SciML · Vaibhavdixit02 · Apr 19, 2024 · Apr 21, 2024 · Apr 22, 2024 · Aug 23, 2024
diff --git a/.buildkite/launch_benchmarks.yml.signature b/.buildkite/launch_benchmarks.yml.signature
@@ -1,2 +1,3 @@
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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;