Codegen issue with `implicit_affect!` and array variables

[SebastianM-C]

Describe the bug 🐞

While looking into https://buildkite.com/julialang/scimldocs/builds/10644#0199cd20-dfc9-4978-9a92-29e23d775259/7-135 I found that implicit affects that are generated from discrete events can lead to codegen where a (vector element) variable is used before it's defined. I'm not sure if this is related to cse or not. I tried to use cse=false in the ODEProblem, but the codegen for the observed function in the affect is still using CSE variables.

The following snippet shows the issue:

var"Initial(nn₊inputs(t))" = var"##cse#6"
var"##cse#7" = begin
       #= /home/sebastian/.julia/packages/SymbolicUtils/N76BL/src/code.jl:510 =#
        (SymbolicUtils.Code.create_array)(Vector{SymbolicUtils.BasicSymbolic{Real}}, nothing, Val{1}(), Val{(1,)}(), (Shift(t, 1))(var"(nn₊inputs(t))[1]"))
end
var"##cse#8" = (ModelingToolkit.StructuralTransformations.change_origin)((1,), var"##cse#7")
var"##cse#9" = (getindex)(var"##cse#8", 1)
var"(nn₊inputs(t))[1]" = var"##cse#9"

Expected behavior

The callback should work.

Minimal Reproducible Example 👇

using ModelingToolkit
using OrdinaryDiffEqDefault
using ModelingToolkit: t_nounits as t, D_nounits as D

@mtkmodel BioreactorMWE begin
    @constants begin
        C_s_in = 50.0
        y_x_s = 0.777
        m = 0.0
    end
    @parameters begin
        controls[1:1] = [1], [tunable = false]
        Q_in = 1.1, [tunable = false]
    end
    @variables begin
        C_s(t)
        C_x(t) = 1.0
        V(t) = 7.0
        μ(t)
        σ(t)
        nn_inputs(t)[1:1] = [C_s_in]
        nn_outputs(t)[1:1] = [2C_s_in/(C_s_in+1)]
    end
    @equations begin
        σ ~ μ / y_x_s + m
        D(C_s) ~ -σ * C_x + Q_in / V * (C_s_in - C_s)
        D(C_x) ~ μ * C_x - Q_in / V * C_x
        D(V) ~ Q_in
        nn_inputs[1] ~ C_s
        nn_outputs[1] ~ 2*(nn_inputs[1])/(nn_inputs[1]+1)
        nn_outputs[1] ~ μ
    end
    @discrete_events begin
        (t == 1.0) => [Q_in ~ controls[1]]
    end
end

@mtkcompile bioreactor_mwe = BioreactorMWE()
mwe_prob = ODEProblem(bioreactor_mwe, [], (0.0, 15.0), tstops = 0:15, save_everystep=false)

integ = init(mwe_prob)
integ.opts.callback.discrete_callbacks[1].affect!.u_getter.obsfn.f_oop

Error & Stacktrace ⚠️

ERROR: UndefVarError: `(nn_inputs(t))[1]` not defined in local scope
Suggestion: check for an assignment to a local variable that shadows a global of the same name.
Stacktrace:
  [1] macro expansion
    @ ~/.julia/packages/SymbolicUtils/N76BL/src/code.jl:510 [inlined]
  [2] macro expansion
    @ ~/.julia/packages/Symbolics/lJiB2/src/build_function.jl:366 [inlined]
  [3] macro expansion
    @ ~/.julia/packages/RuntimeGeneratedFunctions/2SjTC/src/RuntimeGeneratedFunctions.jl:161 [inlined]
  [4] macro expansion
    @ ./none:0 [inlined]
  [5] generated_callfunc
    @ ./none:0 [inlined]
  [6] (::RuntimeGeneratedFunctions.RuntimeGeneratedFunction{…})(::Nothing, ::MTKParameters{…}, ::Float64)
    @ RuntimeGeneratedFunctions ~/.julia/packages/RuntimeGeneratedFunctions/2SjTC/src/RuntimeGeneratedFunctions.jl:148
  [7] macro expansion
    @ ~/.julia/packages/ModelingToolkit/IdXTK/src/systems/codegen_utils.jl:0 [inlined]
  [8] _generated_call(::ModelingToolkit.GeneratedFunctionWrapper{…}, ::Nothing, ::MTKParameters{…}, ::Float64)
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/IdXTK/src/systems/codegen_utils.jl:353
  [9] (::ModelingToolkit.GeneratedFunctionWrapper{…})(::Nothing, ::Vararg{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/IdXTK/src/systems/codegen_utils.jl:350
 [10] (::SymbolicIndexingInterface.TimeDependentObservedFunction{…})(::SymbolicIndexingInterface.NotTimeseries, ::SymbolicIndexingInterface.IndexerBoth, prob::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ SymbolicIndexingInterface ~/.julia/packages/SymbolicIndexingInterface/mg9eW/src/state_indexing.jl:116
 [11] (::SymbolicIndexingInterface.TimeDependentObservedFunction{…})(::SymbolicIndexingInterface.NotTimeseries, ::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ SymbolicIndexingInterface ~/.julia/packages/SymbolicIndexingInterface/mg9eW/src/state_indexing.jl:80
 [12] (::SymbolicIndexingInterface.TimeDependentObservedFunction{…})(prob::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ SymbolicIndexingInterface ~/.julia/packages/SymbolicIndexingInterface/mg9eW/src/value_provider_interface.jl:166
 [13] (::ModelingToolkit.var"#implicit_affect!#687"{…})(integ::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/IdXTK/src/systems/callbacks.jl:976
 [14] apply_discrete_callback!
    @ ~/.julia/packages/DiffEqBase/p82Yh/src/callbacks.jl:625 [inlined]
 [15] handle_callbacks!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/integrators/integrator_utils.jl:401
 [16] _loopfooter!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/integrators/integrator_utils.jl:284
 [17] loopfooter!
    @ ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/integrators/integrator_utils.jl:248 [inlined]
 [18] solve!(integrator::OrdinaryDiffEqCore.ODEIntegrator{…})
    @ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/solve.jl:612
 [19] #__solve#60
    @ ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/solve.jl:7 [inlined]
 [20] __solve
    @ ~/.julia/packages/OrdinaryDiffEqCore/GMkz9/src/solve.jl:1 [inlined]
 [21] #__solve#3
    @ ~/.julia/packages/OrdinaryDiffEqDefault/MdlB6/src/default_alg.jl:48 [inlined]
 [22] __solve
    @ ~/.julia/packages/OrdinaryDiffEqDefault/MdlB6/src/default_alg.jl:47 [inlined]
 [23] #__solve#49
    @ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:741 [inlined]
 [24] __solve
    @ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:732 [inlined]
 [25] solve_call(::ODEProblem{…}; merge_callbacks::Bool, kwargshandle::Nothing, kwargs::@Kwargs{})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:127
 [26] solve_call(::ODEProblem{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:84
 [27] solve_up(::ODEProblem{…}, ::Nothing, ::Vector{…}, ::MTKParameters{…}; originator::SciMLBase.ChainRulesOriginator, kwargs::@Kwargs{})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:547
 [28] solve_up
    @ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:540 [inlined]
 [29] solve(::ODEProblem{…}; sensealg::Nothing, u0::Nothing, p::Nothing, wrap::Val{…}, kwargs::@Kwargs{})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:530
 [30] solve(::ODEProblem{…})
    @ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:520
 [31] top-level scope
    @ ~/dev/cb_obsfn_mwe/mwe.jl:56
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

• Output of using Pkg; Pkg.status()

Status `~/dev/cb_obsfn_mwe/Project.toml`
  [961ee093] ModelingToolkit v10.25.0
  [50262376] OrdinaryDiffEqDefault v1.8.0

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)

Status `~/dev/cb_obsfn_mwe/Manifest.toml`
  [47edcb42] ADTypes v1.18.0
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.42
  [79e6a3ab] Adapt v4.4.0
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.20.0
  [4c555306] ArrayLayouts v1.12.0
  [e2ed5e7c] Bijections v0.2.2
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [8e7c35d0] BlockArrays v1.7.2
  [70df07ce] BracketingNonlinearSolve v1.5.0
  [2a0fbf3d] CPUSummary v0.2.7
  [d360d2e6] ChainRulesCore v1.26.0
  [fb6a15b2] CloseOpenIntervals v0.1.13
⌅ [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.9.1
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.18.1
  [b152e2b5] CompositeTypes v0.1.4
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  [9a962f9c] DataAPI v1.16.0
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  [77a26b50] DiffEqNoiseProcess v5.24.1
  [163ba53b] DiffResults v1.1.0
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  [692b3bcd] JLLWrappers v1.7.1
  [ae98c720] Jieko v0.2.1
  [98e50ef6] JuliaFormatter v2.1.6
⌅ [70703baa] JuliaSyntax v0.4.10
  [ccbc3e58] JumpProcesses v9.19.1
  [ba0b0d4f] Krylov v0.10.2
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  [87fe0de2] LineSearch v0.1.4
  [d3d80556] LineSearches v7.4.0
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  [2ab3a3ac] LogExpFunctions v0.3.29
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.16
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  [bb5d69b7] MaybeInplace v0.1.4
  [e1d29d7a] Missings v1.2.0
  [961ee093] ModelingToolkit v10.25.0
  [2e0e35c7] Moshi v0.3.7
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.13
  [d8a4904e] MutableArithmetics v1.6.6
  [d41bc354] NLSolversBase v7.10.0
  [77ba4419] NaNMath v1.1.3
  [8913a72c] NonlinearSolve v4.12.0
  [be0214bd] NonlinearSolveBase v2.0.0
  [5959db7a] NonlinearSolveFirstOrder v1.9.0
  [9a2c21bd] NonlinearSolveQuasiNewton v1.10.0
  [26075421] NonlinearSolveSpectralMethods v1.5.0
  [6fe1bfb0] OffsetArrays v1.17.0
  [429524aa] Optim v1.13.2
  [bac558e1] OrderedCollections v1.8.1
  [6ad6398a] OrdinaryDiffEqBDF v1.10.1
  [bbf590c4] OrdinaryDiffEqCore v1.36.0
  [50262376] OrdinaryDiffEqDefault v1.8.0
  [4302a76b] OrdinaryDiffEqDifferentiation v1.16.1
  [127b3ac7] OrdinaryDiffEqNonlinearSolve v1.15.0
  [43230ef6] OrdinaryDiffEqRosenbrock v1.18.1
  [2d112036] OrdinaryDiffEqSDIRK v1.7.0
  [b1df2697] OrdinaryDiffEqTsit5 v1.5.0
  [79d7bb75] OrdinaryDiffEqVerner v1.6.0
  [90014a1f] PDMats v0.11.35
  [d96e819e] Parameters v0.12.3
  [e409e4f3] PoissonRandom v0.4.7
  [f517fe37] Polyester v0.7.18
  [1d0040c9] PolyesterWeave v0.2.2
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.34
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.5.0
  [27ebfcd6] Primes v0.5.7
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [74087812] Random123 v1.7.1
  [e6cf234a] RandomNumbers v1.6.0
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.37.1
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.8.0
  [7e49a35a] RuntimeGeneratedFunctions v0.5.15
  [9dfe8606] SCCNonlinearSolve v1.6.0
  [94e857df] SIMDTypes v0.1.0
  [0bca4576] SciMLBase v2.120.0
  [19f34311] SciMLJacobianOperators v0.1.11
  [c0aeaf25] SciMLOperators v1.9.0
  [431bcebd] SciMLPublic v1.0.0
  [53ae85a6] SciMLStructures v1.7.0
  [efcf1570] Setfield v1.1.2
  [727e6d20] SimpleNonlinearSolve v2.9.0
  [699a6c99] SimpleTraits v0.9.5
  [ce78b400] SimpleUnPack v1.1.0
  [a2af1166] SortingAlgorithms v1.2.2
  [0a514795] SparseMatrixColorings v0.4.21
  [276daf66] SpecialFunctions v2.6.1
  [aedffcd0] Static v1.3.0
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [2913bbd2] StatsBase v0.34.6
  [4c63d2b9] StatsFuns v1.5.0
  [7792a7ef] StrideArraysCore v0.5.8
  [2efcf032] SymbolicIndexingInterface v0.3.45
⌃ [19f23fe9] SymbolicLimits v0.2.3
⌅ [d1185830] SymbolicUtils v3.32.0
  [0c5d862f] Symbolics v6.55.0
  [ed4db957] TaskLocalValues v0.1.3
  [8ea1fca8] TermInterface v2.0.0
  [1c621080] TestItems v1.0.0
  [8290d209] ThreadingUtilities v0.5.5
  [a759f4b9] TimerOutputs v0.5.29
  [410a4b4d] Tricks v0.1.12
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.6.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.25.0
  [a7c27f48] Unityper v0.1.6
  [61579ee1] Ghostscript_jll v9.55.1+0
  [1d5cc7b8] IntelOpenMP_jll v2025.2.0+0
  [aacddb02] JpegTurbo_jll v3.1.3+0
  [856f044c] MKL_jll v2025.2.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [1317d2d5] oneTBB_jll v2022.0.0+0
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
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  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.5+0
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2
Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

• Output of versioninfo()

Julia Version 1.11.7
Commit f2b3dbda30a (2025-09-08 12:10 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × Intel(R) Core(TM) i9-14900K
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, alderlake)
Threads: 32 default, 0 interactive, 16 GC (on 32 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_VSCODE_REPL = 1

Additional context

The ODEProblem is overdetermined here while in the original case is not, but when I tried to remove the defaults on nn_outputs or nn_inputs, I got some convert error, probably a separate bug. (Cannot convert an object of type ModelingToolkit.NoValue to an object of type Real)