Bug in function generation with Catalyst.jl v14

[j-fu]

Describe the bug 🐞

There seems to be an error with function generation in Catalyst.jl v14. With Catalyst.jl v13, my code shows correct behavior, while with v14, things appear to be wrong. I tried to cook down to the essentials, resulting in the MRE below which looks at the output of the generated ODE description function. We indeed see a difference of results between v13 and v14.

Minimal Reproducible Example 👇

using Catalyst
using OrdinaryDiffEq

rnv=@reaction_network rnv begin
    (k_1p, k_1m), A + C <--> CA
    (k_2p,k_2m),  B + C <--> CB
    (k_3p,k_3m),  CA + 2CB <--> CAB2 + 2C
    (k_4p, k_4m), CAB2 <--> AB2 + C
end

pcat=(
    k_1p=50, k_1m=0.1,
    k_2p=50, k_2m=0.1,
    k_3p=10, k_3m=0.1,
    k_4p=50, k_4m=0.1)

uv_ini=(A=0, B=0, CA=0, CB=0, CAB2=0, AB2=0, C=1.0)

tvend=200.0

probv=ODEProblem(rnv,Dict(pairs(uv_ini)),(0,tvend),Dict(pairs(pcat)))

du=zeros(7)
probv.f(du,ones(7),pcat,0.0)
println(du)

Expected behavior

With Catalyst.jl v13 this prints

[-49.9, -40.0, 44.949999999999996, -49.9, 40.0, -44.949999999999996, 49.9]

which is correct judging from the results of my example (which is too complex to reproduced here).

With Catalyst.jl v14 this prints

[49.9, -40.0, -49.9, -40.0, 40.0, 49.9, -49.9]

and my example fails.

Environment (please complete the following information):

• Output of using Pkg; Pkg.status() for Catalyst.jl v14

[479239e8] Catalyst v14.1.0
[1dea7af3] OrdinaryDiffEq v6.87.0

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST) for Catalyst.jl v14

[47edcb42] ADTypes v1.6.1
[1520ce14] AbstractTrees v0.4.5
[7d9f7c33] Accessors v0.1.37
[79e6a3ab] Adapt v4.0.4
[66dad0bd] AliasTables v1.1.3
[ec485272] ArnoldiMethod v0.4.0
[4fba245c] ArrayInterface v7.15.0
[4c555306] ArrayLayouts v1.10.2
[e2ed5e7c] Bijections v0.1.7
[62783981] BitTwiddlingConvenienceFunctions v0.1.6
[2a0fbf3d] CPUSummary v0.2.6
[00ebfdb7] CSTParser v3.4.3
[49dc2e85] Calculus v0.5.1
[479239e8] Catalyst v14.1.0
[d360d2e6] ChainRulesCore v1.24.0
[fb6a15b2] CloseOpenIntervals v0.1.13
[861a8166] Combinatorics v1.0.2
[a80b9123] CommonMark v0.8.12
[38540f10] CommonSolve v0.2.4
[bbf7d656] CommonSubexpressions v0.3.0
[f70d9fcc] CommonWorldInvalidations v1.0.0
[34da2185] Compat v4.15.0
[b152e2b5] CompositeTypes v0.1.4
[a33af91c] CompositionsBase v0.1.2
[2569d6c7] ConcreteStructs v0.2.3
[187b0558] ConstructionBase v1.5.6
[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 v6.151.5
[459566f4] DiffEqCallbacks v3.6.2
[77a26b50] DiffEqNoiseProcess v5.22.0
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.15.1
[a0c0ee7d] DifferentiationInterface v0.5.9
[31c24e10] Distributions v0.25.109
[ffbed154] DocStringExtensions v0.9.3
[5b8099bc] DomainSets v0.7.14
[fa6b7ba4] DualNumbers v0.6.8
⌅ [7c1d4256] DynamicPolynomials v0.5.7
⌅ [06fc5a27] DynamicQuantities v0.13.2
[4e289a0a] EnumX v1.0.4
[f151be2c] EnzymeCore v0.7.7
[d4d017d3] ExponentialUtilities v1.26.1
[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
[1a297f60] FillArrays v1.11.0
[64ca27bc] FindFirstFunctions v1.2.0
[6a86dc24] FiniteDiff v2.23.1
[1fa38f19] Format v1.3.7
[f6369f11] ForwardDiff v0.10.36
[069b7b12] FunctionWrappers v1.1.3
[77dc65aa] FunctionWrappersWrappers v0.1.3
[d9f16b24] Functors v0.4.11
[46192b85] GPUArraysCore v0.1.6
[c145ed77] GenericSchur v0.5.4
[c27321d9] Glob v1.3.1
[86223c79] Graphs v1.11.2
[3e5b6fbb] HostCPUFeatures v0.1.17
[34004b35] HypergeometricFunctions v0.3.23
[615f187c] IfElse v0.1.1
[d25df0c9] Inflate v0.1.5
[8197267c] IntervalSets v0.7.10
[3587e190] InverseFunctions v0.1.15
[92d709cd] IrrationalConstants v0.2.2
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.5.0
[682c06a0] JSON v0.21.4
[98e50ef6] JuliaFormatter v1.0.59
[ccbc3e58] JumpProcesses v9.12.0
[ef3ab10e] KLU v0.6.0
[ba0b0d4f] Krylov v0.9.6
[b964fa9f] LaTeXStrings v1.3.1
[2ee39098] LabelledArrays v1.16.0
[984bce1d] LambertW v0.4.6
[23fbe1c1] Latexify v0.16.4
[10f19ff3] LayoutPointers v0.1.17
[5078a376] LazyArrays v2.1.9
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.31.1
[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 v0.1.3
[e1d29d7a] Missings v1.2.0
[961ee093] ModelingToolkit v9.28.0
[46d2c3a1] MuladdMacro v0.2.4
[102ac46a] MultivariatePolynomials v0.5.6
[d8a4904e] MutableArithmetics v1.4.5
[d41bc354] NLSolversBase v7.8.3
[77ba4419] NaNMath v1.0.2
[8913a72c] NonlinearSolve v3.13.1
[6fe1bfb0] OffsetArrays v1.14.1
[429524aa] Optim v1.9.4
[bac558e1] OrderedCollections v1.6.3
[1dea7af3] OrdinaryDiffEq v6.87.0
[90014a1f] PDMats v0.11.31
[65ce6f38] PackageExtensionCompat v1.0.2
[d96e819e] Parameters v0.12.3
[69de0a69] Parsers v2.8.1
[e409e4f3] PoissonRandom v0.4.4
[f517fe37] Polyester v0.7.15
[1d0040c9] PolyesterWeave v0.2.2
[85a6dd25] PositiveFactorizations v0.2.4
[d236fae5] PreallocationTools v0.4.22
[aea7be01] PrecompileTools v1.2.1
[21216c6a] Preferences v1.4.3
[43287f4e] PtrArrays v1.2.0
[1fd47b50] QuadGK v2.10.1
[74087812] Random123 v1.7.0
[e6cf234a] RandomNumbers v1.5.3
[3cdcf5f2] RecipesBase v1.3.4
[731186ca] RecursiveArrayTools v3.26.0
[f2c3362d] RecursiveFactorization v0.2.23
[189a3867] Reexport v1.2.2
[ae029012] Requires v1.3.0
[ae5879a3] ResettableStacks v1.1.1
[79098fc4] Rmath v0.7.1
[7e49a35a] RuntimeGeneratedFunctions v0.5.13
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.43
[0bca4576] SciMLBase v2.48.0
[c0aeaf25] SciMLOperators v0.3.8
[53ae85a6] SciMLStructures v1.4.1
[efcf1570] Setfield v1.1.1
[727e6d20] SimpleNonlinearSolve v1.11.0
[699a6c99] SimpleTraits v0.9.4
[ce78b400] SimpleUnPack v1.1.0
[a2af1166] SortingAlgorithms v1.2.1
[47a9eef4] SparseDiffTools v2.19.0
[0a514795] SparseMatrixColorings v0.3.6
[e56a9233] Sparspak v0.3.9
[276daf66] SpecialFunctions v2.4.0
[aedffcd0] Static v1.1.1
[0d7ed370] StaticArrayInterface v1.5.1
[90137ffa] StaticArrays v1.9.7
[1e83bf80] StaticArraysCore v1.4.3
[82ae8749] StatsAPI v1.7.0
[2913bbd2] StatsBase v0.34.3
[4c63d2b9] StatsFuns v1.3.1
[7792a7ef] StrideArraysCore v0.5.7
[2efcf032] SymbolicIndexingInterface v0.3.27
⌃ [19f23fe9] SymbolicLimits v0.2.1
⌅ [d1185830] SymbolicUtils v2.1.2
[0c5d862f] Symbolics v5.35.0
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.12.0
⌅ [8ea1fca8] TermInterface v0.4.1
[8290d209] ThreadingUtilities v0.5.2
[a759f4b9] TimerOutputs v0.5.24
[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 v1.21.0
[a7c27f48] Unityper v0.1.6
[3d5dd08c] VectorizationBase v0.21.70
[19fa3120] VertexSafeGraphs v0.2.0
[1d5cc7b8] IntelOpenMP_jll v2024.2.0+0
[856f044c] MKL_jll v2024.2.0+0
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[f50d1b31] Rmath_jll v0.4.2+0
[1317d2d5] oneTBB_jll v2021.12.0+0
[0dad84c5] ArgTools v1.1.1
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8ba89e20] Distributed
[f43a241f] Downloads v1.6.0
[7b1f6079] FileWatching
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL v0.6.4
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[ca575930] NetworkOptions v1.2.0
[44cfe95a] Pkg v1.10.0
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA v0.7.0
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays v1.10.0
[10745b16] Statistics v1.10.0
[4607b0f0] SuiteSparse
[fa267f1f] TOML v1.0.3
[a4e569a6] Tar v1.10.0
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll v1.1.1+0
[deac9b47] LibCURL_jll v8.4.0+0
[e37daf67] LibGit2_jll v1.6.4+0
[29816b5a] LibSSH2_jll v1.11.0+1
[c8ffd9c3] MbedTLS_jll v2.28.2+1
[14a3606d] MozillaCACerts_jll v2023.1.10
[4536629a] OpenBLAS_jll v0.3.23+4
[05823500] OpenLibm_jll v0.8.1+2
[bea87d4a] SuiteSparse_jll v7.2.1+1
[83775a58] Zlib_jll v1.2.13+1
[8e850b90] libblastrampoline_jll v5.8.0+1
[8e850ede] nghttp2_jll v1.52.0+1
[3f19e933] p7zip_jll v17.4.0+2```

  - Output of `versioninfo()`

```julia
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 20 × 13th Gen Intel(R) Core(TM) i7-13700H
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, goldmont)
Threads: 1 default, 0 interactive, 1 GC (on 20 virtual cores)
Environment:
LD_LIBRARY_PATH = /home/fuhrmann/local/lib64:/home/fuhrmann/local/lib:/usr/local/cuda-12.3/lib64:.:/usr/local/lib64:/usr/local/lib:/home/fuhrmann/local/lib:/home/fuhrmann/Sys/share/pardiso
JULIA_PKG_DEVDIR = /home/fuhrmann/Wias/work/julia/dev
JULIA_PKG_SERVER_REGISTRY_PREFERENCE = eager
JULIA_PARDISO = /home/fuhrmann/Sys/share/pardiso/panua-pardiso-20240229-linux/lib
JULIA_HISTORY = /home/fuhrmann/.julia_histories/_home_fuhrmann_Wias_work_julia_dev_CatmapInterface

Additional context @smaasz

[ChrisRackauckas]

It looks like the vector is just in a different order. Did you check the symbol order is as you expected? Are you using getu to ensure you get the ordering you want?

[j-fu]

I checked for the symbol order, will update the MWE. Anyway, the vector is ones(7), so the IMHO order should not matter.

[ChrisRackauckas]

Both of your outputs are the same, one is just in a different order.

[j-fu]

But I do't see the 44.949999999999996 value in the output from v14.

[ChrisRackauckas]

Oh interesting, I see now. Are you sure it's function generation? Did you check the generated ODEs?

[isaacsas]

@ChrisRackauckas can’t parameter order also change? (And change from the ordering within Catalyst.)

[isaacsas]

@j-fu what happens if you instead pass probv.p to f?

[ChrisRackauckas]

can’t parameter order also change? (And change from the ordering within Catalyst.)

oh yes that's probably it.

[isaacsas]

(Sorry I’m traveling and have cell phone only connectivity till Sunday.)

[ChrisRackauckas]

I'm actually surprised it didn't just error, since it should use the split form and separate the integer parameters from the float ones.

[isaacsas]

At some low level everything is now upconverted to floats if the symbolics are not explicitly declared as integers.

I’m not sure I agree with this behavior but it is happening in MTK or lower now.

[j-fu]

@j-fu what happens if you instead pass probv.p to f?

Yeah this helps indeed! Thinking about it, it seems that it should be logical to pass probv.p instead of my params tuple, as int might be mangled in whatever way.

Thanks for the quick response!

[isaacsas]

Yeah, you can’t rely on the Catalyst order any more being preserved in generated functions. So using the initial condition and parameter objects from generated problems is the way to go.

[isaacsas]

I’m going to close this issue but feel free to reopen if there are further issues.