`ODESystem` seems to be broken with threading

[AbdAlazezAhmed]

Edit: Well, now it's ODESystem that's broken. In another MRE structural_simplify was the issue :D
It seems like threading breaks something in structural_simplify. Doing the loop in MRE without threading works. IIUC this should not happen since everything is local to the function bar

Minimal Reproducible Example

using Catalyst, ModelingToolkit, ThreadPinning
using ModelingToolkit: t_nounits as t, D_nounits as D

pinthreads(:cores)

function bar()
    @parameters σ ρ β
    @variables x(t) y(t) z(t)

    eqs = [D(x) ~ σ*(y-x),
        D(y) ~ x*(ρ-z)-y,
        D(z) ~ x*y - β*z]

    @named de = ODESystem(eqs,t,[x,y,z],[σ,ρ,β],tspan=(0, 1000.0))
    odess = structural_simplify(de)
end

Threads.@threads :static  for i in 1:1000
    bar()
end

Error & Stacktrace

ERROR: TaskFailedException

    nested task error: UndefRefError: access to undefined reference
    Stacktrace:
      [1] getindex
        @ ./essentials.jl:917 [inlined]
      [2] iterate
        @ ./array.jl:891 [inlined]
      [3] vars!(vars::Set{Any}, O::SymbolicUtils.BasicSymbolic{Real}; op::Type)
        @ ModelingToolkit ~/.julia/packages/ModelingToolkit/iQ7So/src/utils.jl:441
      [4] vars!(vars::Set{Any}, eq::Equation; op::Type)
        @ ModelingToolkit ~/.julia/packages/ModelingToolkit/iQ7So/src/utils.jl:402
      [5] vars!
        @ ~/.julia/packages/ModelingToolkit/iQ7So/src/utils.jl:401 [inlined]
      [6] _check_if_dde(eqs::Vector{Equation}, iv::SymbolicUtils.BasicSymbolic{Real}, subsystems::Vector{ODESystem})
        @ ModelingToolkit ~/.julia/packages/ModelingToolkit/iQ7So/src/systems/diffeqs/abstractodesystem.jl:19
      [7] ODESystem(deqs::Vector{…}, iv::Num, dvs::Vector{…}, ps::Vector{…}; controls::Vector{…}, observed::Vector{…}, systems::Vector{…}, tspan::Tuple{…}, name::Symbol, description::String, default_u0::Dict{…}, default_p::Dict{…}, defaults::Dict{…}, guesses::Dict{…}, initializesystem::Nothing, initialization_eqs::Vector{…}, schedule::Nothing, connector_type::Nothing, preface::Nothing, continuous_events::Nothing, discrete_events::Nothing, parameter_dependencies::Vector{…}, checks::Bool, metadata::Nothing, gui_metadata::Nothing, is_dde::Nothing, tstops::Vector{…})
        @ ModelingToolkit ~/.julia/packages/ModelingToolkit/iQ7So/src/systems/diffeqs/odesystem.jl:287
      [8] macro expansion
        @ ~/.julia/packages/ModelingToolkit/iQ7So/src/systems/abstractsystem.jl:2060 [inlined]
      [9] bar()
        @ Main ~/code/scripts/bug_reproducer.jl:49
     [10] macro expansion
        @ ~/code/scripts/bug_reproducer.jl:54 [inlined]
     [11] (::var"#9#threadsfor_fun#12"{var"#9#threadsfor_fun#11#13"{UnitRange{Int64}}})(tid::Int64; onethread::Bool)
        @ Main ./threadingconstructs.jl:252
     [12] #9#threadsfor_fun
        @ ./threadingconstructs.jl:219 [inlined]
     [13] (::Base.Threads.var"#1#2"{var"#9#threadsfor_fun#12"{var"#9#threadsfor_fun#11#13"{UnitRange{Int64}}}, Int64})()
        @ Base.Threads ./threadingconstructs.jl:154

...and 19 more exceptions.

Stacktrace:
 [1] threading_run(fun::var"#9#threadsfor_fun#12"{var"#9#threadsfor_fun#11#13"{UnitRange{Int64}}}, static::Bool)
   @ Base.Threads ./threadingconstructs.jl:172
 [2] macro expansion
   @ ./threadingconstructs.jl:193 [inlined]
 [3] top-level scope
   @ ~/code/scripts/bug_reproducer.jl:53
Some type information was truncated. Use `show(err)` to see complete types.

Environment:

Output of `using Pkg; Pkg.status()`

   [479239e8] Catalyst v14.4.1
  [03cb29e0] CellMLToolkit v2.13.0
  [a93c6f00] DataFrames v1.7.0
  [8bb1440f] DelimitedFiles v1.9.1
  [0c46a032] DifferentialEquations v7.15.0
  [634d3b9d] DrWatson v2.18.0
  [86b6b26d] Evolutionary v0.11.1
  [d4d017d3] ExponentialUtilities v1.27.0
  [26cc04aa] FiniteDifferences v0.12.32
  [f6369f11] ForwardDiff v0.10.38
  [e9467ef8] GLMakie v0.10.18
  [86223c79] Graphs v1.12.0
  [916415d5] Images v0.26.1
  [b3565e16] Kroki v1.0.0
  [ee78f7c6] Makie v0.21.18
  [961ee093] ModelingToolkit v9.60.0
  [3bd65402] Optimisers v0.4.4
  [7f7a1694] Optimization v4.0.5
  [6f0a0517] OptimizationGCMAES v0.3.0
  [36348300] OptimizationOptimJL v0.4.1
  [500b13db] OptimizationPolyalgorithms v0.3.0
  [1dea7af3] OrdinaryDiffEq v6.90.1
⌃ [91a5bcdd] Plots v1.40.7
  [c3e4b0f8] Pluto v0.20.4
  [3cdcf5f2] RecipesBase v1.3.4
  [0bca4576] SciMLBase v2.70.0
  [90137ffa] StaticArrays v1.9.10
  [c3572dad] Sundials v4.26.1
  [d1185830] SymbolicUtils v3.8.1
  [48a634ad] Tensors v1.16.1
  [811555cd] ThreadPinning v1.0.2
  [3a884ed6] UnPack v1.0.2
  [cb13b1c6] Waveforms v0.1.3
⌃ [e88e6eb3] Zygote v0.6.75
  [0656b61e] GLFW_jll v3.4.0+2
  [ade2ca70] Dates v1.11.0

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

   [47edcb42] ADTypes v1.11.0
  [621f4979] AbstractFFTs v1.5.0
  [1520ce14] AbstractTrees v0.4.5
  [7d9f7c33] Accessors v0.1.41
  [79e6a3ab] Adapt v4.1.1
  [35492f91] AdaptivePredicates v1.2.0
  [66dad0bd] AliasTables v1.1.3
  [a95523ee] AlmostBlockDiagonals v0.1.10
  [27a7e980] Animations v0.4.2
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.18.0
  [4c555306] ArrayLayouts v1.11.0
  [a9b6321e] Atomix v1.0.1
  [67c07d97] Automa v1.1.0
  [13072b0f] AxisAlgorithms v1.1.0
  [39de3d68] AxisArrays v0.4.7
  [fbb218c0] BSON v0.3.9
  [aae01518] BandedMatrices v1.9.0
  [e2ed5e7c] Bijections v0.1.9
  [d1d4a3ce] BitFlags v0.1.9
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [8e7c35d0] BlockArrays v1.3.0
  [764a87c0] BoundaryValueDiffEq v5.13.0
  [7227322d] BoundaryValueDiffEqAscher v1.2.0
  [56b672f2] BoundaryValueDiffEqCore v1.3.0
  [85d9eb09] BoundaryValueDiffEqFIRK v1.3.0
  [1a22d4ce] BoundaryValueDiffEqMIRK v1.3.0
  [9255f1d6] BoundaryValueDiffEqMIRKN v1.1.0
  [ed55bfe0] BoundaryValueDiffEqShooting v1.3.0
  [70df07ce] BracketingNonlinearSolve v1.1.0
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.6
  [00ebfdb7] CSTParser v3.4.3
  [aafaddc9] CatIndices v0.2.2
  [479239e8] Catalyst v14.4.1
  [03cb29e0] CellMLToolkit v2.13.0
  [082447d4] ChainRules v1.72.2
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⌅ [3da002f7] ColorTypes v0.11.5
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⌅ [5ae59095] Colors v0.12.11
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⌅ [6b7a57c9] Expronicon v0.8.5
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⌃ [28b8d3ca] GR v0.72.8
  [c145ed77] GenericSchur v0.5.4
  [68eda718] GeoFormatTypes v0.4.3
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⌅ [5c1252a2] GeometryBasics v0.4.11
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  [a2bd30eb] Graphics v1.1.3
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  [08abe8d2] PrettyTables v2.4.0
  [27ebfcd6] Primes v0.5.6
  [33c8b6b6] ProgressLogging v0.1.4
  [92933f4c] ProgressMeter v1.10.2
  [43287f4e] PtrArrays v1.2.1
  [4b34888f] QOI v1.0.1
  [1fd47b50] QuadGK v2.11.1
  [94ee1d12] Quaternions v0.7.6
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
  [b3c3ace0] RangeArrays v0.3.2
  [c84ed2f1] Ratios v0.4.5
  [c1ae055f] RealDot v0.1.0
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [731186ca] RecursiveArrayTools v3.27.4
  [f2c3362d] RecursiveFactorization v0.2.23
  [189a3867] Reexport v1.2.2
  [dee08c22] RegionTrees v0.3.2
  [2792f1a3] RegistryInstances v0.1.0
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [708f8203] Richardson v1.4.2
  [79098fc4] Rmath v0.8.0
  [6038ab10] Rotations v1.7.1
  [5eaf0fd0] RoundingEmulator v0.2.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.13
  [9dfe8606] SCCNonlinearSolve v1.0.0
  [fdea26ae] SIMD v3.7.1
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.43
  [0bca4576] SciMLBase v2.70.0
  [19f34311] SciMLJacobianOperators v0.1.1
  [c0aeaf25] SciMLOperators v0.3.12
  [53ae85a6] SciMLStructures v1.6.1
  [7e506255] ScopedValues v1.3.0
  [6c6a2e73] Scratch v1.2.1
  [91c51154] SentinelArrays v1.4.8
  [efcf1570] Setfield v1.1.1
⌅ [65257c39] ShaderAbstractions v0.4.1
  [992d4aef] Showoff v1.0.3
  [73760f76] SignedDistanceFields v0.4.0
  [777ac1f9] SimpleBufferStream v1.2.0
  [727e6d20] SimpleNonlinearSolve v2.1.0
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [47aef6b3] SimpleWeightedGraphs v1.4.0
  [45858cf5] Sixel v0.1.3
  [a2af1166] SortingAlgorithms v1.2.1
  [9f842d2f] SparseConnectivityTracer v0.6.9
  [47a9eef4] SparseDiffTools v2.23.1
  [dc90abb0] SparseInverseSubset v0.1.2
  [0a514795] SparseMatrixColorings v0.4.10
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.5.0
  [860ef19b] StableRNGs v1.0.2
  [91464d47] StableTasks v0.1.5
  [cae243ae] StackViews v0.1.1
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.10
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.4
  [4c63d2b9] StatsFuns v1.3.2
  [9672c7b4] SteadyStateDiffEq v2.4.1
  [789caeaf] StochasticDiffEq v6.72.1
  [7792a7ef] StrideArraysCore v0.5.7
  [892a3eda] StringManipulation v0.4.0
⌅ [09ab397b] StructArrays v0.6.21
  [c3572dad] Sundials v4.26.1
  [2efcf032] SymbolicIndexingInterface v0.3.37
  [19f23fe9] SymbolicLimits v0.2.2
  [d1185830] SymbolicUtils v3.8.1
  [0c5d862f] Symbolics v6.22.1
  [90a7ee08] SysInfo v0.3.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [62fd8b95] TensorCore v0.1.1
  [48a634ad] Tensors v1.16.1
  [8ea1fca8] TermInterface v2.0.0
  [5d786b92] TerminalLoggers v0.1.7
  [1c621080] TestItems v1.0.0
  [811555cd] ThreadPinning v1.0.2
  [6f48bc29] ThreadPinningCore v0.4.5
  [8290d209] ThreadingUtilities v0.5.2
  [731e570b] TiffImages v0.11.2
  [06e1c1a7] TiledIteration v0.5.0
  [a759f4b9] TimerOutputs v0.5.26
  [0796e94c] Tokenize v0.5.29
  [3bb67fe8] TranscodingStreams v0.11.3
  [d5829a12] TriangularSolve v0.2.1
  [410a4b4d] Tricks v0.1.9
  [981d1d27] TriplotBase v0.1.0
  [781d530d] TruncatedStacktraces v1.4.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.22.0
  [45397f5d] UnitfulLatexify v1.6.4
  [a7c27f48] Unityper v0.1.6
  [013be700] UnsafeAtomics v0.3.0
  [41fe7b60] Unzip v0.2.0
  [3d5dd08c] VectorizationBase v0.21.71
  [19fa3120] VertexSafeGraphs v0.2.0
  [cb13b1c6] Waveforms v0.1.3
  [897b6980] WeakValueDicts v0.1.0
  [e3aaa7dc] WebP v0.1.3
  [efce3f68] WoodburyMatrices v1.0.0
⌃ [e88e6eb3] Zygote v0.6.75
  [700de1a5] ZygoteRules v0.2.5
  [6e34b625] Bzip2_jll v1.0.8+4
  [4e9b3aee] CRlibm_jll v1.0.1+0
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [5ae413db] EarCut_jll v2.2.4+0
  [2702e6a9] EpollShim_jll v0.0.20230411+1
  [2e619515] Expat_jll v2.6.4+3
⌅ [b22a6f82] FFMPEG_jll v4.4.2+2
  [f5851436] FFTW_jll v3.3.10+3
  [a3f928ae] Fontconfig_jll v2.15.0+0
  [d7e528f0] FreeType2_jll v2.13.3+1
  [559328eb] FriBidi_jll v1.0.16+0
  [0656b61e] GLFW_jll v3.4.0+2
⌅ [d2c73de3] GR_jll v0.72.8+0
  [78b55507] Gettext_jll v0.21.0+0
  [61579ee1] Ghostscript_jll v9.55.0+4
  [59f7168a] Giflib_jll v5.2.3+0
  [7746bdde] Glib_jll v2.82.4+0
  [3b182d85] Graphite2_jll v1.3.14+1
  [2e76f6c2] HarfBuzz_jll v8.5.0+0
  [e33a78d0] Hwloc_jll v2.11.2+3
  [c73af94c] ImageMagick_jll v7.1.1+1
  [905a6f67] Imath_jll v3.1.11+0
  [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
  [aacddb02] JpegTurbo_jll v3.1.1+0
  [c1c5ebd0] LAME_jll v3.100.2+0
⌅ [88015f11] LERC_jll v3.0.0+1
  [dad2f222] LLVMExtra_jll v0.0.34+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.3+0
  [81d17ec3] L_BFGS_B_jll v3.0.1+0
⌅ [e9f186c6] Libffi_jll v3.2.2+2
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.7.0+0
  [7add5ba3] Libgpg_error_jll v1.51.1+0
  [94ce4f54] Libiconv_jll v1.17.0+1
  [4b2f31a3] Libmount_jll v2.40.3+0
⌅ [89763e89] Libtiff_jll v4.4.0+0
  [38a345b3] Libuuid_jll v2.40.3+0
⌃ [d3a379c0] LittleCMS_jll v2.12.0+0
  [856f044c] MKL_jll v2024.2.0+0
  [e7412a2a] Ogg_jll v1.3.5+1
  [18a262bb] OpenEXR_jll v3.2.4+0
⌃ [643b3616] OpenJpeg_jll v2.4.0+0
⌅ [458c3c95] OpenSSL_jll v1.1.23+1
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [91d4177d] Opus_jll v1.3.3+0
  [36c8627f] Pango_jll v1.55.5+0
⌅ [30392449] Pixman_jll v0.43.4+0
  [ea2cea3b] Qt5Base_jll v5.15.3+2
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.3+0
  [a2964d1f] Wayland_jll v1.21.0+2
  [2381bf8a] Wayland_protocols_jll v1.36.0+0
  [02c8fc9c] XML2_jll v2.13.5+0
  [aed1982a] XSLT_jll v1.1.42+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+3
  [0c0b7dd1] Xorg_libXau_jll v1.0.12+0
  [935fb764] Xorg_libXcursor_jll v1.2.3+0
  [a3789734] Xorg_libXdmcp_jll v1.1.5+0
  [1082639a] Xorg_libXext_jll v1.3.6+3
  [d091e8ba] Xorg_libXfixes_jll v6.0.0+0
  [a51aa0fd] Xorg_libXi_jll v1.8.2+0
  [d1454406] Xorg_libXinerama_jll v1.1.5+0
  [ec84b674] Xorg_libXrandr_jll v1.5.4+0
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+1
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.2+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+3
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+1
  [12413925] Xorg_xcb_util_image_jll v0.4.0+1
  [2def613f] Xorg_xcb_util_jll v0.4.0+1
  [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
  [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
  [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
  [35661453] Xorg_xkbcomp_jll v1.4.6+1
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.1+0
  [3161d3a3] Zstd_jll v1.5.7+0
  [214eeab7] fzf_jll v0.56.3+0
  [9a68df92] isoband_jll v0.2.3+0
  [a4ae2306] libaom_jll v3.11.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [b53b4c65] libpng_jll v1.6.45+1
  [075b6546] libsixel_jll v1.10.4+1
  [f27f6e37] libvorbis_jll v1.3.7+2
⌃ [c5f90fcd] libwebp_jll v1.4.0+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+2
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [8bf52ea8] CRC32c 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
  [3fa0cd96] REPL 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
  [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 v1.1.1+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
  [efcefdf7] PCRE2_jll v10.42.0+1
  [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 1.11.1
Commit 8f5b7ca12ad (2024-10-16 10:53 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 20 × 13th Gen Intel(R) Core(TM) i5-13500
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, goldmont)
Threads: 20 default, 0 interactive, 10 GC (on 20 virtual cores)
Environment:
  JULIA_LOAD_PATH = /usr/share/gmsh/api/julia:
  JULIA_EDITOR = code

[ChrisRackauckas]

@bowenszhu is hash consing thread safe?

[bowenszhu]

@bowenszhu is hash consing thread safe?

No. I implemented it only for single thread for now.