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ChrisRackauckasChrisRackauckas
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Bump LinearSolves
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Diff for: ‎benchmarks/AstroChem/Project.toml

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@@ -10,6 +10,7 @@ ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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OrdinaryDiffEqCore = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
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Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
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@@ -18,12 +19,13 @@ BenchmarkTools = "1"
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Catalyst = "14"
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DiffEqDevTools = "2"
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LSODA = "0.7"
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LinearSolve = "2"
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LinearSolve = "3"
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NaNMath = "1"
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ODEInterface = "0.5"
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ODEInterfaceDiffEq = "3"
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OrdinaryDiffEq = "6.89"
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OrdinaryDiffEqCore = "1.9"
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Plots = "1"
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RecursiveFactorization = "0.2.23"
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Sundials = "4"
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Symbolics = "6"

Diff for: ‎benchmarks/AstroChem/astrochem.jmd

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@@ -10,6 +10,7 @@ using Plots
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using Symbolics
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using DiffEqDevTools
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using Sundials, ODEInterface, ODEInterfaceDiffEq, LSODA
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using RecursiveFactorization
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```
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## Without Temperature Dynamics

Diff for: ‎benchmarks/AstroChem/nelson.jmd

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@@ -8,6 +8,7 @@ using OrdinaryDiffEq
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using DiffEqDevTools, Plots
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using Sundials, LSODA
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using ODEInterface, ODEInterfaceDiffEq
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using RecursiveFactorization
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```
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The ODE function defined below models the reduced carbon-oxygen

Diff for: ‎benchmarks/Bio/BCR.jmd

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@@ -17,7 +17,7 @@ Catalyst network model to ODEs.
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools,
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LinearSolve
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LinearSolve, RecursiveFactorization
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gr()
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datadir = joinpath(dirname(pathof(ReactionNetworkImporters)),"../data/bcr")

Diff for: ‎benchmarks/Bio/Bidkhori2012.jmd

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@@ -13,7 +13,8 @@ and the model was parsed to Julia are finally to ODEs using [ModelingToolkit](ht
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```julia
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools, JLD2,
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RecursiveFactorization
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gr()
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Diff for: ‎benchmarks/Bio/Project.toml

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@@ -12,6 +12,7 @@ ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c"
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ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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ReactionNetworkImporters = "b4db0fb7-de2a-5028-82bf-5021f5cfa881"
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SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344"
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Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
@@ -25,13 +26,14 @@ DiffEqDevTools = "2.35"
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IncompleteLU = "0.2"
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JLD2 = "0.4, 0.5"
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LSODA = "0.7"
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LinearSolve = "1, 2"
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LinearSolve = "3"
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ModelingToolkit = "9"
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ODEInterface = "0.5"
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ODEInterfaceDiffEq = "3.8"
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OrdinaryDiffEq = "6"
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Plots = "1.10"
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ReactionNetworkImporters = "0.15"
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RecursiveFactorization = "0.2.23"
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SciMLBenchmarks = "0.1"
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Sundials = "4.4"
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TimerOutputs = "0.5"

Diff for: ‎benchmarks/Bio/egfr_net.jmd

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@@ -18,7 +18,7 @@ Catalyst network model to ODEs.
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools,
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LinearSolve
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LinearSolve, RecursiveFactorization
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gr()
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const to = TimerOutput()

Diff for: ‎benchmarks/Bio/fceri_gamma2.jmd

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@@ -17,7 +17,7 @@ Catalyst network model to ODEs.
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools,
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LinearSolve
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LinearSolve, RecursiveFactorization
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gr()
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const to = TimerOutput()

Diff for: ‎benchmarks/Bio/multisite2.jmd

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@@ -16,7 +16,7 @@ Catalyst network model to ODEs.
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools,
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LinearSolve
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LinearSolve, RecursiveFactorization
2020

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gr()
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const to = TimerOutput()

Diff for: ‎benchmarks/Bio/multistate.jmd

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@@ -15,7 +15,8 @@ Catalyst network model to ODEs.
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```julia
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using DiffEqBase, OrdinaryDiffEq, Catalyst, ReactionNetworkImporters,
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Sundials, Plots, DiffEqDevTools, ODEInterface, ODEInterfaceDiffEq,
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools
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LSODA, TimerOutputs, LinearAlgebra, ModelingToolkit, BenchmarkTools,
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RecursiveFactorization
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gr()
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const to = TimerOutput()

Diff for: ‎benchmarks/ComplicatedPDE/Filament.jmd

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@@ -15,7 +15,7 @@ The model is thus defined as follows:
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```julia
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using OrdinaryDiffEq, ODEInterfaceDiffEq, Sundials, DiffEqDevTools, LSODA, LinearSolve
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using LinearAlgebra
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using LinearAlgebra, RecursiveFactorization
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using Plots
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gr()
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```

Diff for: ‎benchmarks/ComplicatedPDE/Project.toml

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@@ -8,6 +8,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
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ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
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StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
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Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
@@ -17,12 +18,13 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
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DiffEqDevTools = "2"
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GaussianRandomFields = "2"
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LSODA = "0.7"
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LinearSolve = "2"
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LinearSolve = "3"
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ModelingToolkit = "8"
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NonlinearSolve = "1, 2, 4"
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ODEInterfaceDiffEq = "3"
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OrdinaryDiffEq = "6"
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Plots = "1"
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RecursiveFactorization = "0.2.23"
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StableRNGs = "1"
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Sundials = "4"
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Symbolics = "5, 6"

Diff for: ‎benchmarks/ComplicatedPDE/SpringBlockNonLinearResistance.jmd

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@@ -8,7 +8,7 @@ using OrdinaryDiffEq, Symbolics, ModelingToolkit, Sundials, LinearSolve, SparseA
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using NonlinearSolve
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using GaussianRandomFields
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using StableRNGs
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using DiffEqDevTools
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using DiffEqDevTools, RecursiveFactorization
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using Plots; gr()
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Diff for: ‎benchmarks/LinearSolve/LUFactorization.jmd

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@@ -5,7 +5,7 @@ author: Chris Rackauckas
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66
```julia
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using BenchmarkTools, Random, VectorizationBase
8-
using LinearAlgebra, LinearSolve, MKL_jll
8+
using LinearAlgebra, LinearSolve, RecursiveFactorization, MKL_jll
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nc = min(Int(VectorizationBase.num_cores()), Threads.nthreads())
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BLAS.set_num_threads(nc)
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BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.5

Diff for: ‎benchmarks/LinearSolve/Project.toml

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@@ -16,7 +16,7 @@ VectorizationBase = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
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[compat]
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BenchmarkTools = "1"
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LinearSolve = "2.5"
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LinearSolve = "3"
2020
MatrixDepot = "1"
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Pardiso = "0.5.4"
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Plots = "1"

Diff for: ‎benchmarks/MethodOfLinesPDE/MOL_fdm.jmd

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@@ -8,7 +8,7 @@ It is concerned with comparing the performance of various discretization methods
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```julia
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using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra,
11-
LinearSolve, Plots
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LinearSolve, Plots, RecursiveFactorization
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```
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Here is the burgers equation with a Dirichlet and Neumann boundary conditions,

Diff for: ‎benchmarks/MethodOfLinesPDE/MOLxPDESystemLibrary.jmd

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@@ -9,7 +9,7 @@ It is concerned with comparing the performance of various discretization methods
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```julia
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using MethodOfLines, DomainSets, OrdinaryDiffEq, ModelingToolkit, DiffEqDevTools, LinearAlgebra,
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LinearSolve, Plots
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LinearSolve, Plots, RecursiveFactorization
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using PDESystemLibrary
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```
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Diff for: ‎benchmarks/MethodOfLinesPDE/Project.toml

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@@ -7,17 +7,19 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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PDESystemLibrary = "d14f9848-fe58-4297-bd22-c1aba6f3000d"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344"
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Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
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[compat]
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DiffEqDevTools = "2"
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DomainSets = "0.5, 0.6, 0.7"
16-
LinearSolve = "1, 2"
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LinearSolve = "3"
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MethodOfLines = "0.9"
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ModelingToolkit = "8"
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OrdinaryDiffEq = "6"
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PDESystemLibrary = "0.1"
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Plots = "1"
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RecursiveFactorization = "0.2.23"
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SciMLBenchmarks = "0.1"
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Sundials = "4"

Diff for: ‎benchmarks/ModelingToolkit/Project.toml

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@@ -24,7 +24,7 @@ CairoMakie = "0.11.11"
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DataFrames = "1"
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JuliaSimCompiler = "0.1.9"
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JuliaSimCompilerRuntime = "1.0.0"
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LinearSolve = "2.30.0"
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LinearSolve = "3"
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ModelingToolkit = "9.20.0"
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ModelingToolkitStandardLibrary = "2"
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Multibody = "0.1.0"

Diff for: ‎benchmarks/NonlinearProblem/Project.toml

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@@ -17,6 +17,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
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PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0"
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PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
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PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344"
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Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
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SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7"
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PETSc = "0.3"
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PolyesterForwardDiff = "0.1"
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PrettyTables = "2"
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RecursiveFactorization = "0.2.23"
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SciMLBenchmarks = "0.1"
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Setfield = "1"
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SimpleNonlinearSolve = "2"

Diff for: ‎benchmarks/NonlinearProblem/bruss.jmd

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using NonlinearSolve, SparseDiffTools, LinearAlgebra, SparseArrays, DiffEqDevTools,
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CairoMakie, Symbolics, BenchmarkTools, PolyesterForwardDiff, LinearSolve, Sundials,
1313
Enzyme, SparseConnectivityTracer, DifferentiationInterface
14-
import NLsolve, MINPACK, PETSc
14+
import NLsolve, MINPACK, PETSc, RecursiveFactorization
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const RUS = RadiusUpdateSchemes;
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BenchmarkTools.DEFAULT_PARAMETERS.seconds = 0.2;

Diff for: ‎benchmarks/NonlinearProblem/nonlinear_battery_problem.jmd

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```julia
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using NonlinearSolve, LinearSolve, StaticArrays, Sundials, SpeedMapping,
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BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie
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BenchmarkTools, LinearAlgebra, DiffEqDevTools, PolyesterForwardDiff, CairoMakie,
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RecursiveFactorization
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import MINPACK, NLsolve
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import LineSearches
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Diff for: ‎benchmarks/NonlinearProblem/nonlinear_solver_23_tests.jmd

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```julia
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using NonlinearSolve, LinearSolve, StaticArrays, Sundials, Setfield,
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BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie
39+
BenchmarkTools, LinearAlgebra, DiffEqDevTools, NonlinearProblemLibrary, CairoMakie,
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RecursiveFactorization
4041
import PolyesterForwardDiff, MINPACK, NLsolve
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const RUS = RadiusUpdateSchemes;

Diff for: ‎benchmarks/NonlinearProblem/quadratic_nonlinear.jmd

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@@ -7,7 +7,7 @@ This is a test of a simple small nonlinear rootfinding problem.
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```julia
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using NonlinearSolve, StaticArrays, DiffEqDevTools, Sundials, CairoMakie, LinearSolve,
10-
LinearAlgebra, StableRNGs, BenchmarkTools, Setfield
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LinearAlgebra, StableRNGs, BenchmarkTools, Setfield, RecursiveFactorization
1111
import PolyesterForwardDiff, MINPACK, NLsolve, SpeedMapping
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const RUS = RadiusUpdateSchemes;

Diff for: ‎benchmarks/SimpleHandwrittenPDE/Project.toml

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@@ -10,6 +10,7 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
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ODEInterfaceDiffEq = "09606e27-ecf5-54fc-bb29-004bd9f985bf"
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OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
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Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
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RecursiveFactorization = "f2c3362d-daeb-58d1-803e-2bc74f2840b4"
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SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344"
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Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
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ODEInterfaceDiffEq = "3.7"
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OrdinaryDiffEq = "5.41, 6"
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Plots = "1.4"
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RecursiveFactorization = "0.2.23"
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SciMLBenchmarks = "0.1"
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Sundials = "4.2"

Diff for: ‎benchmarks/SimpleHandwrittenPDE/allen_cahn_fdm_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
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using DiffEqDevTools
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using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/allen_cahn_spectral_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
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using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/burgers_fdm_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
88
using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/burgers_spectral_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
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using DiffEqDevTools
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using LinearAlgebra
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using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/kdv_fdm_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
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using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/kdv_spectral_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
88
using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/ks_fdm_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
88
using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/SimpleHandwrittenPDE/ks_spectral_wpd.jmd

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```julia
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using ApproxFun, OrdinaryDiffEq, Sundials, LinearSolve
88
using DiffEqDevTools
9-
using LinearAlgebra
9+
using LinearAlgebra, RecursiveFactorization
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using Plots; gr()
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```
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Diff for: ‎benchmarks/StiffODE/Bruss.jmd

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@@ -6,7 +6,8 @@ author: Chris Rackauckas and Utkarsh
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```julia
77
using OrdinaryDiffEq, DiffEqDevTools, Sundials, ParameterizedFunctions, Plots,
88
ODEInterfaceDiffEq, LSODA, SparseArrays, LinearSolve,
9-
LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit
9+
LinearAlgebra, IncompleteLU, AlgebraicMultigrid, Symbolics, ModelingToolkit,
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RecursiveFactorization
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gr()
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const N = 8

Diff for: ‎benchmarks/StiffODE/Hires.jmd

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```julia
77
using OrdinaryDiffEq, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, DiffEqDevTools, Sundials
8-
using LinearAlgebra, StaticArrays
8+
using LinearAlgebra, StaticArrays, RecursiveFactorization
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gr() #gr(fmt=:png)
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Diff for: ‎benchmarks/StiffODE/Orego.jmd

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@@ -6,7 +6,7 @@ author: Chris Rackauckas
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```julia
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using OrdinaryDiffEq, DiffEqDevTools, ParameterizedFunctions, Plots, ODEInterfaceDiffEq, LSODA, Sundials
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gr() #gr(fmt=:png)
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using LinearAlgebra, StaticArrays
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using LinearAlgebra, StaticArrays, RecursiveFactorization
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f = @ode_def Orego begin
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dy1 = p1*(y2+y1*(1-p2*y1-y2))

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