Changes when updating to v0.9 from v0.8.x
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#### Added

‎Project.toml‎

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name = "Trixi"
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uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
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authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
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version = "0.9.18-DEV"
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version = "0.10.0-DEV"
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[deps]
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Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"

‎docs/src/visualization.md‎

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@@ -174,7 +174,7 @@ julia> compute_vorticity(velocity, semi) =
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compute_vorticity(velocity, Trixi.mesh_equations_solver_cache(semi)...);
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julia> function get_velocity(sol)
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rho, rhou, rhov, E = StructArrays.components(sol.u[end])
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rho, rhou, rhov, E = StructArrays.components(Base.parent(sol.u[end]))
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v1 = rhou ./ rho
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v2 = rhov ./ rho
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return v1, v2

‎examples/dgmulti_1d/elixir_euler_shu_osher_gauss_shock_capturing.jl‎

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equations = CompressibleEulerEquations1D(gamma_gas)
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###############################################################################
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# setup the GSBP DG discretization that uses the Gauss operators from
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# Chan, Del Rey Fernandez, Carpenter (2019).
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# setup the GSBP DG discretization that uses the Gauss operators from
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# Chan, Del Rey Fernandez, Carpenter (2019).
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# [https://doi.org/10.1137/18M1209234](https://doi.org/10.1137/18M1209234)
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# Shu-Osher initial condition for 1D compressible Euler equations
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v_left = 4 * sqrt(35) / 9
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p_left = 31 / 3
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# Replaced v_right = 0 to v_right = 0.1 to avoid positivity issues.
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v_right = 0.1
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v_right = 0.0
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p_right = 1.0
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rho = ifelse(x[1] > x0, 1 + 1 / 5 * sin(5 * x[1]), rho_left)
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analysis_callback = AnalysisCallback(semi, interval = 100, uEltype = real(dg))
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# handles the re-calculation of the maximum Δt after each time step
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stepsize_callback = StepsizeCallback(cfl = 0.1)
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stepsize_callback = StepsizeCallback(cfl = 0.2)
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# collect all callbacks such that they can be passed to the ODE solver
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callbacks = CallbackSet(summary_callback, analysis_callback, stepsize_callback)
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# ###############################################################################
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# # run the simulation
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sol = solve(ode, SSPRK43(), adaptive = true, callback = callbacks, save_everystep = false)
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sol = solve(ode, SSPRK43(), adaptive = false,
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dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
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callback = callbacks, save_everystep = false)

‎src/Trixi.jl‎

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using P4est
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using T8code
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using RecipesBase: RecipesBase
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using RecursiveArrayTools: VectorOfArray
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using Requires: @require
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using Static: Static, One, True, False
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@reexport using StaticArrays: SVector

‎src/semidiscretization/semidiscretization.jl‎

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return J
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end
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# unpack u if it is wrapped in VectorOfArray (mainly for DGMulti solvers)
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jacobian_ad_forward(semi::AbstractSemidiscretization, t0, u0_ode::VectorOfArray) = jacobian_ad_forward(semi,
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t0,
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parent(u0_ode))
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# This version is specialized to `StructArray`s used by some `DGMulti` solvers.
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# We need to convert the numerical solution vectors since ForwardDiff cannot
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# handle arrays of `SVector`s.

‎src/solvers/dgmulti/dg.jl‎

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# interface with semidiscretization_hyperbolic
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wrap_array(u_ode, mesh::DGMultiMesh, equations, dg::DGMulti, cache) = u_ode
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wrap_array_native(u_ode, mesh::DGMultiMesh, equations, dg::DGMulti, cache) = u_ode
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# used to initialize `u_ode` in `semidiscretize`
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function allocate_coefficients(mesh::DGMultiMesh, equations, dg::DGMulti, cache)
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return VectorOfArray(allocate_nested_array(real(dg), nvariables(equations),
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size(mesh.md.x), dg))
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end
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wrap_array(u_ode::VectorOfArray, mesh::DGMultiMesh, equations, dg::DGMulti, cache) = parent(u_ode)
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function digest_boundary_conditions(boundary_conditions::NamedTuple{Keys, ValueTypes},
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mesh::DGMultiMesh,
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dg::DGMulti,
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local_values_threaded, flux_threaded, rotated_flux_threaded)
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end
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function allocate_coefficients(mesh::DGMultiMesh, equations, dg::DGMulti, cache)
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return allocate_nested_array(real(dg), nvariables(equations), size(mesh.md.x), dg)
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end
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function compute_coefficients!(u, initial_condition, t,
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mesh::DGMultiMesh, equations, dg::DGMulti, cache)
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md = mesh.md

‎src/solvers/dgmulti/flux_differencing_gauss_sbp.jl‎

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@inline function tensor_product_gauss_face_operator!(out::AbstractVector,
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A::TensorProductGaussFaceOperator{2, Interpolation},
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x_in::AbstractVector)
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#! format: on
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#! format: on
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(; interp_matrix_gauss_to_face_1d, face_indices_tensor_product) = A
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(; nnodes_1d) = A
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@inline function tensor_product_gauss_face_operator!(out::AbstractVector,
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A::TensorProductGaussFaceOperator{3, Interpolation},
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x::AbstractVector)
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#! format: on
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#! format: on
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(; interp_matrix_gauss_to_face_1d, face_indices_tensor_product) = A
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@inline function tensor_product_gauss_face_operator!(out_vec::AbstractVector,
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#! format: on
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(; interp_matrix_gauss_to_face_1d, face_indices_tensor_product) = A
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@inline function tensor_product_gauss_face_operator!(out_vec::AbstractVector,
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#! format: on
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#! format: on
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@unpack interp_matrix_gauss_to_face_1d, face_indices_tensor_product = A
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@unpack inv_volume_weights_1d, nnodes_1d, nfaces = A
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‎src/visualization/types.jl‎

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# unwrap u if it is VectorOfArray
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PlotData1D(u::VectorOfArray, mesh, equations, dg::DGMulti{1}, cache; kwargs...) = PlotData1D(parent(u),
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mesh,
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equations,
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dg,
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cache;
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kwargs...)
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PlotData2D(u::VectorOfArray, mesh, equations, dg::DGMulti{2}, cache; kwargs...) = PlotData2D(parent(u),
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mesh,
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equations,
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dg,
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cache;
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kwargs...)
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function PlotData1D(u, mesh, equations, solver, cache;
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‎test/test_dgmulti_1d.jl‎

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"elixir_euler_shu_osher_gauss_shock_capturing.jl"),
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cells_per_dimension=(64,), tspan=(0.0, 1.0),
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l2=[
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1.673813320412685,
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5.980737909458242,
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21.587822949251173
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1.6967151731067875,
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6.018445633981826,
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21.77425594743242
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],
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linf=[
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3.1388039126918064,
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10.630952212105246,
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37.682826521024865
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3.2229876650556477,
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10.702690533393842,
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# Ensure that we do not have excessive memory allocations
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approximation_type=SBP(),
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l2=[
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3.002634351734614e-16,
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1.1636653574178203e-15
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3.0300196635805022e-6,
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1.1012004949980629e-15
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linf=[
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5.346754311919e-5,
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2.220446049250313e-15
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])

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