SciML / ModelingToolkit.jl

An acausal modeling framework for automatically parallelized scientific machine learning (SciML) in Julia. A computer algebra system for integrated symbolics for physics-informed machine learning and automated transformations of differential equations
https://mtk.sciml.ai/dev/
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MTK -- linearization bug (?) #2888

Open B-LIE opened 4 months ago

B-LIE commented 4 months ago

When I try to linearize my model, I get an "BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]" error🐞

Here is my Julia/MTK statement with partial error message:

julia> linearize(of_noi, [of_noi.dm.ṁ_i], [of_noi.dm.p], op=Dict(of_noi.dm.ṁ_i => u_ṁ_c2d(0) ))
BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]

Stacktrace:
  [1] getindex
    @ .\essentials.jl:13 [inlined]
  [2] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:369 [inlined]
  [3] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:368 [inlined]
  [4] check_consistency(state::TearingState{ODESystem}, orig_inputs::Set{Any})
...

Expected behavior

I expected Julia to respond with a collection of linearized matrices A, B, C, D, etc.

Minimal Reproducible Example 👇

I have not been able to create a minimal reproducible example (MRE). I tried to make a couple of similar examples, but in both of those cases, my code works.

Still, to illustrate what I do, I include a similar but slightly simpler example. In this simplified example, I consider a Telegraph Line module:

image

which I then cascade into a Telegraph Line system:

# Packages
using ModelingToolkit
using ModelingToolkit: t_nounits as t, D_nounits as Dt
using DifferentialEquations
# 
# Telegraph Line Module
#
@mtkmodel Telegraph_Module begin
    # Model parameters
    @parameters begin 
        # Default parameters X_, X ∈ {R,L,G,C} taken from https://en.wikipedia.org/wiki/Telegrapher%27s_equations
        R_=172.28,      [description = "Unit resistance, Ω/km"]
        L_=612.5e-6,    [description = "Unit inductance, H/km"]
        G_=0.072e-6,    [description = "Unit conductance, S/km"]
        C_=51.57e-9,    [description = "Unit capacitance, F/km"]
        Δx=1,           [description = "Module length, km"]
        R=R_*Δx,        [description = "Resistance, Ω"]
        L=L_*Δx,        [description = "Inductance, H"]
        G=G_*Δx,        [description = "Conductance, S"]
        C=C_*Δx,        [description = "Capacitance, F"]
    end
    #
    # Model variables, with initial values
    @variables begin
        # Inputs
        u(t),           [description = "Voltage at input, V"]
        # Variables
        u₊(t)=0.5,      [description = "Voltage at output, V"]
        i(t)=1e-3,      [description = "Current at input, A"]
        i₊(t),          [description = "Current at output, A"]
    end
    #
    # Telegraph line module equations
    #
    @equations begin
        u ~ R*i + L*Dt(i) + u₊
        i ~ G*u₊ + C*Dt(u₊) + i₊
    end
end
# 
# Telegraph Line System
# -- cascaded modules + input + load
#
@mtkmodel Telegraph_Line begin
    #
    @parameters begin
        R_L=600,    [description = "Load resistance, Ω"]
    end
    #
    @structural_parameters begin
        ℓ = 10 # km
        N = 2
    end
    # Components used
    @components begin 
        tm = [Telegraph_Module(; Δx=ℓ/N) for i in 1:N]
    end
    # Equations for connecting components
    @equations begin
        # Distribution manifold splitting
        tm[1].u ~ sin(2π*1_000*t)                 # Input at 1 kHz
        [tm[j].u ~ tm[j-1].u₊ for j in 2:N]...
        [tm[j].i ~ tm[j-1].i₊ for j in 2:N]...
        tm[N].i₊ ~ tm[N].u₊/R_L                     # Terminal load
    end
end

I then instantiate this model + run the simulation successfully:

ℓ = 18
N = 3
#
@mtkbuild tL = Telegraph_Line(; ℓ=ℓ, N=N)
# 
tspan = (0, 1e-2)
#u_ṁ_c2d(t) = ṁ_c2d_constant(t)
#
prob = ODEProblem(tL, [], tspan)
sol = solve(prob)

This works fine.

Next, I want to linearize the model. To do so, without using ModelingToolkitStandardLibrary and Analysis Points, I create a copy of the system model where I comment out the definition of input(s), i.e., I create a version with "no inputs" (_noi):

@mtkmodel Telegraph_Line_noi begin
    #
    @parameters begin
        R_L=3e3,    [description = "Load resistance, Ω"]
    end
    #
    @structural_parameters begin
        ℓ = 10 # km
        N = 2
    end
    # Components used
    @components begin 
        tm = [Telegraph_Module(; Δx=ℓ/N) for i in 1:N]
    end
    # Equations for connecting components
    @equations begin
        # Distribution manifold splitting
    #    tm[1].u ~ sin(2π*1_000*t)                 # Input
        [tm[j].u ~ tm[j-1].u₊ for j in 2:N]...
        [tm[j].i ~ tm[j-1].i₊ for j in 2:N]...
        tm[N].i₊ ~ tm[N].u₊/R_L
    end
end

which I then instantiate and do the linearization:

@named tL_noi = Telegraph_Line_noi(; ℓ=ℓ, N=N)
tL_noi = complete(tL_noi)
# 
matx_, _ = linearize(tL_noi, [tL_noi.tm_1.u], [tL_noi.tm_3.i₊], op=Dict(tL_noi.tm_1.u => 1))

This works (as expected).

My problem is that when I do the exactly same thing for my other, slightly more complex model, (i) doing simulation with the balanced model works, but (ii) when creating a model with inputs commented out, linearization leads to the error message with BoundsError.

Error & Stacktrace ⚠️

{
    "name": "BoundsError",
    "message": "BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]",
    "stack": "BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]\n\nStacktrace:\n  [1] getindex\n    @ .\\essentials.jl:13 [inlined]\n  [2] 𝑑neighbors\n    @ C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\bipartite_graph.jl:369 [inlined]\n  [3] 𝑑neighbors\n    @ C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\bipartite_graph.jl:368 [inlined]\n  [4] check_consistency(state::TearingState{ODESystem}, orig_inputs::Set{Any})\n    @ ModelingToolkit.StructuralTransformations C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\structural_transformation\\utils.jl:96\n  [5] _structural_simplify!(state::TearingState{ODESystem}, io::Tuple{Vector{Num}, Vector{Num}}; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, dummy_derivative::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\systemstructure.jl:691\n  [6] structural_simplify!(state::TearingState{ODESystem}, io::Tuple{Vector{Num}, Vector{Num}}; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\systemstructure.jl:634\n  [7] __structural_simplify(sys::ODESystem, io::Tuple{Vector{Num}, Vector{Num}}; simplify::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\systems.jl:83\n  [8] structural_simplify(sys::ODESystem, io::Tuple{Vector{Num}, Vector{Num}}; simplify::Bool, split::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\systems.jl:24\n  [9] structural_simplify\n    @ C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\systems.jl:21 [inlined]\n [10] io_preprocessing(sys::ODESystem, inputs::Vector{Num}, outputs::Vector{Num}; simplify::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\abstractsystem.jl:1934\n [11] linearization_function(sys::ODESystem, inputs::Vector{Num}, outputs::Vector{Num}; simplify::Bool, initialize::Bool, op::Dict{Num, Float64}, p::SciMLBase.NullParameters, zero_dummy_der::Bool, initialization_solver_alg::GeneralizedFirstOrderAlgorithm{nothing, :TrustRegion, Missing, NonlinearSolve.GenericTrustRegionScheme{NonlinearSolve.RadiusUpdateSchemes.__Simple, Rational{Int64}, Rational{Int64}, Rational{Int64}, Rational{Int64}, Rational{Int64}, Nothing, Nothing, Nothing, Nothing}, Dogleg{NewtonDescent{Nothing, typeof(NonlinearSolve.DEFAULT_PRECS)}, SteepestDescent{Nothing, typeof(NonlinearSolve.DEFAULT_PRECS)}}, Nothing, Nothing, Nothing}, eval_expression::Bool, eval_module::Module, warn_initialize_determined::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\abstractsystem.jl:1990\n [12] linearization_function\n    @ C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\abstractsystem.jl:1978 [inlined]\n [13] linearize(sys::ODESystem, inputs::Vector{Num}, outputs::Vector{Num}; op::Dict{Num, Float64}, t::Float64, allow_input_derivatives::Bool, zero_dummy_der::Bool, kwargs::@Kwargs{})\n    @ ModelingToolkit C:\\Users\\Bernt\\.julia\\packages\\ModelingToolkit\\7em8Z\\src\\systems\\abstractsystem.jl:2429\n [14] top-level scope\n    @ c:\\Users\\Bernt\\OneDrive\\Documents\\researchUSN\\Supervisor\\PhD\\Kushila_Jayamanne\\Notebooks\\gas-lifted_oil-field_DAE_components.ipynb:1"
}

Environment (please complete the following information):

Status `C:\Users\Bernt\.julia\environments\v1.10\Project.toml`
⌅ [c3fe647b] AbstractAlgebra v0.41.10
  [6e4b80f9] BenchmarkTools v1.5.0
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  [336ed68f] CSV v0.10.14
  [a6e380b2] ControlSystems v1.10.3
  [687d7614] ControlSystemsMTK v2.1.0
  [a93c6f00] DataFrames v1.6.1
⌅ [82cc6244] DataInterpolations v4.8.0
  [6748aba7] DeepEquilibriumNetworks v2.1.4
  [0c46a032] DifferentialEquations v7.13.0
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  [0b43b601] Groebner v0.7.5
  [7073ff75] IJulia v1.25.0
  [b964fa9f] LaTeXStrings v1.3.1
  [23fbe1c1] Latexify v0.16.4
  [b2108857] Lux v0.5.61
  [94925ecb] MethodOfLines v0.11.1
  [961ee093] ModelingToolkit v9.25.0
  [16a59e39] ModelingToolkitStandardLibrary v2.7.5
⌅ [2edaba10] Nemo v0.45.7
  [8913a72c] NonlinearSolve v3.13.1
  [1dea7af3] OrdinaryDiffEq v6.86.0
  [91a5bcdd] Plots v1.40.5
  [98d1487c] PolyesterForwardDiff v0.1.2
  [f27b6e38] Polynomials v4.0.11
  [90137ffa] StaticArrays v1.9.7
  [0c5d862f] Symbolics v5.34.0

Status `C:\Users\Bernt\.julia\environments\v1.10\Manifest.toml`
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Julia Version 1.10.4
Commit 48d4fd4843 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: 12 × 12th Gen Intel(R) Core(TM) i7-1255U
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, alderlake)
Threads: 1 default, 0 interactive, 1 GC (on 12 virtual cores)

Additional context

The problem where I get an error message is somewhat too complex to include here. Also, it is part of a research project, and I'd prefer to not include it in public. However, if some MTK developers need to get access to my code, I can provide it via e-mail.

baggepinnen commented 4 months ago

This is a bug / poor error message in structural simplify

BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]

  [2] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:369 [inlined]
  [3] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:368 [inlined]
  [4] check_consistency(state::TearingState{ODESystem}, orig_inputs::Set{Any})

looks similar to https://github.com/SciML/ModelingToolkit.jl/issues/2727

This issue can probably be closed in favor of other similar ones, this one does not have a reproducer

B-LIE commented 4 months ago

I'm not explicitly using structural_simplify in the code that produces the error. Is structural_simplify used implicitly in the linearize function?

baggepinnen commented 4 months ago

yes, structural simplification is required also for linearization, so that happens internally.

ChrisRackauckas commented 4 months ago

Can we isolate this?

B-LIE commented 4 months ago

Hm. OK. In case #2727, the error seems to be related to equating two parameters.

I have no statements equating parameters. However, I do "reuse" parameters in different components: I have created a component of physical data:

@mtkmodel GasLift_Properties begin
    # Model parameters
    @parameters begin
        g = 9.81,   [description = "Acceleration of gravity, m/s^2"]
        R = 8.3145,   [description = "Ideal gas constant, J/(K*mol)"]
        T = 280,    [description = "Temperature, assumed constant, K"]
        M = 20.2511e-3,  [description = "Molar mas,s kg/mol"]
        ρ_ℓ = 780,  [description = "Liquid density, kg/m^3"]
        z = 0.7,    [description = "Gas compressibility, assumed constant, -"]
        zRT = z*R*T
        p_c = 45.5e5,[description = "Critical pressure, Pa"]
        T_c = 215,  [description = "Critical temperature, K"]
        Ṽ_qc = T_c*R/p_c,   [description = "Quasi-critical molar volume, m^3/mol"]
    end
end

which I used as components in various other models in order to ensure consistency.

Could that be the problem?

pmc4 commented 4 months ago

When I try to linearize my model, I get an "BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]" error🐞

Here is my Julia/MTK statement with partial error message:

julia> linearize(of_noi, [of_noi.dm.ṁ_i], [of_noi.dm.p], op=Dict(of_noi.dm.ṁ_i => u_ṁ_c2d(0) ))
BoundsError: attempt to access 302-element Vector{Vector{Int64}} at index [303]

Stacktrace:
  [1] getindex
    @ .\essentials.jl:13 [inlined]
  [2] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:369 [inlined]
  [3] 𝑑neighbors
    @ C:\Users\Bernt\.julia\packages\ModelingToolkit\7em8Z\src\bipartite_graph.jl:368 [inlined]
  [4] check_consistency(state::TearingState{ODESystem}, orig_inputs::Set{Any})
...

Even though the example is not the same, the error is similar to what happened to me in #2870, where I got

ERROR: BoundsError: attempt to access 2-element Vector{Any} at index [3]

Are the bugs related somehow? I was also using structural_simplify

ChrisRackauckas commented 4 months ago

That's completely unrelated. The other one is just that you didn't define derivatives on your registered function.

pmc4 commented 4 months ago

Oh, I'll review it again. I'm sorry.

ChrisRackauckas commented 4 months ago

I just haven't gotten to answering that one because I want to make it give a better error message, but you can see your stack trace is in expand_derivatives