# Julia crashes when doing parameter estimation for a system of differential equations in VScode

**URL:** https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859
**Category:** Modelling & Simulations
**Tags:** diffeq, differentialequation
**Created:** [September 8, 2021, 8:57am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859 "2021-09-08T08:57:42Z")
**Posts on this page:** 10
**Page:** 1

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 8, 2021, 8:57am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/1 "2021-09-08T08:57:42Z")

</div>

I have written a battery model in Julia. This model already runs without any issues.  
I want to now do parameter estimation w.r.t to testing data using DiffEqFlux.jl . However, whenever I run the diffeqflux.scimltrain command, julia crashes with this message

> The terminal process “julia.exe ‘-i’, ‘–banner=no’, ‘–project=C:\Users\madmin1.julia\environments\v1.6’, ‘c:\Users\madmin1.vscode\extensions\julialang.language-julia-1.3.34\scripts\terminalserver\terminalserver.jl’, ‘\.\pipe\vsc-jl-repl-76ed54af-dfa3-4f44-b40b-ceee81f8fccd’, ‘\.\pipe\vsc-jl-cr-2d720729-fad4-47fe-9903-02a83bb0f643’, ‘USE\_REVISE=true’, ‘USE\_PLOTPANE=true’, ‘USE\_PROGRESS=true’, ‘DEBUG\_MODE=false’” terminated with exit code: 3221226356.

I have already run everything else. Its the sciml line that’s causing the Julia to crash. I have also tried restarting the Julia language server and vscode too.

I am running Windows Server 2019 and have the latest Visual studio and Julia versions respectively.  
‘’’

```julia
'''
using DifferentialEquations
using Plots
using DataFrames
using DiffEqFlux, Optim
using CSV
using Flux

plotly()

global const F = 96485.0 # Faraday's constant 
global const R = 8.314462 # J.K⁻¹.mol⁻¹
T = 298 # K

function Δ!(A,N,D,R,Δr)
    """
    Creates the 2nd order FDM matrix for solid phase concentration equation with Neumann boundary conditions
    Comes from the following paper https://drive.google.com/file/d/1czf_P0tt8ViULMVcxTla_u-zaiGCsRE-/view?usp=sharing Page 41
    """
    #Neumann BCs 
    A[1,1] = -D*(R[2] + Δr)/(R[2] *Δr^2)
    A[1,2] = D*(R[2] + Δr)/(R[2] *Δr^2)
    A[N,N-1] = D*(R[N-1] - Δr)/(R[N-1] *Δr^2)
    A[N,N] = -D*(R[N-1] - Δr)/(R[N-1] *Δr^2)

    for i in 2:N-1
        A[i,i] = -2 * D/ (Δr^2)
        A[i,i-1] = D*(R[i] - Δr)/(R[i] *Δr^2)
        A[i,i+1] = D*(R[i] + Δr)/(R[i] *Δr^2)
    end  
end

function U₊_vs_c(θ)
    """
    Returns Cathode equilibrium potential. Source: https://drive.google.com/file/d/16WE-LDKcFBVcLXrl-y-Y5UyfWY1u4GvE/view?usp=sharing 
    """
    return 4.4875 - 0.8090*θ - 0.0428*tanh(18.5138*(θ-0.5542)) - 17.732*tanh(15.789*(θ-0.3117)) + 17.5842*tanh(15.9308*(θ-0.3120))
end

function U₋_vs_c(θ)
    """
    Returns Anode equilibrium potential. Source: https://drive.google.com/file/d/16WE-LDKcFBVcLXrl-y-Y5UyfWY1u4GvE/view?usp=sharing
    """
    return 0.2482 - 0.0909*tanh(29.8538*(θ-0.1234)) - 0.04478*tanh(14.9159*(θ-0.2769)) - 0.0205*tanh(30.4444*(θ-0.6103)) + 1.9793*exp(-39.3631*θ)
end

function Butler_Volmer(c⁺ₛ , c⁻ₛ , p,T=298,I=6.5)
    """
    Returns the cell voltage using Butler_Volmer equation. From paper: https://drive.google.com/file/d/1KwhI43EkDnFEZ2QGybs4o6bq7SOnPugx/view?usp=sharing
    """
    R⁺ₛ ,R⁻ₛ , ε₊ , ε₋ , A , L₊ , L₋ , D₊ , D₋ , k⁺ , k⁻ , C⁰Lᵢ , cₘₐₓ⁺ , cₘₐₓ⁻ ,Rᶠ = p
    α⁺ = α⁻ = 0.5
    try
        i₀⁺ = k⁺ * sqrt(C⁰Lᵢ * c⁺ₛ * (cₘₐₓ⁺ - c⁺ₛ ))
        i₀⁻ = k⁻ * sqrt(C⁰Lᵢ * c⁻ₛ * (cₘₐₓ⁻ - c⁻ₛ ))
        return (R*T/(α⁺*F)) * asinh(I*R⁺ₛ/(2*ε₊*A*i₀⁺)) - (R*T/(α⁻*F)) * asinh(I*R⁻ₛ/(2*ε₋*A*i₀⁻)) + U₊_vs_c(c⁺ₛ/cₘₐₓ⁺) - U₋_vs_c(c⁻ₛ/cₘₐₓ⁻) - (Rᶠ * I)
    catch
        return 0.0# Cell_parameters["Lower cutoff voltage"]
    end
    
end

#Initial Conditions
Cₛ⁺ = ones(Float64,50) .* 17038.0 # calculated concentrations for Cathode
Cₛ⁻ = ones(Float64,50) .* 29866.0 # calculated concentrations for Anode
dCₜ = 0.0 .* ArrayPartition(Cₛ⁺,Cₛ⁻) #Intial fluxes are zero
Cₛ = ArrayPartition(Cₛ⁺,Cₛ⁻)

function SPM!(dCₜ,Cₛ,p,t)
    Cell_R⁺ₛ ,Cell_R⁻ₛ , ε₊ , ε₋ , A , L₊ , L₋ , D₊ , D₋ , k⁺ , k⁻ , C⁰Lᵢ , cₘₐₓ⁺ , cₘₐₓ⁻ ,Rᶠ = p
    
    I = 6.5
    N₊ = 50
    N₋ = 50

    Δr₊ = Cell_R⁺ₛ/(N₊ - 1)
    Δr₋ = Cell_R⁻ₛ/(N₋ -1)
    Rs⁺ₛ = collect(0.0:Δr₊:Cell_R⁺ₛ)
    Rs⁻ₛ = collect(0.0:Δr₋:Cell_R⁻ₛ)
    Acs⁺ = zeros(Float64,N₊,N₊) #FDM matrix for positive solid phase concentration
    Acs⁻ = zeros(Float64,N₋,N₋) #FDM matrix for negative solid phase concentration
    Bcs⁺ = zeros(Float64,N₊,1)
    Bcs⁺[N₊] = (Rs⁺ₛ[N₊ - 1] + Δr₊ )*Cell_R⁺ₛ/(Rs⁺ₛ[N₊-1] * Δr₊ * 3 * ε₊ * F * A * L₊) #Neumann BC source term for positive
    Bcs⁻ = zeros(Float64,N₋,1)
    Bcs⁻[N₋] = -(Rs⁻ₛ[N₋ - 1] + Δr₋ )*Cell_R⁻ₛ/(Rs⁻ₛ[N₋ - 1] * Δr₋ * 3 * ε₋ * F * A * L₋) #Neumann BC source term for negative
    Δ!(Acs⁺,N₊,D₊,Rs⁺ₛ,Δr₊)
    Δ!(Acs⁻,N₋,D₋,Rs⁻ₛ,Δr₋)

    dCₜ[1:N₊] = Acs⁺ * Cₛ[1:N₊] + Bcs⁺ .* I  
    dCₜ[N₊+1:N₋+N₊] = Acs⁻ * Cₛ[N₊+1:N₋+N₊] + Bcs⁻ .* I   
    
end

tspan = (0.0,2300)
p = [5.22e-6,5.86e-6,0.75,0.665,0.1027,7.56e-5,8.52e-5,4.0e-15,3.3e-14,3.42e-6,6.48e-7,1000,63104.0,33133.0,0.1]

SPM_model = ODEProblem(SPM!,Cₛ,tspan,p)
sol = solve(SPM_model,alg_hints = [:stiff])
ts_BV = collect(sol.t[1]:1:sol.t[end])
V1=[]
for t in ts_BV
    push!(V1,Butler_Volmer(sol(t)[50],sol(t)[100],p))
end

plot(ts_BV,V1,label="Initial SPM Prediction")

df = DataFrame(CSV.File("D:\\Shwetank files\\Google Drive\\Life_prediction_data_sets\\CSV_data\\SNL_18650_NCA_25C_0-100_0.5-2C_b_timeseries.csv"))
df = df[!,["Test_Time (s)","Cycle_Index","Current (A)" , "Voltage (V)"]]
dropmissing(df)
filter!(row -> row."Current (A)" < 0.0,df)

Cycle1 = filter(row -> row."Cycle_Index"==6.0,df)
Cycle1[!,"Current (A)"] = Cycle1[!,"Current (A)"].*-1
Cycle1[!,"Test_Time (s)"] = Cycle1[!,"Test_Time (s)"] .- Cycle1[!,"Test_Time (s)"][1]
plot!(Cycle1[!,"Test_Time (s)"],Cycle1[!,"Voltage (V)"],label = "SNL_1C")

function loss(p)
    tmp_prob = remake(SPM_model,p=p)
    tmp_sol = solve(tmp_prob,alg_hints = [:stiff])
    
    V1 = []
    for t in Cycle1[!,"Test_Time (s)"]
        push!(V1,Butler_Volmer(tmp_sol(t)[50],tmp_sol(t)[100],p))
    end
    l = sum(abs2,V1 - Cycle1[!,"Voltage (V)"]) |> sqrt
    return l, tmp_sol
end

pinit = p

cb= function (p,l,pred)
    println("Loss: $l")
    return false
end

res = DiffEqFlux.sciml_train(loss,pinit,ADAM(0.01),cb=cb,maxiters=10)

```

```julia

julia> versioninfo()
Julia Version 1.6.2
Commit 1b93d53fc4 (2021-07-14 15:36 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Xeon(R) Gold 5220 CPU @ 2.20GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, cascadelake)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS =
```

---

<div class="post-metadata">

### Author: ![pfitzseb](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/pfitzseb/32/45566_2.png) [@pfitzseb](https://discourse.julialang.org/u/pfitzseb)
#### Post date: [September 8, 2021, 10:41am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/2 "2021-09-08T10:41:54Z")

</div>

Try running your code in a normal REPL session outside of VSCode; you might get more info that way.

Anyways, the error code you’re getting [apparently indicates heap corruption](https://stackoverflow.com/a/13413054/12113178), so there’s probably not much you can do about it in your code at all.

---

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 8, 2021, 11:28am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/3 "2021-09-08T11:28:46Z")

</div>

> Try running your code in a normal REPL session outside of VSCode; you might get more info that way.

Just tried and it closed before showing anything.  
I will try running the code in a different PC to see if anything changes.

Edit: Nothing changed with my personal PC

Forgot put this:

```julia
(@v1.6) pkg> st
      Status `C:\Users\madmin1\.julia\environments\v1.6\Project.toml`
  [c52e3926] Atom v0.12.34
  [aae01518] BandedMatrices v0.16.10
  [a134a8b2] BlackBoxOptim v0.6.0
  [336ed68f] CSV v0.9.1
  [a93c6f00] DataFrames v1.2.2
  [aae7a2af] DiffEqFlux v1.43.0
  [9fdde737] DiffEqOperators v4.31.0
  [0c46a032] DifferentialEquations v6.18.0
  [ced4e74d] DistributionsAD v0.6.29
  [5b8099bc] DomainSets v0.5.4
  [7a1cc6ca] FFTW v1.4.3
  [587475ba] Flux v0.12.6
  [e5e0dc1b] Juno v0.8.4
  [23fbe1c1] Latexify v0.15.6
  [961ee093] ModelingToolkit v6.4.7
  [429524aa] Optim v1.4.1
  [1dea7af3] OrdinaryDiffEq v5.61.1
  [f0f68f2c] PlotlyJS v0.18.7
  [91a5bcdd] Plots v1.21.3
  [d330b81b] PyPlot v2.9.0
  [37e2e3b7] ReverseDiff v1.9.0
  [c3572dad] Sundials v4.5.3
  [0c5d862f] Symbolics v3.2.3
  [fce5fe82] Turing v0.17.4
  [fdbf4ff8] XLSX v0.7.7

```

---

<div class="post-metadata">

### Author: ![Dan.phi](https://avatars.discourse-cdn.com/v4/letter/d/c89c15/32.png) [@Dan.phi](https://discourse.julialang.org/u/Dan.phi)
#### Post date: [September 10, 2021, 10:28am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/4 "2021-09-10T10:28:35Z")

</div>

I’m curious whether you solved this? I am getting the same exit code, also running fairly simple code.

---

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 10, 2021, 10:48am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/5 "2021-09-10T10:48:21Z")

</div>

Nope. I have raised it as an issue on DiffEqFlux.jl github. Link:  
[Julia crashes during parameter estimation for a system of differential equations](https://github.com/SciML/DiffEqFlux.jl/issues/619)

---

<div class="post-metadata">

### Author: ![Dan.phi](https://avatars.discourse-cdn.com/v4/letter/d/c89c15/32.png) [@Dan.phi](https://discourse.julialang.org/u/Dan.phi)
#### Post date: [September 10, 2021, 10:58am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/6 "2021-09-10T10:58:23Z")

</div>

I only recently updated to Julia 1.6.2 and I am thinking it might be a VS Code thing rather than specific packages.

---

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 10, 2021, 11:03am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/7 "2021-09-10T11:03:27Z")

</div>

I did try running this in a standalone REPL and it still crashed. I don’t think its a vscode issue

---

<div class="post-metadata">

### Author: ![pfitzseb](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/pfitzseb/32/45566_2.png) [@pfitzseb](https://discourse.julialang.org/u/pfitzseb)
#### Post date: [September 10, 2021, 11:06am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/8 "2021-09-10T11:06:17Z")

</div>

Do try starting a terminal and then start Julia inside. That way you won’t lose the crash output.

---

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 11, 2021, 10:14am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/9 "2021-09-11T10:14:09Z")

</div>

I ran this on my PC in Atom/Juno and I got a better message:

```julia
Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7ff919a74408 -- RtlSetUserValueHeap at C:\Windows\SYSTEM32\ntdll.dll (unknown line)
in expression starting at C:\Users\verma\OneDrive\Desktop\Modelling\SPM.jl:140
RtlSetUserValueHeap at C:\Windows\SYSTEM32\ntdll.dll (unknown line)
RtlAllocateHeap at C:\Windows\SYSTEM32\ntdll.dll (unknown line)
RtlAllocateHeap at C:\Windows\SYSTEM32\ntdll.dll (unknown line)
malloc at C:\Windows\System32\msvcrt.dll (unknown line)

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7ff919a9e3cb --

```

```julia
julia> versioninfo()
Julia Version 1.6.2
Commit 1b93d53fc4 (2021-07-14 15:36 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)      
  CPU: AMD Ryzen 5 3500 6-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, znver2)
Environment:
  JULIA_EDITOR = "C:\Users\verma\AppData\Local\atom\app-1.58.0\atom.exe" -a
  JULIA_NUM_THREADS = 6

```

---

<div class="post-metadata">

### Author: ![shwetank\_verma](https://avatars.discourse-cdn.com/v4/letter/s/22d042/32.png) [@shwetank\_verma](https://discourse.julialang.org/u/shwetank_verma)
#### Post date: [September 12, 2021, 8:48am UTC](https://discourse.julialang.org/t/julia-crashes-when-doing-parameter-estimation-for-a-system-of-differential-equations-in-vscode/67859/10 "2021-09-12T08:48:18Z")

</div>

I have finally fixed the issue!  
In my ODE function, I had a collect function:

```julia
    Δr₊ = Cell_R⁺ₛ/(N₊ - 1)
    Δr₋ = Cell_R⁻ₛ/(N₋ -1)
    Rs⁺ₛ = collect(0.0:Δr₊:Cell_R⁺ₛ)
    Rs⁻ₛ = collect(0.0:Δr₋:Cell_R⁻ₛ)

```

I replaced the collect function with a for loop:

```julia
Δr₊ = Cell_R⁺ₛ/(N₊ - 1)
Δr₋ = Cell_R⁻ₛ/(N₋ -1)

Rs⁺ₛ = zeros(Float64,50,1)
Rs⁻ₛ = zeros(Float64,50,1)
for i in 1:50
 Rs⁺ₛ[i] = Cell_R⁺ₛ * (i-1)
 Rs⁻ₛ[i] = Cell_R⁻ₛ * (i-1)
end

```

And now it works!