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Update the Hodgkin-Huxley benchmark some more
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@nathanaelbosch
nathanaelbosch committed Nov 7, 2023
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29 changes: 12 additions & 17 deletions benchmarks/hodgkinhuxley.jmd
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Original file line number Diff line number Diff line change
@@ -1,11 +1,8 @@
# Hodgkin-Huxley benchmark

Adapted from
[SciMLBenchmarks.jl](https://docs.sciml.ai/SciMLBenchmarksOutput/stable/NonStiffODE/LotkaVolterra_wpd/).

```julia
using LinearAlgebra, Statistics
using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Plots
using DiffEqDevTools, SciMLBase, OrdinaryDiffEq, Plots, SimpleUnPack
using ProbNumDiffEq

# Plotting theme
Expand All @@ -29,15 +26,14 @@ theme(:dao;
αh(V, VT) = 0.128 * exp(-(V - VT - 17) / 18)
βh(V, VT) = 4 / (1 + exp(-(V - VT - 40) / 5))


I(t) = 500
Inj(t) = (10 <= t <= 90) ? 500one(t) : zero(t)

function f(du, u, p, t)
@unpack gNa, gK, ENa, EK, area, C, Eleak, VT, gleak = p

V, m, n, h = u

I_inj = I(t) * 1e-6 # uA
I_inj = Inj(t) * 1e-6 # uA

du[2] = dmdt = (αm(V, VT) * (1 - m) - βm(V, VT) * m)
du[3] = dndt = (αn(V, VT) * (1 - n) - βn(V, VT) * n)
Expand Down Expand Up @@ -77,19 +73,18 @@ plot(test_sol,
DENSE = SAVE_EVERYSTEP = false

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -122,19 +117,18 @@ plot(
DENSE = SAVE_EVERYSTEP = true

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -167,7 +161,7 @@ plot(
```julia
DENSE = SAVE_EVERYSTEP = false

dts = 10.0 .^ range(-2, -3, length=10)
dts = 10.0 .^ range(-2, -3, length=10)[begin:end-1]
abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
Expand Down Expand Up @@ -210,7 +204,8 @@ plot(
```julia
DENSE = SAVE_EVERYSTEP = true

dts = 10.0 .^ range(-2, -3, length=length(abstols))
dts = 10.0 .^ range(-2, -3, length=10)[begin:end-1]
abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
_setups = [
Expand Down
834 changes: 417 additions & 417 deletions docs/src/benchmarks/figures/hodgkinhuxley_2_1.svg
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434 changes: 196 additions & 238 deletions docs/src/benchmarks/figures/hodgkinhuxley_3_1.svg
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424 changes: 192 additions & 232 deletions docs/src/benchmarks/figures/hodgkinhuxley_4_1.svg
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391 changes: 157 additions & 234 deletions docs/src/benchmarks/figures/hodgkinhuxley_5_1.svg
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385 changes: 152 additions & 233 deletions docs/src/benchmarks/figures/hodgkinhuxley_6_1.svg
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65 changes: 32 additions & 33 deletions docs/src/benchmarks/hodgkinhuxley.md
View file
Original file line number Diff line number Diff line change
@@ -1,11 +1,8 @@
# Hodgkin-Huxley benchmark

Adapted from
[SciMLBenchmarks.jl](https://docs.sciml.ai/SciMLBenchmarksOutput/stable/NonStiffODE/LotkaVolterra_wpd/).

```julia
using LinearAlgebra, Statistics
using DiffEqDevTools, ParameterizedFunctions, SciMLBase, OrdinaryDiffEq, Plots
using DiffEqDevTools, SciMLBase, OrdinaryDiffEq, Plots, SimpleUnPack
using ProbNumDiffEq

# Plotting theme
Expand All @@ -32,15 +29,14 @@ theme(:dao;
αh(V, VT) = 0.128 * exp(-(V - VT - 17) / 18)
βh(V, VT) = 4 / (1 + exp(-(V - VT - 40) / 5))


I(t) = 500
Inj(t) = (10 <= t <= 90) ? 500one(t) : zero(t)

function f(du, u, p, t)
@unpack gNa, gK, ENa, EK, area, C, Eleak, VT, gleak = p

V, m, n, h = u

I_inj = I(t) * 1e-6 # uA
I_inj = Inj(t) * 1e-6 # uA

du[2] = dmdt = (αm(V, VT) * (1 - m) - βm(V, VT) * m)
du[3] = dndt = (αn(V, VT) * (1 - n) - βn(V, VT) * n)
Expand Down Expand Up @@ -84,19 +80,18 @@ plot(test_sol,
DENSE = SAVE_EVERYSTEP = false

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -133,19 +128,18 @@ plot(
DENSE = SAVE_EVERYSTEP = true

_setups = [
"EK0(2)" => Dict(:alg=>EK0(order=2, smooth=DENSE))
"EK0(3)" => Dict(:alg=>EK0(order=3, smooth=DENSE))
"EK0(5)" => Dict(:alg=>EK0(order=5, smooth=DENSE))
"EK1(2)" => Dict(:alg=>EK1(order=2, smooth=DENSE))
"EK1(3)" => Dict(:alg=>EK1(order=3, smooth=DENSE))
"EK1(5)" => Dict(:alg=>EK1(order=5, smooth=DENSE))
"EK1(8)" => Dict(:alg=>EK1(order=8, smooth=DENSE))
"RosenbrockExpEK1(3)" => Dict(:alg=>RosenbrockExpEK(order=3, smooth=DENSE))
"RosenbrockExpEK1(5)" => Dict(:alg=>RosenbrockExpEK(order=5, smooth=DENSE))
"RosenbrockExpEK1(8)" => Dict(:alg=>RosenbrockExpEK(order=8, smooth=DENSE))
]

labels = first.(_setups)
setups = last.(_setups)
colors = [1 1 2 2 2 3 3 3]
colors = [1 1 2 2 2 3 3]

abstols = 1.0 ./ 10.0 .^ (6:10)
reltols = 1.0 ./ 10.0 .^ (3:7)
Expand Down Expand Up @@ -182,7 +176,7 @@ plot(
```julia
DENSE = SAVE_EVERYSTEP = false

dts = 10.0 .^ range(-2, -3, length=10)
dts = 10.0 .^ range(-2, -3, length=10)[begin:end-1]
abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
Expand Down Expand Up @@ -229,7 +223,8 @@ plot(
```julia
DENSE = SAVE_EVERYSTEP = true

dts = 10.0 .^ range(-2, -3, length=length(abstols))
dts = 10.0 .^ range(-2, -3, length=10)[begin:end-1]
abstols = reltols = repeat([missing], length(dts))

DM = FixedDiffusion()
_setups = [
Expand Down Expand Up @@ -319,13 +314,16 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Project.toml`
[65888b18] ParameterizedFunctions v5.16.0
[91a5bcdd] Plots v1.39.0
[bf3e78b0] ProbNumDiffEq v0.13.0 `~/.julia/dev/ProbNumDiffEq`
[0bca4576] SciMLBase v2.6.0
[0bca4576] SciMLBase v2.7.3
[505e40e9] SciPyDiffEq v0.2.1
[ce78b400] SimpleUnPack v1.1.0
[90137ffa] StaticArrays v1.6.5
[c3572dad] Sundials v4.20.1
[44d3d7a6] Weave v0.10.12
[0518478a] deSolveDiffEq v0.1.1
Warning The project dependencies or compat requirements have changed since
the manifest was last resolved. It is recommended to `Pkg.resolve()` or con
sider `Pkg.update()` if necessary.
```


Expand All @@ -347,7 +345,6 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[ec485272] ArnoldiMethod v0.2.0
[c9d4266f] ArrayAllocators v0.3.0
[4fba245c] ArrayInterface v7.5.1
[30b0a656] ArrayInterfaceCore v0.1.29
[6e4b80f9] BenchmarkTools v1.3.2
[e2ed5e7c] Bijections v0.1.6
[d1d4a3ce] BitFlags v0.1.7
Expand Down Expand Up @@ -384,14 +381,14 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[864edb3b] DataStructures v0.18.15
[e2d170a0] DataValueInterfaces v1.0.0
[8bb1440f] DelimitedFiles v1.9.1
[2b5f629d] DiffEqBase v6.136.0
⌃ [2b5f629d] DiffEqBase v6.138.0
[459566f4] DiffEqCallbacks v2.33.1
[f3b72e0c] DiffEqDevTools v2.39.0
[77a26b50] DiffEqNoiseProcess v5.19.0
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.15.1
[b4f34e82] Distances v0.10.10
[31c24e10] Distributions v0.25.102
[31c24e10] Distributions v0.25.103
[ffbed154] DocStringExtensions v0.9.3
⌅ [5b8099bc] DomainSets v0.6.7
[fa6b7ba4] DualNumbers v0.6.8
Expand Down Expand Up @@ -457,10 +454,10 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[50d2b5c4] Lazy v0.15.1
[1d6d02ad] LeftChildRightSiblingTrees v0.2.0
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.15.0
⌃ [7ed4a6bd] LinearSolve v2.15.0
[2ab3a3ac] LogExpFunctions v0.3.26
[e6f89c97] LoggingExtras v1.0.3
⌃ [bdcacae8] LoopVectorization v0.12.165
[bdcacae8] LoopVectorization v0.12.166
[10e44e05] MATLAB v0.8.4
[e2752cbe] MATLABDiffEq v1.2.0
[33e6dc65] MKL v0.6.1
Expand All @@ -479,7 +476,7 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[2774e3e8] NLsolve v4.5.1
[77ba4419] NaNMath v1.0.2
⌅ [356022a1] NamedDims v0.2.50
[8913a72c] NonlinearSolve v2.6.0
⌃ [8913a72c] NonlinearSolve v2.6.1
[54ca160b] ODEInterface v0.5.0
[09606e27] ODEInterfaceDiffEq v3.13.3
[6fd5a793] Octavian v0.3.27
Expand All @@ -500,7 +497,7 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[995b91a9] PlotUtils v1.3.5
[91a5bcdd] Plots v1.39.0
[e409e4f3] PoissonRandom v0.4.4
[f517fe37] Polyester v0.7.8
⌃ [f517fe37] Polyester v0.7.8
[1d0040c9] PolyesterWeave v0.2.1
⌅ [f27b6e38] Polynomials v3.2.13
[2dfb63ee] PooledArrays v1.4.3
Expand Down Expand Up @@ -532,12 +529,12 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[fdea26ae] SIMD v3.4.5
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.42
[0bca4576] SciMLBase v2.6.0
[0bca4576] SciMLBase v2.7.3
[e9a6253c] SciMLNLSolve v0.1.9
[c0aeaf25] SciMLOperators v0.3.6
⌃ [c0aeaf25] SciMLOperators v0.3.6
[505e40e9] SciPyDiffEq v0.2.1
⌃ [6c6a2e73] Scratch v1.2.0
[91c51154] SentinelArrays v1.4.0
[6c6a2e73] Scratch v1.2.1
⌃ [91c51154] SentinelArrays v1.4.0
[efcf1570] Setfield v1.1.1
[1277b4bf] ShiftedArrays v2.0.0
[992d4aef] Showoff v1.0.3
Expand All @@ -548,7 +545,7 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[66db9d55] SnoopPrecompile v1.0.3
[b85f4697] SoftGlobalScope v1.1.0
[a2af1166] SortingAlgorithms v1.2.0
[47a9eef4] SparseDiffTools v2.9.2
⌃ [47a9eef4] SparseDiffTools v2.9.2
[e56a9233] Sparspak v0.3.9
[276daf66] SpecialFunctions v2.3.1
[928aab9d] SpecialMatrices v3.0.0
Expand Down Expand Up @@ -578,7 +575,7 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[a759f4b9] TimerOutputs v0.5.23
[c751599d] ToeplitzMatrices v0.8.2
[0796e94c] Tokenize v0.5.25
[3bb67fe8] TranscodingStreams v0.10.1
[3bb67fe8] TranscodingStreams v0.10.2
[a2a6695c] TreeViews v0.3.0
[d5829a12] TriangularSolve v0.1.20
[410a4b4d] Tricks v0.1.8
Expand All @@ -597,7 +594,6 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[1b915085] WinReg v1.0.0
[ddb6d928] YAML v0.4.9
[c2297ded] ZMQ v1.2.2
[700de1a5] ZygoteRules v0.2.4
[0518478a] deSolveDiffEq v0.1.1
[6e34b625] Bzip2_jll v1.0.8+0
[83423d85] Cairo_jll v1.16.1+1
Expand Down Expand Up @@ -636,7 +632,7 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[91d4177d] Opus_jll v1.3.2+0
[30392449] Pixman_jll v0.42.2+0
[c0090381] Qt6Base_jll v6.5.2+2
⌃ [c0090381] Qt6Base_jll v6.5.2+2
[f50d1b31] Rmath_jll v0.4.0+0
⌅ [fb77eaff] Sundials_jll v5.2.1+0
[a44049a8] Vulkan_Loader_jll v1.3.243+0
Expand Down Expand Up @@ -737,6 +733,9 @@ Status `~/.julia/dev/ProbNumDiffEq/benchmarks/Manifest.toml`
Info Packages marked with ⌃ and ⌅ have new versions available, but those wi
th ⌅ are restricted by compatibility constraints from upgrading. To see why
use `status --outdated -m`
Warning The project dependencies or compat requirements have changed since
the manifest was last resolved. It is recommended to `Pkg.resolve()` or con
sider `Pkg.update()` if necessary.
```


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