EnsembleSummary deprecated?

Specific Domains Modelling & Simulations
1

I’m very new to Julia so I might be misinterpreting what’s happening here.

The EnsembleSummary function stopped working for me which doesn’t seem to make sense since it is part of SciMLBase so maybe dependencies are messed up somewhere but here’s a MWE from Turing documentation

using Turing, DifferentialEquations, Plots

u0 = [1.0,1.0]
tspan = (0.0,10.0)
function multiplicative_noise!(du,u,p,t)
  x,y = u
  du[1] = p[5]*x
  du[2] = p[6]*y
end
p = [1.5,1.0,3.0,1.0,0.1,0.1]

function lotka_volterra!(du,u,p,t)
  x,y = u
  α,β,γ,δ = p
  du[1] = dx = α*x - β*x*y
  du[2] = dy = δ*x*y - γ*y
end


prob_sde = SDEProblem(lotka_volterra!,multiplicative_noise!,u0,tspan,p)

ensembleprob = EnsembleProblem(prob_sde)
data = solve(ensembleprob,SOSRI(),saveat=0.1,trajectories=1000)

Turing.setadbackend(:forwarddiff)
@model function fitlv(data, prob)
    σ ~ InverseGamma(2,3)
    α ~ truncated(Normal(1.3,0.5),0.5,2.5)
    β ~ truncated(Normal(1.2,0.25),0.5,2)
    γ ~ truncated(Normal(3.2,0.25),2.2,4.0)
    δ ~ truncated(Normal(1.2,0.25),0.5,2.0)
    ϕ1 ~ truncated(Normal(0.12,0.3),0.05,0.25)
    ϕ2 ~ truncated(Normal(0.12,0.3),0.05,0.25)
    α = 1.5
    p = [α,β,γ,δ,ϕ1,ϕ2]
    prob = remake(prob, p=p)
    predicted = solve(prob,SOSRI(),saveat=0.1)

    if predicted.retcode != :Success
        Turing.acclogp!(_varinfo, -Inf)
    end
    for j in 1:length(data)
        for i = 1:length(predicted)
            data[j][i] ~ MvNormal(predicted[i],σ)
        end
    end
end;

EnsembleSummary(data)

and this is the error message

StackOverflowError:

Stacktrace:
 [1] depwarn(::String, ::Symbol; force::Bool) at ./deprecated.jl:79
 [2] depwarn(::String, ::Symbol) at ./deprecated.jl:80
 [3] EnsembleSummary(::EnsembleSolution{Float64,3,Array{RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}},true},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}},true},RSWM{Float64},Nothing,RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Array{Float64,1},Nothing,SDEFunction{true,typeof(lotka_volterra!),typeof(multiplicative_noise!),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(multiplicative_noise!),Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}},Nothing},SOSRI,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}},DiffEqBase.DEStats},1}}) at ./deprecated.jl:71
 [4] EnsembleSummary(::EnsembleSolution{Float64,3,Array{RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}},true},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}},true},RSWM{Float64},Nothing,RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Array{Float64,1},Nothing,SDEFunction{true,typeof(lotka_volterra!),typeof(multiplicative_noise!),LinearAlgebra.UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(multiplicative_noise!),Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}},Nothing},SOSRI,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}},DiffEqBase.DEStats},1}}) at ./deprecated.jl:72 (repeats 32472 times)
 [5] top-level scope at In[5]:1
 [6] include_string(::Function, ::Module, ::String, ::String) at ./loading.jl:1091
2

Indeed the movement of a bunch of code to SciMLBase was a pretty big internal change and there’s a few hiccups. Fixed in SciMLBase v1.6.0 which will release in about 30 minutes.

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