diff --git a/.buildkite/launch_benchmarks.yml.signature b/.buildkite/launch_benchmarks.yml.signature index b1d2dae2c..220d613b1 100644 --- a/.buildkite/launch_benchmarks.yml.signature +++ b/.buildkite/launch_benchmarks.yml.signature @@ -1,2 +1,3 @@ -Salted__�c? �ު��DwL�J�/���)��|p��5 +c��\~o�.�� RR�hAZR�� -$'���� 6���!�m�^����S�j�Y����� \ No newline at end of file +Salted__�c? +�ު��DwL�J�/���)��|p��5 +c��\~o�.�� RR�hAZR�� +$'���� 6���!�m�^����S�j�Y����� \ No newline at end of file diff --git a/.buildkite/run_benchmark.yml b/.buildkite/run_benchmark.yml index d104b044d..a5fa7c416 100644 --- a/.buildkite/run_benchmark.yml +++ b/.buildkite/run_benchmark.yml @@ -19,8 +19,8 @@ steps: - JuliaCI/julia#v1: version: "1.10" - staticfloat/sandbox: - rootfs_url: "https://github.com/thazhemadam/openmodelica-rootfs-image/releases/download/v1.23.0/rootfs-openmodelica-v1.23.0.amd64.tar.gz" - rootfs_treehash: "82970243dc4f188e599a976abc20951f4aba2912" + rootfs_url: "https://github.com/thazhemadam/ScimlBenchmarks-rootfs-image/releases/download/rootfs-image/rootfs-script.amd64.tar.gz" + rootfs_treehash: "943bde824554f0afad5a939341f05e3bdb393051" uid: 1000 gid: 1000 workspaces: diff --git a/benchmarks/AstroChem/Project.toml b/benchmarks/AstroChem/Project.toml index 62e4e2e02..5da665d4b 100644 --- a/benchmarks/AstroChem/Project.toml +++ b/benchmarks/AstroChem/Project.toml @@ -10,6 +10,7 @@ ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" @@ -18,12 +19,13 @@ BenchmarkTools = "1" Catalyst = "14" DiffEqDevTools = "2" LSODA = "0.7" -LinearSolve = "2" +LinearSolve = "3" NaNMath = "1" ODEInterface = "0.5" ODEInterfaceDiffEq = "3" OrdinaryDiffEq = "6.89" OrdinaryDiffEqCore = "1.9" Plots = "1" +RecursiveFactorization = "0.2.23" Sundials = "4" Symbolics = "6" diff --git a/benchmarks/AstroChem/astrochem.jmd b/benchmarks/AstroChem/astrochem.jmd index 5bfe913b6..954544630 100644 --- a/benchmarks/AstroChem/astrochem.jmd +++ b/benchmarks/AstroChem/astrochem.jmd @@ -10,6 +10,7 @@ using Plots using Symbolics using DiffEqDevTools using Sundials, ODEInterface, ODEInterfaceDiffEq, LSODA +using RecursiveFactorization ``` ## Without Temperature Dynamics diff --git a/benchmarks/AstroChem/nelson.jmd b/benchmarks/AstroChem/nelson.jmd index bbe7f9924..78d7a4e8a 100644 --- a/benchmarks/AstroChem/nelson.jmd +++ b/benchmarks/AstroChem/nelson.jmd @@ -8,6 +8,7 @@ using OrdinaryDiffEq using DiffEqDevTools, Plots using Sundials, LSODA using ODEInterface, ODEInterfaceDiffEq +using RecursiveFactorization ``` The ODE function defined below models the reduced carbon-oxygen diff --git a/benchmarks/Bio/BCR.jmd b/benchmarks/Bio/BCR.jmd index cbc4b70a9..9aab1beaa 100644 --- a/benchmarks/Bio/BCR.jmd +++ b/benchmarks/Bio/BCR.jmd @@ -17,7 +17,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() datadir = joinpath(dirname(pathof(ReactionNetworkImporters)),"../data/bcr") diff --git a/benchmarks/Bio/Bidkhori2012.jmd b/benchmarks/Bio/Bidkhori2012.jmd index 1bdac2e40..8f9a460a3 100644 --- a/benchmarks/Bio/Bidkhori2012.jmd +++ b/benchmarks/Bio/Bidkhori2012.jmd @@ -13,7 +13,8 @@ and the model was parsed to Julia are finally to ODEs using [ModelingToolkit](ht ```julia using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, - LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2 + LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2, + RecursiveFactorization gr() diff --git a/benchmarks/Bio/Project.toml b/benchmarks/Bio/Project.toml index be541a358..4a502e021 100644 --- a/benchmarks/Bio/Project.toml +++ b/benchmarks/Bio/Project.toml @@ -12,6 +12,7 @@ ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" ReactionNetworkImporters = "b4db0fb7-de2a-5028-82bf-5021f5cfa881" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -25,13 +26,14 @@ DiffEqDevTools = "2.35" IncompleteLU = "0.2" JLD2 = "0.4, 0.5" LSODA = "0.7" -LinearSolve = "1, 2" +LinearSolve = "3" ModelingToolkit = "9" ODEInterface = "0.5" ODEInterfaceDiffEq = "3.8" OrdinaryDiffEq = "6" Plots = "1.10" ReactionNetworkImporters = "0.15" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4.4" TimerOutputs = "0.5" diff --git a/benchmarks/Bio/egfr_net.jmd b/benchmarks/Bio/egfr_net.jmd index 96cc5c802..b9d604448 100644 --- a/benchmarks/Bio/egfr_net.jmd +++ b/benchmarks/Bio/egfr_net.jmd @@ -18,7 +18,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() diff --git a/benchmarks/Bio/fceri_gamma2.jmd b/benchmarks/Bio/fceri_gamma2.jmd index 1e6178557..1e9bc1fd6 100644 --- a/benchmarks/Bio/fceri_gamma2.jmd +++ b/benchmarks/Bio/fceri_gamma2.jmd @@ -17,7 +17,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() diff --git a/benchmarks/Bio/multisite2.jmd b/benchmarks/Bio/multisite2.jmd index 9f7370154..0dd7c3599 100644 --- a/benchmarks/Bio/multisite2.jmd +++ b/benchmarks/Bio/multisite2.jmd @@ -16,7 +16,7 @@ Catalyst network model to ODEs. using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, - LinearSolve + LinearSolve, RecursiveFactorization gr() const to = TimerOutput() diff --git a/benchmarks/Bio/multistate.jmd b/benchmarks/Bio/multistate.jmd index 953a8e0d9..3d2a05c64 100644 --- a/benchmarks/Bio/multistate.jmd +++ b/benchmarks/Bio/multistate.jmd @@ -15,7 +15,8 @@ Catalyst network model to ODEs. ```julia using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters, Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq, - LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools + LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, + RecursiveFactorization gr() const to = TimerOutput() diff --git a/benchmarks/ComplicatedPDE/Filament.jmd b/benchmarks/ComplicatedPDE/Filament.jmd index 08883b727..7c85a6cd5 100644 --- a/benchmarks/ComplicatedPDE/Filament.jmd +++ b/benchmarks/ComplicatedPDE/Filament.jmd @@ -15,7 +15,7 @@ The model is thus defined as follows: ```julia using OrdinaryDiffEq, ODEInterfaceDiffEq, Sundials, DiffEqDevTools, LSODA, LinearSolve -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots gr() ``` diff --git a/benchmarks/ComplicatedPDE/Project.toml b/benchmarks/ComplicatedPDE/Project.toml index 59f99b135..62ee3335b 100644 --- a/benchmarks/ComplicatedPDE/Project.toml +++ b/benchmarks/ComplicatedPDE/Project.toml @@ -8,6 +8,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -17,12 +18,13 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" DiffEqDevTools = "2" GaussianRandomFields = "2" LSODA = "0.7" -LinearSolve = "2" +LinearSolve = "3" ModelingToolkit = "8" NonlinearSolve = "1, 2, 4" ODEInterfaceDiffEq = "3" OrdinaryDiffEq = "6" Plots = "1" +RecursiveFactorization = "0.2.23" StableRNGs = "1" Sundials = "4" Symbolics = "5, 6" diff --git a/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd b/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd index c2490db5f..dcc536039 100644 --- a/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd +++ b/benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd @@ -8,7 +8,7 @@ using OrdinaryDiffEq, Symbolics, ModelingToolkit, Sundials, LinearSolve, SparseA using NonlinearSolve using GaussianRandomFields using StableRNGs -using DiffEqDevTools +using DiffEqDevTools, RecursiveFactorization using Plots; gr() diff --git a/benchmarks/LinearSolve/LUFactorization.jmd b/benchmarks/LinearSolve/LUFactorization.jmd index 0ca556c60..4c29a2fd7 100644 --- a/benchmarks/LinearSolve/LUFactorization.jmd +++ b/benchmarks/LinearSolve/LUFactorization.jmd @@ -5,7 +5,7 @@ author: Chris Rackauckas ```julia using BenchmarkTools, Random, VectorizationBase -using LinearAlgebra, LinearSolve, MKL_jll +using LinearAlgebra, LinearSolve, RecursiveFactorization, MKL_jll nc = min(Int(VectorizationBase.num_cores()), Threads.nthreads()) BLAS.set_num_threads(nc) BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.5 diff --git a/benchmarks/LinearSolve/Project.toml b/benchmarks/LinearSolve/Project.toml index 04ab21e57..a61352d59 100644 --- a/benchmarks/LinearSolve/Project.toml +++ b/benchmarks/LinearSolve/Project.toml @@ -16,7 +16,7 @@ VectorizationBase = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" [compat] BenchmarkTools = "1" -LinearSolve = "2.5" +LinearSolve = "3" MatrixDepot = "1" Pardiso = "0.5.4" Plots = "1" diff --git a/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd b/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd index 2fbf2f597..794c49203 100644 --- a/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd +++ b/benchmarks/MethodOfLinesPDE/MOL_fdm.jmd @@ -8,7 +8,7 @@ It is concerned with comparing the performance of various discretization methods ```julia using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra, - LinearSolve, Plots + LinearSolve, Plots, RecursiveFactorization ``` Here is the burgers equation with a Dirichlet and Neumann boundary conditions, diff --git a/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd b/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd index 0a9c4dc58..7338c5195 100644 --- a/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd +++ b/benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd @@ -9,7 +9,7 @@ It is concerned with comparing the performance of various discretization methods ```julia using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra, - LinearSolve, Plots + LinearSolve, Plots, RecursiveFactorization using PDESystemLibrary ``` diff --git a/benchmarks/MethodOfLinesPDE/Project.toml b/benchmarks/MethodOfLinesPDE/Project.toml index e5cf7986e..8e12d11e8 100644 --- a/benchmarks/MethodOfLinesPDE/Project.toml +++ b/benchmarks/MethodOfLinesPDE/Project.toml @@ -7,17 +7,19 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" PDESystemLibrary = "d14f9848-fe58-4297-bd22-c1aba6f3000d" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" [compat] DiffEqDevTools = "2" DomainSets = "0.5, 0.6, 0.7" -LinearSolve = "1, 2" +LinearSolve = "3" MethodOfLines = "0.9" ModelingToolkit = "8" OrdinaryDiffEq = "6" PDESystemLibrary = "0.1" Plots = "1" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4" diff --git a/benchmarks/ModelingToolkit/Project.toml b/benchmarks/ModelingToolkit/Project.toml index 2ad635cbc..b395b0b63 100644 --- a/benchmarks/ModelingToolkit/Project.toml +++ b/benchmarks/ModelingToolkit/Project.toml @@ -24,7 +24,7 @@ CairoMakie = "0.11.11" DataFrames = "1" JuliaSimCompiler = "0.1.9" JuliaSimCompilerRuntime = "1.0.0" -LinearSolve = "2.30.0" +LinearSolve = "3" ModelingToolkit = "9.20.0" ModelingToolkitStandardLibrary = "2" Multibody = "0.1.0" diff --git a/benchmarks/NonlinearProblem/Project.toml b/benchmarks/NonlinearProblem/Project.toml index 1eb0b8b11..c37371cd1 100644 --- a/benchmarks/NonlinearProblem/Project.toml +++ b/benchmarks/NonlinearProblem/Project.toml @@ -17,6 +17,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46" SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7" @@ -47,6 +48,7 @@ NonlinearSolve = "4" PETSc = "0.3" PolyesterForwardDiff = "0.1" PrettyTables = "2" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Setfield = "1" SimpleNonlinearSolve = "2" diff --git a/benchmarks/NonlinearProblem/bruss.jmd b/benchmarks/NonlinearProblem/bruss.jmd index 598f94b77..14b33302a 100644 --- a/benchmarks/NonlinearProblem/bruss.jmd +++ b/benchmarks/NonlinearProblem/bruss.jmd @@ -11,7 +11,7 @@ Fetch required packages using NonlinearSolve, SparseDiffTools, LinearAlgebra, SparseArrays, DiffEqDevTools, CairoMakie, Symbolics, BenchmarkTools, PolyesterForwardDiff, LinearSolve, Sundials, Enzyme, SparseConnectivityTracer, DifferentiationInterface -import NLsolve, MINPACK, PETSc +import NLsolve, MINPACK, PETSc, RecursiveFactorization const RUS = RadiusUpdateSchemes; BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.2; diff --git a/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd b/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd index 8bddf2395..10b283e79 100644 --- a/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd +++ b/benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd @@ -21,7 +21,8 @@ Fetch required packages. ```julia using NonlinearSolve, LinearSolve, StaticArrays, Sundials, SpeedMapping, - BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie + BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie, + RecursiveFactorization import MINPACK, NLsolve import LineSearches diff --git a/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd b/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd index f043b05b7..ed7577df5 100644 --- a/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd +++ b/benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd @@ -36,7 +36,8 @@ Fetch required packages. ```julia using NonlinearSolve, LinearSolve, StaticArrays, Sundials, Setfield, - BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie + BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie, + RecursiveFactorization import PolyesterForwardDiff, MINPACK, NLsolve const RUS = RadiusUpdateSchemes; diff --git a/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd b/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd index 043445ae3..9129ee964 100644 --- a/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd +++ b/benchmarks/NonlinearProblem/quadratic_nonlinear.jmd @@ -7,7 +7,7 @@ This is a test of a simple small nonlinear rootfinding problem. ```julia using NonlinearSolve, StaticArrays, DiffEqDevTools, Sundials, CairoMakie, LinearSolve, - LinearAlgebra, StableRNGs, BenchmarkTools, Setfield + LinearAlgebra, StableRNGs, BenchmarkTools, Setfield, RecursiveFactorization import PolyesterForwardDiff, MINPACK, NLsolve, SpeedMapping const RUS = RadiusUpdateSchemes; diff --git a/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd b/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd new file mode 100644 index 000000000..3900e52d7 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_bounded.jmd @@ -0,0 +1,141 @@ +--- +title: CUTEst Bounded Constrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + #Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + @info "here 1" + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + @info "here 2" + + for prob_name in problems + @info prob_name + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Equality/Inequality constrained problems with bounded variables + +Now we analyze the subset of problems with equality/inequality constraints and whose +variables are bounded. There are 666 such problems. + +The following figure shows the results of the same benchmarks previously described for the +problems on this section. + +```julia +@info "before" +eq_bou_problems = CUTEst.select(min_con=1, only_equ_con=true, only_free_var=false) +@info "after1" + +# Analysis +eq_bou_results = run_benchmarks(eq_bou_problems, optimizers) +@info "after2" + +@df eq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +@info "after3" +``` + +Next, we examine the same relationship for problems with inequality-constrained problems, +of which there are 244. + +```julia +@info "after4" +neq_bou_problems = CUTEst.select(min_con=1, only_ineq_con=true, only_free_var=false) +@info "after5" + +# Analysis +neq_bou_results = run_benchmarks(neq_bou_problems, optimizers) +@info "after6" + +@df neq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` diff --git a/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd b/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd new file mode 100644 index 000000000..8a35e2562 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_quadratic.jmd @@ -0,0 +1,108 @@ +--- +title: CUTEst Quadratic Programming with Linear Constraints Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +# Quadratic programs with linear constraints + +Lastly, we examine the problems with a quadratic objective function and only linear +constraints. There are 252 such problems in the suite. + +```julia +quad_problems = CUTEst.select_sif_problems(objtype="quadratic", contype="linear") + +# Analysis +quad_results = run_benchmarks(quad_problems, optimizers) + +@df neq_bou_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd b/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd new file mode 100644 index 000000000..a8038e396 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_unbounded.jmd @@ -0,0 +1,129 @@ +--- +title: CUTEst Unbounded Constrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Equality/Inequality constrained problems with unbounded variables + +These problems have a constraint function that's subject to either equality or inequality +constraints, but the variables themselves are free. CUTEst contains 285 problems with +equality constraints and 114 with inequality constraints for a total of 299. + +We start by analyzing the equality-constrained problems, of which there are 285. The +following figure shows the time to solution as a function of number of variables by +optimizer. + +```julia +eq_unb_problems = CUTEst.select_sif_problems(min_con=1, only_equ_con=true, only_free_var=true) + +# Analysis +eq_unb_results = run_benchmarks(eq_unb_problems, optimizers) + +@df eq_unb_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +Next, we examine the same relationship for problems with inequality-constrained problems. + +```julia +neq_unb_problems = CUTEst.select(min_con=1, only_ineq_con=true, only_free_var=true) + +# Analysis +neq_unb_results = run_benchmarks(neq_unb_problems, optimizers) + +@df neq_unb_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd b/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd new file mode 100644 index 000000000..da2fe781f --- /dev/null +++ b/benchmarks/OptimizationCUTEst/CUTEst_unconstrained.jmd @@ -0,0 +1,109 @@ +--- +title: CUTEst Unconstrained Nonlinear Optimization Benchmarks +author: Alonso M. Cisneros +--- + +# Introduction + +CUTEst, the Constraind and Unconstrained Testing Environment is, as the name suggests is a +collection of around 1500 problems for general nonlinear optimization used to test +optimization routines. The wrapper +[CUTEst.jl](https://github.com/JuliaSmoothOptimizers/CUTEst.jl) provides convenient access +to the problem collection, which we can leverage to test the optimizers made available by +Optimization.jl. + +This benchmark uses the following packages: + +```julia +using Optimization +using OptimizationNLPModels +using CUTEst +using OptimizationOptimJL +using Ipopt +using OptimizationMOI +using OptimizationMOI: MOI as MOI +# Analysis and plotting +using DataFrames +using Plots +using StatsPlots +``` + +# Benchmarks + +We will be testing the [Ipopt]() and the [LBFGS]() optimizers on these classes of +problems. + +```julia +optimizers = [ + Optimization.LBFGS(), + MOI.OptimizerWithAttributes(Ipopt.Optimizer, "print_level" => 0) + ] + +function get_stats(sol, ::Optimization.LBFGS) + return (length(sol.u), sol.stats.time, "LBFGS", Symbol(sol.retcode)) +end + +function get_stats(sol, ::OptimizationMOI.MOI.OptimizerWithAttributes) + return (length(sol.u), MOI.get(sol.original.model, MOI.SolveTimeSec()), + "Ipopt", Symbol(sol.retcode)) +end + +function run_benchmarks(problems, optimizers) + problem = String[] + n_vars = Int64[] + secs = Float64[] + solver = String[] + retcode = Symbol[] + + optz = length(optimizers) + n = length(problems) + + broadcast(c -> sizehint!(c, optz * n), [problem, n_vars, secs, solver, retcode]) + + for prob_name in problems + nlp_prob = CUTEstModel(prob_name) + prob = OptimizationNLPModels.OptimizationProblem(nlp_prob, Optimization.AutoForwardDiff()) + for optimizer in optimizers + sol = solve(prob, optimizer; maxiters = 1e7) + + @info "Solved $(prob_name) with $(optimizer)" + vars, time, alg, code = get_stats(sol, optimizer) + + push!(problem, prob_name) + push!(n_vars, vars) + push!(secs, time) + push!(solver, alg) + push!(retcode, code) + + end + finalize(nlp_prob) + end + + return DataFrame(problem = problem, n_vars = n_vars, secs = secs, solver = solver, + retcode = retcode) +end +``` + +## Unconstrained problems + +CUTEst contains 286 unconstrained problems. We will compare how the optimizers behave in +terms of the time to solution with respect to the number of variables. + +```julia +unc_problems = CUTEst.select(contype="unc") + +# Analysis +unc_results = run_benchmarks(unc_problems, optimizers) + +@df unc_results scatter(:n_vars, :secs, + group = :solver, + xlabel = "n. variables", + ylabel = "secs.", + title = "Time to solution by optimizer and number of vars", + ) +``` + +```julia, echo = false +using SciMLBenchmarks +SciMLBenchmarks.bench_footer(WEAVE_ARGS[:folder],WEAVE_ARGS[:file]) +``` \ No newline at end of file diff --git a/benchmarks/OptimizationCUTEst/Manifest.toml b/benchmarks/OptimizationCUTEst/Manifest.toml new file mode 100644 index 000000000..5db5e97e6 --- /dev/null +++ b/benchmarks/OptimizationCUTEst/Manifest.toml @@ -0,0 +1,2932 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.9" +manifest_format = "2.0" +project_hash = "6772cd706a6b63c91ac654033fe106c262910b2c" + 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["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d5a767a3bb77135a99e433afe0eb14cd7f6914c3" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2022.0.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" + +[[deps.x264_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" +version = "2021.5.5+0" + +[[deps.x265_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "63406453ed9b33a0df95d570816d5366c92b7809" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+2" diff --git a/benchmarks/OptimizationCUTEst/Project.toml b/benchmarks/OptimizationCUTEst/Project.toml new file mode 100644 index 000000000..7709c365b --- /dev/null +++ b/benchmarks/OptimizationCUTEst/Project.toml @@ -0,0 +1,13 @@ +[deps] +CUTEst = "1b53aba6-35b6-5f92-a507-53c67d53f819" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9" +NLPModels = "a4795742-8479-5a88-8948-cc11e1c8c1a6" +Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" +OptimizationMOI = "fd9f6733-72f4-499f-8506-86b2bdd0dea1" +OptimizationNLPModels = "064b21be-54cf-11ef-1646-cdfee32b588f" +OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" +Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" diff --git a/benchmarks/SimpleHandwrittenPDE/Project.toml b/benchmarks/SimpleHandwrittenPDE/Project.toml index fb9735020..32801ff6d 100644 --- a/benchmarks/SimpleHandwrittenPDE/Project.toml +++ b/benchmarks/SimpleHandwrittenPDE/Project.toml @@ -10,6 +10,7 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf" OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4" @@ -24,5 +25,6 @@ ModelingToolkit = "8" ODEInterfaceDiffEq = "3.7" OrdinaryDiffEq = "5.41, 6" Plots = "1.4" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" Sundials = "4.2" diff --git a/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd index 1c736ce6b..b2de3efee 100644 --- a/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd index e2b2b05a6..a4b423a76 100644 --- a/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd index 00ec2785a..0f100f351 100644 --- a/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd index 2c46dd471..502ebf658 100644 --- a/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd index 136543791..4a862dfe8 100644 --- a/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd index 109b0fd93..f285c417f 100644 --- a/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd index 9c58f8852..224929e14 100644 --- a/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd b/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd index 80ff66386..f096e90f0 100644 --- a/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd +++ b/benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd @@ -6,7 +6,7 @@ author: HAO HAO ```julia using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve using DiffEqDevTools -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization using Plots; gr() ``` diff --git a/benchmarks/StiffODE/Bruss.jmd b/benchmarks/StiffODE/Bruss.jmd index 59530f22c..07d0e6b7d 100644 --- a/benchmarks/StiffODE/Bruss.jmd +++ b/benchmarks/StiffODE/Bruss.jmd @@ -6,7 +6,8 @@ author: Chris Rackauckas and Utkarsh ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, SparseArrays, LinearSolve, - LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit + LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit, + RecursiveFactorization gr() const N = 8 diff --git a/benchmarks/StiffODE/Hires.jmd b/benchmarks/StiffODE/Hires.jmd index f888ebb14..c4028347b 100644 --- a/benchmarks/StiffODE/Hires.jmd +++ b/benchmarks/StiffODE/Hires.jmd @@ -5,7 +5,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, DiffEqDevTools, Sundials -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization gr() #gr(fmt=:png) diff --git a/benchmarks/StiffODE/Orego.jmd b/benchmarks/StiffODE/Orego.jmd index e113ab9c9..f5974a1c9 100644 --- a/benchmarks/StiffODE/Orego.jmd +++ b/benchmarks/StiffODE/Orego.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, Sundials gr() #gr(fmt=:png) -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization f = @ode_def Orego begin dy1 = p1*(y2+y1*(1-p2*y1-y2)) diff --git a/benchmarks/StiffODE/Pollution.jmd b/benchmarks/StiffODE/Pollution.jmd index ea7ae39f9..730bb9943 100644 --- a/benchmarks/StiffODE/Pollution.jmd +++ b/benchmarks/StiffODE/Pollution.jmd @@ -7,7 +7,7 @@ author: Chris Rackauckas using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, LinearSolve using ProfileSVG, BenchmarkTools, Profile gr() # gr(fmt=:png) -using LinearAlgebra +using LinearAlgebra, RecursiveFactorization const k1=.35e0 const k2=.266e2 diff --git a/benchmarks/StiffODE/Project.toml b/benchmarks/StiffODE/Project.toml index 3f08d98e4..59bf75ab7 100644 --- a/benchmarks/StiffODE/Project.toml +++ b/benchmarks/StiffODE/Project.toml @@ -15,6 +15,7 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" ParameterizedFunctions = "65888b18-ceab-5e60-b2b9-181511a3b968" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" ProfileSVG = "132c30aa-f267-4189-9183-c8a63c7e05e6" +RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" @@ -30,7 +31,7 @@ DomainSets = "0.7" GeometricIntegratorsDiffEq = "0.2" IncompleteLU = "0.2" LSODA = "0.7" -LinearSolve = "1, 2" +LinearSolve = "3" MethodOfLines = "0.11" ModelingToolkit = "9" ODEInterfaceDiffEq = "3.10" @@ -38,6 +39,7 @@ OrdinaryDiffEq = "6.19" ParameterizedFunctions = "5.3" Plots = "1.4" ProfileSVG = "0.2" +RecursiveFactorization = "0.2.23" SciMLBenchmarks = "0.1" StaticArrays = "1" Sundials = "4.2" diff --git a/benchmarks/StiffODE/ROBER.jmd b/benchmarks/StiffODE/ROBER.jmd index 6f9b4c9c5..5f04a4cb3 100644 --- a/benchmarks/StiffODE/ROBER.jmd +++ b/benchmarks/StiffODE/ROBER.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA gr() -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization rober = @ode_def begin dy₁ = -k₁*y₁+k₃*y₂*y₃ diff --git a/benchmarks/StiffODE/VanDerPol.jmd b/benchmarks/StiffODE/VanDerPol.jmd index e1f76ae53..5f62fe4d3 100644 --- a/benchmarks/StiffODE/VanDerPol.jmd +++ b/benchmarks/StiffODE/VanDerPol.jmd @@ -6,7 +6,7 @@ author: Chris Rackauckas ```julia using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA gr() -using LinearAlgebra, StaticArrays +using LinearAlgebra, StaticArrays, RecursiveFactorization van = @ode_def begin dy = μ*((1-x^2)*y - x)