Cannot solve SDE with Catalyst #1327
Description
Describe the bug 🐞
Starting from yesterday (2025-10-09), trying to solve a Catalyst generated SDE fails.
Expected behavior
Should be able to solve the SDE.
Minimal Reproducible Example 👇
using Catalyst, StochasticDiffEq
model = @reaction_network begin
kB, S + E --> SE
kD, SE --> S + E
kP, SE --> P + E
end
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]
sde = SDEProblem(model, u0, tspan, ps)
sol = solve(sde, LambaEM())Error & Stacktrace
ERROR: MethodError: no method matching _initialize_dae!(::StochasticDiffEq.SDEIntegrator{…}, ::SDEProblem{…}, ::OverrideInit{…}, ::Val{…})
The function `_initialize_dae!` exists, but no method is defined for this combination of argument types.
Closest candidates are:
_initialize_dae!(::OrdinaryDiffEqCore.ODEIntegrator, ::SciMLBase.AbstractDEProblem, ::OverrideInit, ::Union{Val{true}, Val{false}})
@ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/Y97Yg/src/initialize_dae.jl:111
_initialize_dae!(::Union{SciMLBase.AbstractSDDEIntegrator, SciMLBase.AbstractSDEIntegrator}, ::Union{SciMLBase.AbstractRODEProblem, SciMLBase.AbstractSDDEProblem}, ::DefaultInit, ::Any)
@ StochasticDiffEq ~/.julia/packages/StochasticDiffEq/sNZzr/src/initialize_dae.jl:8
_initialize_dae!(::OrdinaryDiffEqCore.ODEIntegrator, ::SciMLBase.AbstractDEProblem, ::CheckInit, ::Union{Val{true}, Val{false}})
@ OrdinaryDiffEqCore ~/.julia/packages/OrdinaryDiffEqCore/Y97Yg/src/initialize_dae.jl:153
...
Stacktrace:
[1] _initialize_dae!(integrator::StochasticDiffEq.SDEIntegrator{…}, prob::SDEProblem{…}, ::DefaultInit, isinplace::Val{…})
@ StochasticDiffEq ~/.julia/packages/StochasticDiffEq/sNZzr/src/initialize_dae.jl:13
[2] initialize_dae!(integrator::StochasticDiffEq.SDEIntegrator{…}, initializealg::DefaultInit)
@ StochasticDiffEq ~/.julia/packages/StochasticDiffEq/sNZzr/src/initialize_dae.jl:4
[3] __init(_prob::SDEProblem{…}, alg::LambaEM{…}, timeseries_init::Vector{…}, ts_init::Vector{…}, ks_init::Type, recompile::Type{…}; saveat::Tuple{}, tstops::Tuple{}, d_discontinuities::Tuple{}, save_idxs::Nothing, save_everystep::Bool, save_noise::Bool, save_on::Bool, save_start::Bool, save_end::Nothing, callback::Nothing, dense::Bool, calck::Bool, dt::Float64, adaptive::Bool, gamma::Rational{…}, abstol::Nothing, reltol::Nothing, qmin::Rational{…}, qmax::Rational{…}, qsteady_min::Int64, qsteady_max::Int64, beta2::Nothing, beta1::Nothing, qoldinit::Rational{…}, controller::Nothing, fullnormalize::Bool, failfactor::Int64, delta::Rational{…}, maxiters::Int64, dtmax::Float64, dtmin::Float64, internalnorm::typeof(DiffEqBase.ODE_DEFAULT_NORM), isoutofdomain::typeof(DiffEqBase.ODE_DEFAULT_ISOUTOFDOMAIN), unstable_check::typeof(DiffEqBase.ODE_DEFAULT_UNSTABLE_CHECK), verbose::Bool, force_dtmin::Bool, timeseries_errors::Bool, dense_errors::Bool, advance_to_tstop::Bool, stop_at_next_tstop::Bool, initialize_save::Bool, progress::Bool, progress_steps::Int64, progress_name::String, progress_message::typeof(DiffEqBase.ODE_DEFAULT_PROG_MESSAGE), progress_id::Symbol, userdata::Nothing, initialize_integrator::Bool, seed::UInt64, alias::Nothing, initializealg::DefaultInit, kwargs::@Kwargs{})
@ StochasticDiffEq ~/.julia/packages/StochasticDiffEq/sNZzr/src/solve.jl:694
[4] __init (repeats 2 times)
@ ~/.julia/packages/StochasticDiffEq/sNZzr/src/solve.jl:20 [inlined]
[5] #__solve#69
@ ~/.julia/packages/StochasticDiffEq/sNZzr/src/solve.jl:6 [inlined]
[6] __solve (repeats 4 times)
@ ~/.julia/packages/StochasticDiffEq/sNZzr/src/solve.jl:1 [inlined]
[7] #solve_call#23
@ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:127 [inlined]
[8] solve_call
@ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:84 [inlined]
[9] #solve_up#30
@ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:563 [inlined]
[10] solve_up
@ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:540 [inlined]
[11] #solve#29
@ ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:530 [inlined]
[12] solve(prob::SDEProblem{…}, args::LambaEM{…})
@ DiffEqBase ~/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:520
[13] 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 v15.0.8
[789caeaf] StochasticDiffEq v6.82.0- Output of
using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)
[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 v1.4.0
[2a0fbf3d] CPUSummary v0.2.7
[479239e8] Catalyst v15.0.8
[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
[a33af91c] CompositionsBase v0.1.2
[2569d6c7] ConcreteStructs v0.2.3
[187b0558] ConstructionBase v1.6.0
[adafc99b] CpuId v0.3.1
[9a962f9c] DataAPI v1.16.0
⌅ [864edb3b] DataStructures v0.18.22
[2b5f629d] DiffEqBase v6.190.2
[459566f4] DiffEqCallbacks v4.10.0
[77a26b50] DiffEqNoiseProcess v5.24.1
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.15.1
⌅ [a0c0ee7d] DifferentiationInterface v0.6.54
[8d63f2c5] DispatchDoctor v0.4.26
[b4f34e82] Distances v0.10.12
[31c24e10] Distributions v0.25.122
[ffbed154] DocStringExtensions v0.9.5
[5b8099bc] DomainSets v0.7.16
⌃ [7c1d4256] DynamicPolynomials v0.6.3
[06fc5a27] DynamicQuantities v1.10.0
[4e289a0a] EnumX v1.0.5
[f151be2c] EnzymeCore v0.8.14
[e2ba6199] ExprTools v0.1.10
[55351af7] ExproniconLite v0.10.14
[7034ab61] FastBroadcast v0.3.5
[9aa1b823] FastClosures v0.3.2
[a4df4552] FastPower v1.1.3
[1a297f60] FillArrays v1.14.0
[64ca27bc] FindFirstFunctions v1.4.2
[6a86dc24] FiniteDiff v2.28.1
[1fa38f19] Format v1.3.7
⌃ [f6369f11] ForwardDiff v0.10.39
[069b7b12] FunctionWrappers v1.1.3
[77dc65aa] FunctionWrappersWrappers v0.1.3
[46192b85] GPUArraysCore v0.2.0
[c27321d9] Glob v1.3.1
[86223c79] Graphs v1.13.1
[34004b35] HypergeometricFunctions v0.3.28
[615f187c] IfElse v0.1.1
[d25df0c9] Inflate v0.1.5
[18e54dd8] IntegerMathUtils v0.1.3
[8197267c] IntervalSets v0.7.11
[3587e190] InverseFunctions v0.1.17
[92d709cd] IrrationalConstants v0.2.4
[82899510] IteratorInterfaceExtensions v1.0.0
[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
[b964fa9f] LaTeXStrings v1.4.0
[23fbe1c1] Latexify v0.16.10
[10f19ff3] LayoutPointers v0.1.17
[5078a376] LazyArrays v2.8.0
[2d8b4e74] LevyArea v1.0.0
[87fe0de2] LineSearch v0.1.4
[d3d80556] LineSearches v7.4.0
[7ed4a6bd] LinearSolve v3.43.0
[2ab3a3ac] LogExpFunctions v0.3.29
[d8e11817] MLStyle v0.4.17
[1914dd2f] MacroTools v0.5.16
[d125e4d3] ManualMemory v0.1.8
[bb5d69b7] MaybeInplace v0.1.4
[e1d29d7a] Missings v1.2.0
⌅ [961ee093] ModelingToolkit v9.83.0
[2e0e35c7] Moshi v0.3.7
[46d2c3a1] MuladdMacro v0.2.4
⌃ [102ac46a] MultivariatePolynomials v0.5.9
[d8a4904e] MutableArithmetics v1.6.6
[d41bc354] NLSolversBase v7.10.0
[2774e3e8] NLsolve v4.5.1
[77ba4419] NaNMath v1.1.3
⌃ [8913a72c] NonlinearSolve v4.10.0
⌅ [be0214bd] NonlinearSolveBase v1.16.1
⌃ [5959db7a] NonlinearSolveFirstOrder v1.8.0
⌃ [9a2c21bd] NonlinearSolveQuasiNewton v1.9.0
⌃ [26075421] NonlinearSolveSpectralMethods v1.4.0
[6fe1bfb0] OffsetArrays v1.17.0
[429524aa] Optim v1.13.2
[bac558e1] OrderedCollections v1.8.1
[bbf590c4] OrdinaryDiffEqCore v1.35.0
[4302a76b] OrdinaryDiffEqDifferentiation v1.16.1
⌃ [127b3ac7] OrdinaryDiffEqNonlinearSolve v1.14.1
[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 v1.3.3
[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 v1.8.0
[431bcebd] SciMLPublic v1.0.0
[53ae85a6] SciMLStructures v1.7.0
[efcf1570] Setfield v1.1.2
⌃ [727e6d20] SimpleNonlinearSolve v2.7.0
[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
[789caeaf] StochasticDiffEq v6.82.0
[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
[ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
[4af54fe1] LazyArtifacts v1.11.0
[b27032c2] LibCURL v0.6.4
[76f85450] LibGit2 v1.11.0
[8f399da3] Libdl v1.11.0
[37e2e46d] LinearAlgebra v1.12.0
[56ddb016] Logging v1.11.0
[d6f4376e] Markdown v1.11.0
[a63ad114] Mmap v1.11.0
[ca575930] NetworkOptions v1.3.0
[44cfe95a] Pkg v1.12.0
[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 v1.12.0
[f489334b] StyledStrings 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 v1.3.0+1
[deac9b47] LibCURL_jll v8.11.1+1
[e37daf67] LibGit2_jll v1.9.0+0
[29816b5a] LibSSH2_jll v1.11.3+1
[14a3606d] MozillaCACerts_jll v2025.5.20
[4536629a] OpenBLAS_jll v0.3.29+0
[05823500] OpenLibm_jll v0.8.7+0
[458c3c95] OpenSSL_jll v3.5.1+0
[bea87d4a] SuiteSparse_jll v7.8.3+2
[83775a58] Zlib_jll v1.3.1+2
[8e850b90] libblastrampoline_jll v5.13.1+1
[8e850ede] nghttp2_jll v1.64.0+1
[3f19e933] p7zip_jll v17.5.0+2- Output of
versioninfo()
Julia Version 1.12.0
Commit b907bd0600f (2025-10-07 15:42 UTC)
Build Info:
Official https://julialang.org release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 14 × Intel(R) Core(TM) Ultra 7 165U
WORD_SIZE: 64
LLVM: libLLVM-18.1.7 (ORCJIT, alderlake)
GC: Built with stock GC
Threads: 1 default, 1 interactive, 1 GC (on 14 virtual cores)
Environment:
JULIA_EDITOR = code
JULIA_VSCODE_REPL = 1Additional context
From running the SBMLImporter workflows, the occurrence of this bug happened at the same time DiffEqCallbacks.jl updated to 4.10.