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Merge branch 'main' into CommentsAllocs
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DanielDoehring authored Sep 13, 2024
2 parents 725ad2a + ef78716 commit 9798b53
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2 changes: 1 addition & 1 deletion .github/workflows/FormatCheck.yml
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ jobs:
# TODO: Change the call below to
# format(".")
run: |
julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.60"))'
julia -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
- name: Format check
run: |
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4 changes: 3 additions & 1 deletion Project.toml
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
name = "Trixi"
uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
version = "0.8.9-DEV"
version = "0.8.11-DEV"

[deps]
Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
Expand Down Expand Up @@ -60,6 +61,7 @@ TrixiConvexECOSExt = ["Convex", "ECOS"]
TrixiMakieExt = "Makie"

[compat]
Accessors = "0.1.12"
CodeTracking = "1.0.5"
ConstructionBase = "1.3"
Convex = "0.16"
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2 changes: 1 addition & 1 deletion docs/src/styleguide.md
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ PRs that verify that running JuliaFormatter.jl again will not change the source
To format your contributions before created a PR (or, at least, before requesting a review
of your PR), you need to install JuliaFormatter.jl first by running
```shell
julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))'
julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.60"))'
```
You can then recursively format the core Julia files in the Trixi.jl repo by executing
```shell
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1 change: 1 addition & 0 deletions src/Trixi.jl
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ module Trixi
# Include other packages that are used in Trixi.jl
# (standard library packages first, other packages next, all of them sorted alphabetically)

using Accessors: @reset
using LinearAlgebra: LinearAlgebra, Diagonal, diag, dot, mul!, norm, cross, normalize, I,
UniformScaling, det
using Printf: @printf, @sprintf, println
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5 changes: 5 additions & 0 deletions src/auxiliary/math.jl
Original file line number Diff line number Diff line change
Expand Up @@ -284,6 +284,11 @@ end
# when using `@fastmath`, which we also get from
# [Fortran](https://godbolt.org/z/Yrsa1js7P)
# or [C++](https://godbolt.org/z/674G7Pccv).
#
# Note however that such a custom reimplementation can cause incompatibilities with other
# packages. Currently we are affected by an issue with MPI.jl on ARM, see
# https://github.com/trixi-framework/Trixi.jl/issues/1922
# The workaround is to resort to Base.min / Base.max when using MPI reductions.
"""
Trixi.max(x, y, ...)
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2 changes: 1 addition & 1 deletion src/callbacks_step/alive.jl
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ function Base.show(io::IO, ::MIME"text/plain",
alive_callback = cb.affect!

setup = [
"interval" => alive_callback.alive_interval,
"interval" => alive_callback.alive_interval
]
summary_box(io, "AliveCallback", setup)
end
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3 changes: 2 additions & 1 deletion src/callbacks_step/analysis.jl
Original file line number Diff line number Diff line change
Expand Up @@ -434,7 +434,8 @@ function (analysis_callback::AnalysisCallback)(io, du, u, u_ode, t, semi)
res = maximum(abs, view(du, v, ..))
if mpi_isparallel()
# TODO: Debugging, here is a type instability
global_res = MPI.Reduce!(Ref(res), max, mpi_root(), mpi_comm())
# Base.max instead of max needed, see comment in src/auxiliary/math.jl
global_res = MPI.Reduce!(Ref(res), Base.max, mpi_root(), mpi_comm())
if mpi_isroot()
res::eltype(du) = global_res[]
end
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33 changes: 31 additions & 2 deletions src/callbacks_step/analysis_dg2d.jl
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,39 @@ function create_cache_analysis(analyzer, mesh::TreeMesh{2},
return (; u_local, u_tmp1, x_local, x_tmp1)
end

# Specialized cache for P4estMesh to allow for different ambient dimension from mesh dimension
function create_cache_analysis(analyzer, mesh::P4estMesh{2, NDIMS_AMBIENT},
equations, dg::DG, cache,
RealT, uEltype) where {NDIMS_AMBIENT}

# pre-allocate buffers
# We use `StrideArray`s here since these buffers are used in performance-critical
# places and the additional information passed to the compiler makes them faster
# than native `Array`s.
u_local = StrideArray(undef, uEltype,
StaticInt(nvariables(equations)), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)))
u_tmp1 = StrideArray(undef, uEltype,
StaticInt(nvariables(equations)), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(dg)))
x_local = StrideArray(undef, RealT,
StaticInt(NDIMS_AMBIENT), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)))
x_tmp1 = StrideArray(undef, RealT,
StaticInt(NDIMS_AMBIENT), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(dg)))
jacobian_local = StrideArray(undef, RealT,
StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)))
jacobian_tmp1 = StrideArray(undef, RealT,
StaticInt(nnodes(analyzer)), StaticInt(nnodes(dg)))

return (; u_local, u_tmp1, x_local, x_tmp1, jacobian_local, jacobian_tmp1)
end

function create_cache_analysis(analyzer,
mesh::Union{StructuredMesh{2}, StructuredMeshView{2},
UnstructuredMesh2D,
P4estMesh{2}, T8codeMesh{2}},
UnstructuredMesh2D, T8codeMesh{2}},
equations, dg::DG, cache,
RealT, uEltype)

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3 changes: 2 additions & 1 deletion src/callbacks_step/analysis_dg2d_parallel.jl
Original file line number Diff line number Diff line change
Expand Up @@ -131,7 +131,8 @@ function calc_error_norms(func, u, t, analyzer,
global_l2_error = Vector(l2_error)
global_linf_error = Vector(linf_error)
MPI.Reduce!(global_l2_error, +, mpi_root(), mpi_comm())
MPI.Reduce!(global_linf_error, max, mpi_root(), mpi_comm())
# Base.max instead of max needed, see comment in src/auxiliary/math.jl
MPI.Reduce!(global_linf_error, Base.max, mpi_root(), mpi_comm())
total_volume = MPI.Reduce(volume, +, mpi_root(), mpi_comm())
if mpi_isroot()
l2_error = convert(typeof(l2_error), global_l2_error)
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46 changes: 44 additions & 2 deletions src/callbacks_step/analysis_dg3d.jl
Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,51 @@ function create_cache_analysis(analyzer, mesh::TreeMesh{3},
return (; u_local, u_tmp1, u_tmp2, x_local, x_tmp1, x_tmp2)
end

# Specialized cache for P4estMesh to allow for different ambient dimension from mesh dimension
function create_cache_analysis(analyzer,
mesh::Union{StructuredMesh{3}, P4estMesh{3},
T8codeMesh{3}},
mesh::P4estMesh{3, NDIMS_AMBIENT},
equations, dg::DG, cache,
RealT, uEltype) where {NDIMS_AMBIENT}

# pre-allocate buffers
# We use `StrideArray`s here since these buffers are used in performance-critical
# places and the additional information passed to the compiler makes them faster
# than native `Array`s.
u_local = StrideArray(undef, uEltype,
StaticInt(nvariables(equations)), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)), StaticInt(nnodes(analyzer)))
u_tmp1 = StrideArray(undef, uEltype,
StaticInt(nvariables(equations)), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(dg)), StaticInt(nnodes(dg)))
u_tmp2 = StrideArray(undef, uEltype,
StaticInt(nvariables(equations)), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)), StaticInt(nnodes(dg)))
x_local = StrideArray(undef, RealT,
StaticInt(NDIMS_AMBIENT), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)), StaticInt(nnodes(analyzer)))
x_tmp1 = StrideArray(undef, RealT,
StaticInt(NDIMS_AMBIENT), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(dg)), StaticInt(nnodes(dg)))
x_tmp2 = StrideArray(undef, RealT,
StaticInt(NDIMS_AMBIENT), StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)), StaticInt(nnodes(dg)))
jacobian_local = StrideArray(undef, RealT,
StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)))
jacobian_tmp1 = StrideArray(undef, RealT,
StaticInt(nnodes(analyzer)), StaticInt(nnodes(dg)),
StaticInt(nnodes(dg)))
jacobian_tmp2 = StrideArray(undef, RealT,
StaticInt(nnodes(analyzer)),
StaticInt(nnodes(analyzer)), StaticInt(nnodes(dg)))

return (; u_local, u_tmp1, u_tmp2, x_local, x_tmp1, x_tmp2, jacobian_local,
jacobian_tmp1, jacobian_tmp2)
end

function create_cache_analysis(analyzer,
mesh::Union{StructuredMesh{3}, T8codeMesh{3}},
equations, dg::DG, cache,
RealT, uEltype)

Expand Down
3 changes: 2 additions & 1 deletion src/callbacks_step/analysis_dg3d_parallel.jl
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,8 @@ function calc_error_norms(func, u, t, analyzer,
global_l2_error = Vector(l2_error)
global_linf_error = Vector(linf_error)
MPI.Reduce!(global_l2_error, +, mpi_root(), mpi_comm())
MPI.Reduce!(global_linf_error, max, mpi_root(), mpi_comm())
# Base.max instead of max needed, see comment in src/auxiliary/math.jl
MPI.Reduce!(global_linf_error, Base.max, mpi_root(), mpi_comm())
total_volume = MPI.Reduce(volume, +, mpi_root(), mpi_comm())
if mpi_isroot()
l2_error = convert(typeof(l2_error), global_l2_error)
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/averaging.jl
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ function Base.show(io::IO, ::MIME"text/plain",

setup = [
"Start time" => first(averaging_callback.tspan),
"Final time" => last(averaging_callback.tspan),
"Final time" => last(averaging_callback.tspan)
]
summary_box(io, "AveragingCallback", setup)
end
Expand Down
7 changes: 5 additions & 2 deletions src/callbacks_step/glm_speed.jl
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ function Base.show(io::IO, ::MIME"text/plain",
setup = [
"GLM wave speed scaling" => glm_speed_callback.glm_scale,
"Expected CFL number" => glm_speed_callback.cfl,
"Selected semidiscretizations" => glm_speed_callback.semi_indices,
"Selected semidiscretizations" => glm_speed_callback.semi_indices
]
summary_box(io, "GlmSpeedCallback", setup)
end
Expand Down Expand Up @@ -83,7 +83,10 @@ function update_cleaning_speed!(semi, glm_speed_callback, dt)
c_h_deltat = calc_dt_for_cleaning_speed(cfl, mesh, equations, solver, cache)

# c_h is proportional to its own time step divided by the complete MHD time step
equations.c_h = glm_scale * c_h_deltat / dt
# We use @reset here since the equations are immutable (to work on GPUs etc.).
# Thus, we need to modify the equations field of the semidiscretization.
@reset equations.c_h = glm_scale * c_h_deltat / dt
semi.equations = equations

return semi
end
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/save_restart.jl
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ function Base.show(io::IO, ::MIME"text/plain",
"interval" => save_restart_callback.interval,
"save final solution" => save_restart_callback.save_final_restart ? "yes" :
"no",
"output directory" => abspath(normpath(save_restart_callback.output_directory)),
"output directory" => abspath(normpath(save_restart_callback.output_directory))
]
summary_box(io, "SaveRestartCallback", setup)
end
Expand Down
4 changes: 2 additions & 2 deletions src/callbacks_step/save_solution.jl
Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ function Base.show(io::IO, ::MIME"text/plain",
"yes" : "no",
"save final solution" => save_solution_callback.save_final_solution ?
"yes" : "no",
"output directory" => abspath(normpath(save_solution_callback.output_directory)),
"output directory" => abspath(normpath(save_solution_callback.output_directory))
]
summary_box(io, "SaveSolutionCallback", setup)
end
Expand All @@ -85,7 +85,7 @@ function Base.show(io::IO, ::MIME"text/plain",
"yes" : "no",
"save final solution" => save_solution_callback.save_final_solution ?
"yes" : "no",
"output directory" => abspath(normpath(save_solution_callback.output_directory)),
"output directory" => abspath(normpath(save_solution_callback.output_directory))
]
summary_box(io, "SaveSolutionCallback", setup)
end
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/steady_state.jl
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ function Base.show(io::IO, ::MIME"text/plain",

setup = [
"absolute tolerance" => steady_state_callback.abstol,
"relative tolerance" => steady_state_callback.reltol,
"relative tolerance" => steady_state_callback.reltol
]
summary_box(io, "SteadyStateCallback", setup)
end
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/stepsize.jl
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ function Base.show(io::IO, ::MIME"text/plain",
stepsize_callback = cb.affect!

setup = [
"CFL number" => stepsize_callback.cfl_number,
"CFL number" => stepsize_callback.cfl_number
]
summary_box(io, "StepsizeCallback", setup)
end
Expand Down
18 changes: 12 additions & 6 deletions src/callbacks_step/stepsize_dg2d.jl
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,8 @@ function max_dt(u, t, mesh::ParallelTreeMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -70,7 +71,8 @@ function max_dt(u, t, mesh::ParallelTreeMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand Down Expand Up @@ -154,7 +156,8 @@ function max_dt(u, t, mesh::ParallelP4estMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -170,7 +173,8 @@ function max_dt(u, t, mesh::ParallelP4estMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -186,7 +190,8 @@ function max_dt(u, t, mesh::ParallelT8codeMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -202,7 +207,8 @@ function max_dt(u, t, mesh::ParallelT8codeMesh{2},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand Down
12 changes: 8 additions & 4 deletions src/callbacks_step/stepsize_dg3d.jl
Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,8 @@ function max_dt(u, t, mesh::ParallelP4estMesh{3},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -146,7 +147,8 @@ function max_dt(u, t, mesh::ParallelP4estMesh{3},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -162,7 +164,8 @@ function max_dt(u, t, mesh::ParallelT8codeMesh{3},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand All @@ -178,7 +181,8 @@ function max_dt(u, t, mesh::ParallelT8codeMesh{3},
typeof(constant_speed), typeof(equations), typeof(dg),
typeof(cache)},
u, t, mesh, constant_speed, equations, dg, cache)
dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[]
# Base.min instead of min needed, see comment in src/auxiliary/math.jl
dt = MPI.Allreduce!(Ref(dt), Base.min, mpi_comm())[]

return dt
end
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/time_series.jl
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ function Base.show(io::IO, ::MIME"text/plain",
"interval" => time_series_callback.interval,
"solution_variables" => time_series_callback.solution_variables,
"output_directory" => time_series_callback.output_directory,
"filename" => time_series_callback.filename,
"filename" => time_series_callback.filename
]
summary_box(io, "TimeSeriesCallback", setup)
end
Expand Down
2 changes: 1 addition & 1 deletion src/callbacks_step/visualization.jl
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ function Base.show(io::IO, ::MIME"text/plain",
"variable names" => visualization_callback.variable_names,
"show mesh" => visualization_callback.show_mesh,
"plot creator" => visualization_callback.plot_creator,
"plot data creator" => visualization_callback.plot_data_creator,
"plot data creator" => visualization_callback.plot_data_creator
]
summary_box(io, "VisualizationCallback", setup)
end
Expand Down
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