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structural_simplify fails on SDESystem #3261

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sebapersson opened this issue Dec 5, 2024 · 6 comments · Fixed by #3266
Closed

structural_simplify fails on SDESystem #3261

sebapersson opened this issue Dec 5, 2024 · 6 comments · Fixed by #3266
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bug Something isn't working

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@sebapersson
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Describe the bug 🐞

structural_simplify fails on SDESystem generated from a Catalyst ReactionSystem.

Expected behavior

The code should not error.

Minimal Reproducible Example 👇

using ModelingToolkit, Catalyst

rn = @reaction_network begin
    kB, S + E --> SE
    kD, SE --> S + E
    kP, SE --> P + E
end

# Creating an ODEProblem works
u0 = [:S => 50.0, :E => 10.0, :SE => 0.0, :P => 0.0]
tspan = (0., 200.)
ps = [:kB => 0.01, :kD => 0.1, :kP => 0.1]
osys = structural_simplify(convert(ODESystem, rn))
ode = ODEProblem(osys, [50.0, 10.0, 0.0, 0.0], tspan, ps)

ssys = convert(SDESystem, rn)
structural_simplify(ssys)

Error & Stacktrace ⚠️

ERROR: This should never happen. Trying to set DataType with @NamedTuple{substitutions::ModelingToolkit.Substitutions}.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] #s335#288
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/abstractsystem.jl:1132 [inlined]
  [3] var"#s335#288"(::Any, obj::Any, patch::Any)
    @ ModelingToolkit ./none:0
  [4] (::Core.GeneratedFunctionStub)(::UInt64, ::LineNumberNode, ::Any, ::Vararg{Any})
    @ Core ./boot.jl:707
  [5] set
    @ ~/.julia/packages/Setfield/PdKfV/src/lens.jl:122 [inlined]
  [6] macro expansion
    @ ~/.julia/packages/Setfield/PdKfV/src/sugar.jl:197 [inlined]
  [7] tearing_reassemble(state::TearingState{…}, var_eq_matching::ModelingToolkit.BipartiteGraphs.Matching{…}, full_var_eq_matching::Nothing; simplify::Bool, mm::ModelingToolkit.SparseMatrixCLIL{…}, cse_hack::Bool, array_hack::Bool)
    @ ModelingToolkit.StructuralTransformations ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:601
  [8] tearing_reassemble (repeats 2 times)
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:240 [inlined]
  [9] #dummy_derivative#140
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/structural_transformation/symbolics_tearing.jl:839 [inlined]
 [10] _structural_simplify!(state::TearingState{…}, io::Nothing; simplify::Bool, check_consistency::Bool, fully_determined::Bool, warn_initialize_determined::Bool, dummy_derivative::Bool, kwargs::@Kwargs{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:701
 [11] _structural_simplify!
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:676 [inlined]
 [12] #structural_simplify!#1353
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systemstructure.jl:669 [inlined]
 [13] __structural_simplify(sys::SDESystem, io::Nothing; simplify::Bool, kwargs::@Kwargs{…})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:94
 [14] __structural_simplify
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:75 [inlined]
 [15] structural_simplify(sys::SDESystem, io::Nothing; simplify::Bool, split::Bool, allow_symbolic::Bool, allow_parameter::Bool, conservative::Bool, fully_determined::Bool, kwargs::@Kwargs{})
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:33
 [16] structural_simplify
    @ ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:28 [inlined]
 [17] structural_simplify(sys::SDESystem)
    @ ModelingToolkit ~/.julia/packages/ModelingToolkit/0O7FS/src/systems/systems.jl:28
 [18] top-level scope
    @ ~/Dropbox/PhD/tmp/test_fail/MVE.jl:17
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()
  [479239e8] Catalyst v14.4.1
  [961ee093] ModelingToolkit v9.54.0
  • Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
  [47edcb42] ADTypes v1.11.0
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.38
  [79e6a3ab] Adapt v4.1.1
  [66dad0bd] AliasTables v1.1.3
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.17.1
  [4c555306] ArrayLayouts v1.10.4
  [e2ed5e7c] Bijections v0.1.9
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [8e7c35d0] BlockArrays v1.2.0
  [70df07ce] BracketingNonlinearSolve v1.1.0
  [2a0fbf3d] CPUSummary v0.2.6
  [00ebfdb7] CSTParser v3.4.3
  [7057c7e9] Cassette v0.3.14
  [479239e8] Catalyst v14.4.1
  [d360d2e6] ChainRulesCore v1.25.0
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [861a8166] Combinatorics v1.0.2
  [a80b9123] CommonMark v0.8.15
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.16.0
  [b152e2b5] CompositeTypes v0.1.4
  [a33af91c] CompositionsBase v0.1.2
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.5.8
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.20
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.160.0
  [459566f4] DiffEqCallbacks v4.2.2
  [77a26b50] DiffEqNoiseProcess v5.24.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [a0c0ee7d] DifferentiationInterface v0.6.24
  [8d63f2c5] DispatchDoctor v0.4.17
  [31c24e10] Distributions v0.25.113
  [ffbed154] DocStringExtensions v0.9.3
  [5b8099bc] DomainSets v0.7.14
  [7c1d4256] DynamicPolynomials v0.6.1
  [06fc5a27] DynamicQuantities v1.4.0
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.8.7
  [e2ba6199] ExprTools v0.1.10
⌅ [6b7a57c9] Expronicon v0.8.5
  [7034ab61] FastBroadcast v0.3.5
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.4
  [a4df4552] FastPower v1.1.1
  [1a297f60] FillArrays v1.13.0
  [64ca27bc] FindFirstFunctions v1.4.1
  [6a86dc24] FiniteDiff v2.26.2
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.38
  [f62d2435] FunctionProperties v0.1.2
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.5.2
  [46192b85] GPUArraysCore v0.2.0
  [c27321d9] Glob v1.3.1
  [86223c79] Graphs v1.12.0
  [3e5b6fbb] HostCPUFeatures v0.1.17
  [34004b35] HypergeometricFunctions v0.3.25
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [18e54dd8] IntegerMathUtils v0.1.2
  [8197267c] IntervalSets v0.7.10
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.6.1
  [98e50ef6] JuliaFormatter v1.0.62
  [ccbc3e58] JumpProcesses v9.14.0
  [ef3ab10e] KLU v0.6.0
  [ba0b0d4f] Krylov v0.9.8
  [b964fa9f] LaTeXStrings v1.4.0
  [23fbe1c1] Latexify v0.16.5
  [10f19ff3] LayoutPointers v0.1.17
  [5078a376] LazyArrays v2.2.4
  [87fe0de2] LineSearch v0.1.4
  [d3d80556] LineSearches v7.3.0
  [7ed4a6bd] LinearSolve v2.38.0
  [2ab3a3ac] LogExpFunctions v0.3.28
  [bdcacae8] LoopVectorization v0.12.171
  [d8e11817] MLStyle v0.4.17
  [1914dd2f] MacroTools v0.5.13
  [d125e4d3] ManualMemory v0.1.8
  [bb5d69b7] MaybeInplace v0.1.4
  [e1d29d7a] Missings v1.2.0
  [961ee093] ModelingToolkit v9.54.0
  [46d2c3a1] MuladdMacro v0.2.4
  [102ac46a] MultivariatePolynomials v0.5.7
  [d8a4904e] MutableArithmetics v1.6.0
  [d41bc354] NLSolversBase v7.8.3
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v4.2.0
  [be0214bd] NonlinearSolveBase v1.3.3
  [5959db7a] NonlinearSolveFirstOrder v1.1.0
  [9a2c21bd] NonlinearSolveQuasiNewton v1.0.0
  [26075421] NonlinearSolveSpectralMethods v1.0.0
  [6fe1bfb0] OffsetArrays v1.14.1
  [429524aa] Optim v1.10.0
  [bac558e1] OrderedCollections v1.7.0
  [90014a1f] PDMats v0.11.31
  [d96e819e] Parameters v0.12.3
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.16
  [1d0040c9] PolyesterWeave v0.2.2
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.24
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [27ebfcd6] Primes v0.5.6
  [43287f4e] PtrArrays v1.2.1
  [1fd47b50] QuadGK v2.11.1
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.27.4
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [79098fc4] Rmath v0.8.0
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
  [0bca4576] SciMLBase v2.65.1
  [19f34311] SciMLJacobianOperators v0.1.1
  [c0aeaf25] SciMLOperators v0.3.12
  [53ae85a6] SciMLStructures v1.6.1
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v2.0.0
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [0a514795] SparseMatrixColorings v0.4.10
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.4.0
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [4c63d2b9] StatsFuns v1.3.2
  [7792a7ef] StrideArraysCore v0.5.7
  [2efcf032] SymbolicIndexingInterface v0.3.35
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.7.2
  [0c5d862f] Symbolics v6.22.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [8ea1fca8] TermInterface v2.0.0
  [1c621080] TestItems v1.0.0
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.25
  [0796e94c] Tokenize v0.5.29
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1986cc42] Unitful v1.21.1
  [a7c27f48] Unityper v0.1.6
  [3d5dd08c] VectorizationBase v0.21.71
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [856f044c] MKL_jll v2024.2.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [1317d2d5] oneTBB_jll v2021.12.0+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
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [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
  • Output of versioninfo()
Julia Version 1.11.2
Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 8 × 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, tigerlake)
Threads: 4 default, 0 interactive, 2 GC (on 8 virtual cores)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 4
@sebapersson sebapersson added the bug Something isn't working label Dec 5, 2024
@sebapersson
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Ping @AayushSabharwal

@AayushSabharwal
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AayushSabharwal commented Dec 11, 2024 •
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Right, thanks for the ping. I looked into this, and we support/test simplification of "stochastic ODEs" (for lack of a better name) created using @brownian. SDESystems can't be simplified this way. Since you're creating your SDEs through Catalyst, it's reasonable to assume Catalyst will do some simplification on its own. This happens during convert(SDESystem, rn). This specific system also doesn't change when passed through structural_simplify.

@sebapersson
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Thanks for looking into this! So it is not possible (or on the roadmap) to add structural_simplify for more generic SDESystem, and there is no other way to inline equations? Specifically, I am interested in inlinining equations on the form

x ~ ...

into the SDESystem, where x then appears in the model dynamics.

@AayushSabharwal
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I see. It's possible to round-trip through an equivalent ODESystem with @brownian variables instead of noise_eqs. I'll try and get this done soon. In the meantime, can I ask why you're going the SDESystem approach instead of using @brownian?

@sebapersson
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Great thanks!

The reason why I go via the SDESystem is because I want the Chemical Langevin Equation (CLE) for a model imported into a Catalyst ReactionSystem with SBMLImporter. The SDESystem (or SDEProblem which does not work here as I need to inline equations) is the only why I think it is possible to get the CLE (which is a SDE with non-diagonal noise). So in short, I do not think Catalyst works with @brownian.

@AayushSabharwal
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That makes sense

@AayushSabharwal AayushSabharwal mentioned this issue Dec 11, 2024
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feat: enable structural_simplify(::SDESystem) AayushSabharwal/ModelingToolkit.jl
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@AayushSabharwal @sebapersson