Updating ParameterEstimation Benchmarks #1160
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…into ParameterEstimation
…123/SciMLBenchmarks.jl into ParameterEstimation
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The build for ParameterEstimation and PINNErrorVsTime hasn't started on the CI since the last 10 hours |
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@ChrisRackauckas in LotkaVolterraParameterEstimation.jmd I got the following error on running the code which seems to be related to the blackbox optim @btime res1 = solve(optprob, BBO_adaptive_de_rand_1_bin(), maxiters = 4e3) Any fixes you might suggest for this?? |
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Do you have the latest version of OptimizationBBO and Optimization? Can you try and make an MWE? |
Yes. I am using the latest version of OptimizationBBO and Optimization. Here's the code for the MWE: using ParameterizedFunctions, OrdinaryDiffEq, DiffEqParamEstim, Optimization, ForwardDiff
using OptimizationBBO, OptimizationNLopt, Plots, RecursiveArrayTools, BenchmarkTools
using ModelingToolkit: t_nounits as t, D_nounits as D
gr(fmt=:png)
loc_bounds = Tuple{Float64, Float64}[(0, 5), (0, 5), (0, 5), (0, 5)]
glo_bounds = Tuple{Float64, Float64}[(0, 10), (0, 10), (0, 10), (0, 10)]
loc_init = [1,0.5,3.5,1.5]
glo_init = [5,5,5,5]
@mtkmodel LotkaVolterraTest begin
@parameters begin
a = 1.5 # Growth rate of prey
b = 1.0 # Predation rate
c = 3.0 # Death rate of predators
d = 1.0 # Reproduction rate of predators
e = 0.0 # Additional parameter (if needed)
end
@variables begin
x(t) = 1.0 # Population of prey with initial condition
y(t) = 1.0 # Population of predators with initial condition
end
@equations begin
D(x) ~ a * x - b * x * y
D(y) ~ -c * y + d * x * y
end
end
@mtkbuild f = LotkaVolterraTest()
u0 = [1.0,1.0] #initial values
tspan = (0.0,10.0)
p = [1.5,1.0,3.0,1,0] #parameters used, these need to be estimated from the data
tspan = (0.0, 30.0) # sample of 3000 observations over the (0,30) timespan
prob = ODEProblem(f, u0, tspan,p)
tspan2 = (0.0, 3.0) # sample of 3000 observations over the (0,30) timespan
prob_short = ODEProblem(f, u0, tspan2,p)
dt = 30.0/3000
tf = 30.0
tinterval = 0:dt:tf
time_points = collect(tinterval)
h = 0.01
M = 300
tstart = 0.0
tstop = tstart + M * h
tinterval_short = 0:h:tstop
t_short = collect(tinterval_short)
#Generate Data
data_sol_short = solve(prob_short,Tsit5(),saveat=t_short,reltol=1e-9,abstol=1e-9)
data_short = convert(Array, data_sol_short)
data_sol = solve(prob,Tsit5(),saveat=time_points,reltol=1e-9,abstol=1e-9)
data = convert(Array, data_sol)
t_concrete = collect(0.0:dt:tf)
obj = build_loss_objective(prob,Vern9(),L2Loss(t_concrete,data),tstops=t_concrete,reltol=1e-9,abstol=1e-9)
optprob = OptimizationProblem(obj, glo_init, lb = first.(glo_bounds), ub = last.(glo_bounds))
@btime res1 = solve(optprob, BBO_adaptive_de_rand_1_bin(), maxiters = 4e3)The error: |
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All packages updated with the manifest resolved. |
The MWE code will probably now give the following error |
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Only one built? |
Actually, I modified the code for all the three and all three were building on the CI but since the past few runs and commits, I found that only one was building on the CI, for some reason |
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@ChrisRackauckas All the errors here have been fixed and all the three algorithms have been built successfully. Can you please review ?? I think we are ready to merge this. |
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