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Merged
merged 9 commits into from
Nov 19, 2024
Merged

Bump Bio for Catalyst v14 and MTK v9 #1022

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7016ad1
Bump Bio for Catalyst v14 and MTK v9
ChrisRackauckas Jul 28, 2024
87a26f9
complete all
ChrisRackauckas Jul 28, 2024
ffb64af
complete converted sys and get u0 and p from oprob
isaacsas Aug 12, 2024
4fecc66
manifest bump
ChrisRackauckas Sep 11, 2024
f49e30f
remove broken and unnecessary plot limit calculation
ChrisRackauckas Sep 14, 2024
b497130
Manifest
ChrisRackauckas Nov 8, 2024
b71e60b
lts
ChrisRackauckas Nov 9, 2024
b2bd2f1
bumps
ChrisRackauckas Nov 11, 2024
e1a5758
should fix the polyesterthreads issue
ChrisRackauckas Nov 17, 2024
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43 changes: 12 additions & 31 deletions benchmarks/Bio/BCR.jmd
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@ tf = 100000.0
# generate ModelingToolkit ODEs
@timeit to "Parse Network" prnbng = loadrxnetwork(BNGNetwork(), joinpath(datadir, "bcr.net"))
show(to)
rn = prnbng.rn
rn = complete(prnbng.rn)
obs = [eq.lhs for eq in observed(rn)]

@timeit to "Create ODESys" osys = convert(ODESystem, rn)
@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn))
show(to)

tspan = (0.,tf)
Expand All @@ -56,12 +56,12 @@ As compiling the ODE derivative functions has in the past taken longer than
running a simulation, we first force compilation by evaluating these functions
one time.
```julia
u = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn))
u = oprob.u0
du = copy(u)
p = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn))
p = oprob.p
@timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.)
@timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.)
sparsejacprob.f(du,u,p,0.)
@timeit to "ODE rhs spjac Eval1" sparsejacprob.f(du,u,p,0.)
show(to)
```

We also time the ODE rhs function with BenchmarkTools as it is more accurate
Expand Down Expand Up @@ -99,18 +99,6 @@ test_sol = TestSolution(sol);
default(legendfontsize=7,framestyle=:box,gridalpha=0.3,gridlinewidth=2.5)
```

#### Declares a plotting helper function

```julia
function plot_settings(wp)
times = vcat(map(wp -> wp.times, wp.wps)...)
errors = vcat(map(wp -> wp.errors, wp.wps)...)
xlimit = 10 .^ (floor(log10(minimum(errors))), ceil(log10(maximum(errors))))
ylimit = 10 .^ (floor(log10(minimum(times))), ceil(log10(maximum(times))))
return xlimit,ylimit
end
```

#### Declare pre-conditioners
```julia
using IncompleteLU, LinearAlgebra
Expand Down Expand Up @@ -189,8 +177,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups;
saveat=tf/10000.,appxsol=[test_sol,test_sol,test_sol],maxiters=Int(1e6),numruns=1)

names = ["lsoda" "CVODE_BDF" "CVODE_BDF (LapackDense)" "CVODE_BDF (GMRES)" "CVODE_BDF (GMRES, iLU)" "CVODE_BDF (KLU, sparse jac)"]
xlimit,ylimit = plot_settings(wp)
plot(wp;label=names,xlimit=xlimit,ylimit=ylimit)
plot(wp;label=names)
```

## Work-Precision Diagrams (various Julia solvers)
Expand All @@ -213,8 +200,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2,
saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1)

names = ["TRBDF2" "QNDF" "FBDF" "KenCarp4"]
xlimit,ylimit = plot_settings(wp)
plot(wp;label=names,xlimit=xlimit,ylimit=ylimit)
plot(wp;label=names)
```

#### Declare solvers (using GMRES linear solver).
Expand All @@ -235,8 +221,7 @@ wp = WorkPrecisionSet(oprob,abstols,reltols,setups;error_estimate=:l2,
saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1)

names = ["TRBDF2 (GMRES)" "QNDF (GMRES)" "FBDF (GMRES)" "KenCarp4 (GMRES)"]
xlimit,ylimit = plot_settings(wp)
plot(wp;label=names,xlimit=xlimit,ylimit=ylimit)
plot(wp;label=names)
```

#### Declare solvers (using GMRES linear solver, with pre-conditioner).
Expand All @@ -257,8 +242,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2,
saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1)

names = ["TRBDF2 (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "KenCarp4 (GMRES, iLU)"]
xlimit,ylimit = plot_settings(wp)
plot(wp;label=names,xlimit=xlimit,ylimit=ylimit)
plot(wp;label=names)
```

#### Declare solvers (using sparse jacobian)
Expand All @@ -282,8 +266,7 @@ wp = WorkPrecisionSet(sparsejacprob,abstols,reltols,setups;error_estimate=:l2,
saveat=tf/10000.,appxsol=test_sol,maxiters=Int(1e6),numruns=1)

names = ["TRBDF2 (KLU, sparse jac)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"]
xlimit,ylimit = plot_settings(wp)
plot(wp;label=names,xlimit=xlimit,ylimit=ylimit)
plot(wp;label=names)
```

## Summary of results
Expand Down Expand Up @@ -312,9 +295,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups;
names = ["CVODE_BDF (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"]
colors = [:green :deepskyblue1 :dodgerblue2 :royalblue2 :slateblue3 :lightskyblue]
markershapes = [:octagon :hexagon :rtriangle :pentagon :ltriangle :star5]
xlimit,ylimit = plot_settings(wp)
xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95];
plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
```

```julia, echo = false
Expand Down
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