Use OrdinaryDiffEqTsit5.jl and OrdinaryDiffEqLowStorageRK.jl (#163)

* use OrdinaryDiffEqTsit5.jl everywhere * also use OrdinaryDiffEqLowStorageRK where necessary * drop support for Julia v1.9 * skipt Test * compat bound for OrdinaryDiffEqLowStorage * bump compat of DiffEqBase * bump compat of SciMLBase * bump compat of FastBroadcast to 0.3.1 * bump compat of RecursiveArrayTools * bump compat of RecipesBase * bump compat of FastBroadcast * bump compat of RecursiveArrayTools * bump compat of Interpolations * bump compat of Reexport * bump compat of FastBroadcast * bump compat of RecursiveArrayToools * bump compat of StaticArrays * bump compat of DiffEqBase * bump compat of SciMLBase * bump compat of OrdinaryDiffEq* * try (temporarily) fixing benchmark * remove OrdinaryDiffEq again * allow higher allocations Julia v1.11 reports more allocations in some cases
JoshuaLampert · Dec 4, 2024 · 83a753a · 83a753a
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -54,7 +54,7 @@ jobs:
           - macos-latest
           - windows-latest
         include:
-          - version: '1.9'
+          - version: '1.11'
             os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
@@ -35,7 +35,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.9'
+          version: '1.10'
           show-versioninfo: true
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1

diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml
@@ -35,7 +35,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.9'
+          - '1.10'
           # - '~1.9.0-0' # including development versions
           # - 'nightly'
         os:
@@ -49,7 +49,7 @@ jobs:
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-downgrade-compat@v1
         with:
-          skip: LinearAlgebra,Printf,SparseArrays
+          skip: LinearAlgebra,Printf,SparseArrays,Test
           projects: ., test
       - uses: julia-actions/julia-buildpkg@v1
         env:

diff --git a/Project.toml b/Project.toml
@@ -25,21 +25,21 @@ TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
 BandedMatrices = "1"
-DiffEqBase = "6.143"
-FastBroadcast = "0.2.8, 0.3"
-Interpolations = "0.14.2, 0.15"
+DiffEqBase = "6.157"
+FastBroadcast = "0.3.5"
+Interpolations = "0.15.1"
 LinearAlgebra = "1"
 PolynomialBases = "0.4.15"
 Printf = "1"
-RecipesBase = "1.2"
-RecursiveArrayTools = "3.3"
-Reexport = "1.0"
+RecipesBase = "1.3.4"
+RecursiveArrayTools = "3.27"
+Reexport = "1.2.2"
 Roots = "2.0.17"
-SciMLBase = "2.11"
+SciMLBase = "2.56"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
-StaticArrays = "1"
+StaticArrays = "1.9.7"
 SummationByPartsOperators = "0.5.63"
 TimerOutputs = "0.5.7"
 TrixiBase = "0.1.3"
-julia = "1.9"
+julia = "1.10"
diff --git a/README.md b/README.md
@@ -25,35 +25,46 @@ A more detailed documentation can be found [online](https://JoshuaLampert.github
 ## Installation
 
 If you have not yet installed Julia, then you first need to [download Julia](https://julialang.org/downloads/). Please [follow the instructions for your operating system](https://julialang.org/downloads/platform/).
-DispersiveShallowWater.jl works with Julia v1.9 and newer. DispersiveShallowWater.jl is a registered Julia package. Therefore, you can install it by executing the following commands from the Julia REPL
+DispersiveShallowWater.jl works with Julia v1.10 and newer. DispersiveShallowWater.jl is a registered Julia package. Therefore, you can install it by executing the following commands from the Julia REPL
+
 ```julia
 julia> using Pkg
 
-julia> Pkg.add(["DispersiveShallowWater", "OrdinaryDiffEq", "Plots"])
+julia> Pkg.add(["DispersiveShallowWater", "OrdinaryDiffEqTsit5", "Plots"])
 ```
-In addition, this installs the packages [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) used for time-integration and [Plots.jl](https://github.com/JuliaPlots/Plots.jl) to visualize the results.
+
+In addition, this installs the packages OrdinaryDiffEqTsit5.jl from [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl)
+used for time-integration and [Plots.jl](https://github.com/JuliaPlots/Plots.jl) to visualize the results. If you want to use
+other time integration methods than `Tsit5`, you can install the respective subpackage or OrdinaryDiffEq.jl, which will install
+every available solver.
 If you want to use other SBP operators than the default operators that DispersiveShallowWater.jl uses, then you also need [SummationByPartsOperators.jl](https://github.com/ranocha/SummationByPartsOperators.jl),
 which can be installed running
+
 ```julia
 julia> Pkg.add("SummationByPartsOperators")
 ```
 
 ## Usage
 
 In the Julia REPL, first load the package DispersiveShallowWater.jl
+
 ```julia
 julia> using DispersiveShallowWater
 ```
 
 You can run a basic simulation that solves the BBM-BBM equations by executing
+
 ```julia
 julia> include(default_example());
 ```
+
 The result can be visualized by using the package Plots.jl
+
 ```julia
 julia> using Plots
 julia> plot(semi => sol)
 ```
+
 The command `plot` expects a `Pair` consisting of a `Semidiscretization` and an `ODESolution`. The visualization can also be customized, see the [documentation](https://JoshuaLampert.github.io/DispersiveShallowWater.jl/stable/overview#visualize_results)
 for more details. Other examples can be found in the subdirectory [examples/](https://github.com/JoshuaLampert/DispersiveShallowWater.jl/tree/main/examples).
 A list of all examples is returned by running `get_examples()`. You can pass the filename of one of the examples or your own simulation file to `include` in order to run it,
@@ -62,6 +73,7 @@ e.g., `include(joinpath(examples_dir(), "svaerd_kalisch_1d", "svaerd_kalisch_1d_
 ## Referencing
 
 You can directly refer to DispersiveShallowWater.jl as
+
 ```bibtex
 @misc{lampert2023dispersive,
   title={{D}ispersive{S}hallow{W}ater.jl: {S}tructure-preserving numerical

diff --git a/benchmark/Project.toml b/benchmark/Project.toml
@@ -1,9 +1,11 @@
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqLowStorageRK = "b0944070-b475-4768-8dec-fb6eb410534d"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 SummationByPartsOperators = "9f78cca6-572e-554e-b819-917d2f1cf240"
 
 [compat]
 BenchmarkTools = "1"
-OrdinaryDiffEq = "6.49.1"
+OrdinaryDiffEqLowStorageRK = "1"
+OrdinaryDiffEqTsit5 = "1"
 SummationByPartsOperators = "0.5.63"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,15 +1,15 @@
 [deps]
 Changelog = "5217a498-cd5d-4ec6-b8c2-9b85a09b6e3e"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 SummationByPartsOperators = "9f78cca6-572e-554e-b819-917d2f1cf240"
 TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
 Changelog = "1"
 Documenter = "1"
-OrdinaryDiffEq = "6.49.1"
+OrdinaryDiffEqTsit5 = "1"
 Plots = "1.9"
 SummationByPartsOperators = "0.5.41"
 TrixiBase = "0.1.1"
diff --git a/docs/src/development.md b/docs/src/development.md
@@ -19,7 +19,7 @@ cd DispersiveShallowWater
 mkdir run
 cd run
 julia --project=. -e 'using Pkg; Pkg.develop(PackageSpec(path=".."))' # Install local DispersiveShallowWater.jl clone
-julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots", "SummationByPartsOperators"])' # Install additional packages
+julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEqTsit5", "Plots", "SummationByPartsOperators"])' # Install additional packages
 ```
 
 If you use other packages for executing DispersiveShallowWater.jl, you can add them to the project in the `run`

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -24,35 +24,46 @@ Fully discrete entropy-conservative methods can be obtained by using the [relaxa
 ## Installation
 
 If you have not yet installed Julia, then you first need to [download Julia](https://julialang.org/downloads/). Please [follow the instructions for your operating system](https://julialang.org/downloads/platform/).
-DispersiveShallowWater.jl works with Julia v1.9 and newer. DispersiveShallowWater.jl is a registered Julia package. Therefore, you can install it by executing the following commands from the Julia REPL
+DispersiveShallowWater.jl works with Julia v1.10 and newer. DispersiveShallowWater.jl is a registered Julia package. Therefore, you can install it by executing the following commands from the Julia REPL
+
 ```julia
 julia> using Pkg
 
-julia> Pkg.add(["DispersiveShallowWater", "OrdinaryDiffEq", "Plots"])
+julia> Pkg.add(["DispersiveShallowWater", "OrdinaryDiffEqTsit5", "Plots"])
 ```
-In addition, this installs the packages [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) used for time-integration and [Plots.jl](https://github.com/JuliaPlots/Plots.jl) to visualize the results.
+
+In addition, this installs the packages OrdinaryDiffEqTsit5.jl from [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl)
+used for time-integration and [Plots.jl](https://github.com/JuliaPlots/Plots.jl) to visualize the results. If you want to use
+other time integration methods than `Tsit5`, you can install the respective subpackage or OrdinaryDiffEq.jl, which will install
+every available solver.
 If you want to use other SBP operators than the default operators that DispersiveShallowWater.jl uses, then you also need [SummationByPartsOperators.jl](https://github.com/ranocha/SummationByPartsOperators.jl),
 which can be installed running
+
 ```julia
 julia> Pkg.add("SummationByPartsOperators")
 ```
 
 ## Usage
 
 In the Julia REPL, first load the package DispersiveShallowWater.jl
+
 ```julia
 julia> using DispersiveShallowWater
 ```
 
 You can run a basic simulation that solves the BBM-BBM equations by executing
+
 ```julia
 julia> include(default_example());
 ```
+
 The result can be visualized by using the package Plots.jl
+
 ```julia
 julia> using Plots
 julia> plot(semi => sol)
 ```
+
 The command `plot` expects a `Pair` consisting of a [`Semidiscretization`](@ref) and an `ODESolution`. The visualization can also be customized, see the [documentation](@ref visualize_results)
 for more details. Other examples can be found in the subdirectory [examples/](https://github.com/JoshuaLampert/DispersiveShallowWater.jl/tree/main/examples).
 A list of all examples is returned by running [`get_examples()`](@ref). You can pass the filename of one of the examples or your own simulation file to `include` in order to run it,
@@ -61,6 +72,7 @@ e.g., `include(joinpath(examples_dir(), "svaerd_kalisch_1d", "svaerd_kalisch_1d_
 ## Referencing
 
 You can directly refer to DispersiveShallowWater.jl as
+
 ```bibtex
 @misc{lampert2023dispersive,
   title={{D}ispersive{S}hallow{W}ater.jl: {S}tructure-preserving numerical

diff --git a/docs/src/overview.md b/docs/src/overview.md
@@ -27,7 +27,7 @@ In order to conduct a numerical simulation with DispersiveShallowWater.jl, we pe
 First, we load the necessary libraries:
 
 ```@example overview
-using DispersiveShallowWater, OrdinaryDiffEq
+using DispersiveShallowWater, OrdinaryDiffEqTsit5
 ```
 
 ## Define physical setup
@@ -106,7 +106,9 @@ is a nonlinear invariant and should be constant over time as well. During the si
 
 Finally, the `ode` can be `solve`d using the interface from [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl). This means, we can specify a time-stepping
 scheme we want to use the tolerances for the adaptive time-stepping and the time values, where the solution values should be saved. In this case, we use the adaptive
-explicit Runge-Kutta method `Tsit5` by Tsitouras of order 5(4). Here, we save the solution at 100 equidistant points.
+explicit Runge-Kutta method `Tsit5` by Tsitouras of order 5(4), which is implemented in the subpackage OrdinaryDiffEqTsit5.jl. If you want to use other time-stepping
+schemes, you can install the respective subpackage or the whole package OrdinaryDiffEq.jl, which will install every available solver.
+Here, we save the solution at 100 equidistant points.
 
 ```@example overview
 tspan = (0.0, 25.0)
@@ -214,7 +216,6 @@ nothing # hide
 
 ![analysis callback relaxation](analysis_callback_relaxation.png)
 
-
 ## [Customize solver](@id customize_solver)
 
 In the semidiscretization created above, we used the default SBP operators, which are periodic finite difference operators. Using different SBP operators for the
@@ -307,4 +308,3 @@ and [plot_examples.jl](https://github.com/JoshuaLampert/2023-master-thesis/blob/
     Ranocha, Sayyari, Dalcin, Parsani, Ketcheson (2020):
     Relaxation Runge–Kutta Methods: Fully-Discrete Explicit Entropy-Stable Schemes for the Compressible Euler and Navier–Stokes Equations
     [DOI: 10.1137/19M1263480](https://doi.org/10.1137/19M1263480)
-
diff --git a/examples/bbm_1d/bbm_1d_basic.jl b/examples/bbm_1d/bbm_1d_basic.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_1d/bbm_1d_fourier.jl b/examples/bbm_1d/bbm_1d_fourier.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: fourier_derivative_operator
 

diff --git a/examples/bbm_1d/bbm_1d_hamiltonian_relaxation.jl b/examples/bbm_1d/bbm_1d_hamiltonian_relaxation.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_1d/bbm_1d_manufactured.jl b/examples/bbm_1d/bbm_1d_manufactured.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_1d/bbm_1d_relaxation.jl b/examples/bbm_1d/bbm_1d_relaxation.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_basic.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_basic.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_basic_reflecting.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_basic_reflecting.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: MattssonNordström2004, derivative_operator
 

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_dg.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_dg.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using SummationByPartsOperators: legendre_derivative_operator,
                                  UniformPeriodicMesh1D,
                                  couple_discontinuously

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_dingemans.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_dingemans.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_fourier.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_fourier.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: fourier_derivative_operator
 

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_manufactured.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_manufactured.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_relaxation.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_relaxation.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_upwind_relaxation.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_upwind_relaxation.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: upwind_operators, periodic_derivative_operator
 using SparseArrays: sparse

diff --git a/examples/bbm_bbm_1d/bbm_bbm_1d_well_balanced.jl b/examples/bbm_bbm_1d/bbm_bbm_1d_well_balanced.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: periodic_derivative_operator
 using SparseArrays: sparse

diff --git a/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_conservation.jl b/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_conservation.jl
@@ -6,7 +6,7 @@
 #   equations in standard and hyperbolic form
 #   [arXiv: 2408.02665](https://arxiv.org/abs/2408.02665)
 
-using OrdinaryDiffEq
+using OrdinaryDiffEqLowStorageRK
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_dingemans.jl b/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_dingemans.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqLowStorageRK
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_manufactured.jl b/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_manufactured.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_soliton.jl b/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_soliton.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqLowStorageRK
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/...ples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_soliton_relaxation.jl b/...ples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_soliton_relaxation.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqLowStorageRK
 using DispersiveShallowWater
 using SummationByPartsOperators: fourier_derivative_operator
 

diff --git a/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_well_balanced.jl b/examples/hyperbolic_serre_green_naghdi_1d/hyperbolic_serre_green_naghdi_well_balanced.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqLowStorageRK
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/serre_green_naghdi_1d/serre_green_naghdi_conservation.jl b/examples/serre_green_naghdi_1d/serre_green_naghdi_conservation.jl
@@ -6,7 +6,7 @@
 #   equations in standard and hyperbolic form
 #   [arXiv: 2408.02665](https://arxiv.org/abs/2408.02665)
 
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 
 ###############################################################################

diff --git a/examples/serre_green_naghdi_1d/serre_green_naghdi_dingemans.jl b/examples/serre_green_naghdi_1d/serre_green_naghdi_dingemans.jl
@@ -1,4 +1,4 @@
-using OrdinaryDiffEq
+using OrdinaryDiffEqTsit5
 using DispersiveShallowWater
 using SummationByPartsOperators: upwind_operators, periodic_derivative_operator