Documentation Serialization Example No Longer Works

[rconnorjohnstone]

Describe the example

Documentation Example for serialization using JLD2 no longer works: https://docs.sciml.ai/DiffEqDocs/stable/features/io/

Minimal Reproducible Example 👇

using OrdinaryDiffEq
f_2dlinear = (du, u, p, t) -> du .= 1.01u
tspan = (0.0, 1.0)
prob = ODEProblem(f_2dlinear, rand(2, 2), tspan)
sol = solve(prob, Euler(); dt = 1 // 2^(4))
using JLD2
@save "out.jld2" sol

Error & Stacktrace ⚠️

ERROR: UndefRefError: access to undefined reference
Stacktrace:
  [1] getproperty
    @ ./Base.jl:32 [inlined]
  [2] h5convert!(out::JLD2.IndirectPointer, ::JLD2.OnDiskRepresentation{…}, f::JLD2.JLDFile{…}, T::DataType, wsession::JLD2.JLDWriteSession{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:448
  [3] write_data(io::JLD2.MmapIO, f::JLD2.JLDFile{…}, data::Type, odr::JLD2.OnDiskRepresentation{…}, ::JLD2.HasReferences, wsession::JLD2.JLDWriteSession{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/dataio.jl:96
  [4] write_attribute(io::JLD2.MmapIO, f::JLD2.JLDFile{…}, attr::JLD2.WrittenAttribute{…}, wsession::JLD2.JLDWriteSession{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/attributes.jl:47
  [5] write_header_message(io::JLD2.MmapIO, f::JLD2.JLDFile{…}, msg::JLD2.WrittenAttribute{…}, wsession::JLD2.JLDWriteSession{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/explicit_datasets.jl:233
  [6] write_header_message
    @ ~/.julia/packages/JLD2/JyzIz/src/explicit_datasets.jl:232 [inlined]
  [7] commit(f::JLD2.JLDFile{…}, dt::JLD2.H5Datatype, attrs::Tuple{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/datatypes.jl:302
  [8] commit(::JLD2.JLDFile{…}, ::Any, ::DataType, ::DataType, ::JLD2.WrittenAttribute{…}, ::Vararg{…})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:248
  [9] commit_compound(f::JLD2.JLDFile{JLD2.MmapIO}, names::Vector{Symbol}, writtenas::DataType, readas::Type)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:199
 [10] h5fieldtype(f::JLD2.JLDFile{JLD2.MmapIO}, writeas::Any, readas::Type, initialized::Type{Val{true}})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:104
 [11] commit_compound(f::JLD2.JLDFile{JLD2.MmapIO}, names::Vector{Symbol}, writtenas::DataType, readas::Type)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:160
 [12] h5fieldtype(f::JLD2.JLDFile{JLD2.MmapIO}, writeas::Any, readas::Type, initialized::Type{Val{true}})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:104
 [13] commit_compound(f::JLD2.JLDFile{JLD2.MmapIO}, names::Vector{Symbol}, writtenas::DataType, readas::Type)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:160
 [14] h5type(f::JLD2.JLDFile{JLD2.MmapIO}, writtenas::Any, x::Any)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:136
 [15] h5type(f::JLD2.JLDFile{JLD2.MmapIO}, x::Any)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/data/writing_datatypes.jl:141
 [16] write_dataset(f::JLD2.JLDFile{JLD2.MmapIO}, x::Any, wsession::JLD2.JLDWriteSession{Dict{UInt64, JLD2.RelOffset}})
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/datasets.jl:389
 [17] write(g::JLD2.Group{…}, name::String, obj::ODESolution{…}, wsession::JLD2.JLDWriteSession{…}; compress::Nothing)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/compression.jl:87
 [18] write(f::JLD2.JLDFile{JLD2.MmapIO}, name::String, obj::Any, wsession::JLD2.JLDWriteSession{Dict{UInt64, JLD2.RelOffset}}; compress::Nothing)
    @ JLD2 ~/.julia/packages/JLD2/JyzIz/src/compression.jl:71
 [19] macro expansion
    @ ~/.julia/packages/JLD2/JyzIz/src/loadsave.jl:72 [inlined]
 [20] top-level scope
    @ REPL[7]:1
Some type information was truncated. Use `show(err)` to see complete types.

Not Working Environment (please complete the following information):

• Output of using Pkg; Pkg.status()

Status `~/.julia/environments/v1.10/Project.toml`
  [9db2cae5] Gtk4 v0.6.9
  [033835bb] JLD2 v0.5.2
  [2b0e0bc5] LanguageServer v4.5.1
  [1dea7af3] OrdinaryDiffEq v6.89.0
  [f0f68f2c] PlotlyJS v0.18.14
  [295af30f] Revise v3.5.18
  [6ac157d9] SatelliteToolbox v0.12.3
  [5d786b92] TerminalLoggers v0.1.7

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

Status `~/.julia/environments/v1.10/Manifest.toml`
⌃ [47edcb42] ADTypes v1.7.1
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  [692b3bcd] JLLWrappers v1.6.0
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⌃ [aa1ae85d] JuliaInterpreter v0.9.35
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  [2ab3a3ac] LogExpFunctions v0.3.28
  [e6f89c97] LoggingExtras v1.0.3
  [bdcacae8] LoopVectorization v0.12.171
⌃ [6f1432cf] LoweredCodeUtils v3.0.1
  [6c6e2e6c] MIMEs v0.1.4
  [d8e11817] MLStyle v0.4.17
  [3da0fdf6] MPIPreferences v0.1.11
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  [77ba4419] NaNMath v1.0.2
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  [8913a72c] NonlinearSolve v3.14.0
  [510215fc] Observables v0.5.5
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  [fbd9d27c] OptionalData v1.0.0
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  [1dea7af3] OrdinaryDiffEq v6.89.0
  [89bda076] OrdinaryDiffEqAdamsBashforthMoulton v1.1.0
  [6ad6398a] OrdinaryDiffEqBDF v1.1.2
  [bbf590c4] OrdinaryDiffEqCore v1.6.0
  [50262376] OrdinaryDiffEqDefault v1.1.0
  [4302a76b] OrdinaryDiffEqDifferentiation v1.1.0
  [9286f039] OrdinaryDiffEqExplicitRK v1.1.0
  [e0540318] OrdinaryDiffEqExponentialRK v1.1.0
  [becaefa8] OrdinaryDiffEqExtrapolation v1.1.0
  [5960d6e9] OrdinaryDiffEqFIRK v1.1.1
  [101fe9f7] OrdinaryDiffEqFeagin v1.1.0
  [d3585ca7] OrdinaryDiffEqFunctionMap v1.1.1
  [d28bc4f8] OrdinaryDiffEqHighOrderRK v1.1.0
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  [521117fe] OrdinaryDiffEqLinear v1.1.0
  [1344f307] OrdinaryDiffEqLowOrderRK v1.2.0
  [b0944070] OrdinaryDiffEqLowStorageRK v1.2.1
  [127b3ac7] OrdinaryDiffEqNonlinearSolve v1.2.1
  [c9986a66] OrdinaryDiffEqNordsieck v1.1.0
  [5dd0a6cf] OrdinaryDiffEqPDIRK v1.1.0
  [5b33eab2] OrdinaryDiffEqPRK v1.1.0
  [04162be5] OrdinaryDiffEqQPRK v1.1.0
  [af6ede74] OrdinaryDiffEqRKN v1.1.0
  [43230ef6] OrdinaryDiffEqRosenbrock v1.2.0
  [2d112036] OrdinaryDiffEqSDIRK v1.1.0
  [669c94d9] OrdinaryDiffEqSSPRK v1.2.0
  [e3e12d00] OrdinaryDiffEqStabilizedIRK v1.1.0
  [358294b1] OrdinaryDiffEqStabilizedRK v1.1.0
  [fa646aed] OrdinaryDiffEqSymplecticRK v1.1.0
  [b1df2697] OrdinaryDiffEqTsit5 v1.1.0
  [79d7bb75] OrdinaryDiffEqVerner v1.1.1
  [df9a0d86] Oxygen v1.5.13
  [90014a1f] PDMats v0.11.31
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [fa939f87] Pidfile v1.3.0
  [a03496cd] PlotlyBase v0.8.19
  [f0f68f2c] PlotlyJS v0.18.14
  [f2990250] PlotlyKaleido v2.2.5
  [e409e4f3] PoissonRandom v0.4.4
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  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
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  [438e738f] PyCall v1.96.4
⌃ [1fd47b50] QuadGK v2.11.0
  [74087812] Random123 v1.7.0
  [e6cf234a] RandomNumbers v1.6.0
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  [ae029012] Requires v1.3.0
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⌃ [777ac1f9] SimpleBufferStream v1.1.0
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⌅ [76b0de8b] TestItemDetection v0.2.0
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⌃ [0234f1f7] HDF5_jll v1.14.2+1
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⌅ [88015f11] LERC_jll v3.0.0+1
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⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.8.11+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.49.0+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [4b2f31a3] Libmount_jll v2.40.1+0
  [925c91fb] Librsvg_jll v2.54.5+0
  [89763e89] Libtiff_jll v4.6.0+0
  [38a345b3] Libuuid_jll v2.40.1+0
  [5ced341a] Lz4_jll v1.10.0+0
  [856f044c] MKL_jll v2024.2.0+0
  [7cb0a576] MPICH_jll v4.2.2+0
  [f1f71cc9] MPItrampoline_jll v5.4.0+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+2
⌃ [7243133f] NetCDF_jll v400.902.209+0
⌅ [4c82536e] Nettle_jll v3.7.2+0
  [fe0851c0] OpenMPI_jll v5.0.5+0
  [458c3c95] OpenSSL_jll v3.0.15+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [c2071276] P11Kit_jll v0.24.1+0
  [36c8627f] Pango_jll v1.54.1+0
  [30392449] Pixman_jll v0.43.4+0
  [f50d1b31] Rmath_jll v0.5.1+0
⌅ [fb77eaff] Sundials_jll v5.2.2+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.3+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.4.6+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [0aeada51] Xorg_libXdamage_jll v1.1.5+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [d091e8ba] Xorg_libXfixes_jll v5.0.3+4
  [a51aa0fd] Xorg_libXi_jll v1.7.10+4
  [d1454406] Xorg_libXinerama_jll v1.1.4+4
  [ec84b674] Xorg_libXrandr_jll v1.5.2+4
  [ea2f1a96] Xorg_libXrender_jll v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [35661453] Xorg_xkbcomp_jll v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] Zstd_jll v1.5.6+0
  [b437f822] adwaita_icon_theme_jll v43.0.1+0
  [da03df04] gdk_pixbuf_jll v2.42.10+0
  [059c91fe] hicolor_icon_theme_jll v0.17.0+3
  [bf975903] iso_codes_jll v4.15.1+0
  [477f73a3] libaec_jll v1.1.2+0
⌅ [b53b4c65] libpng_jll v1.6.40+0
  [337d8026] libzip_jll v1.10.1+0
  [1317d2d5] oneTBB_jll v2021.12.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [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
  [781609d7] GMP_jll v6.2.1+6
  [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
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
  [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 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 22 × Intel(R) Core(TM) Ultra 7 155H
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, goldmont)
Threads: 1 default, 0 interactive, 1 GC (on 22 virtual cores)

Additional context

It seems like for this example, the Base.Serialization.serialize function does work, but for a more complicated example in my code, I get a pretty similar error message to this (upon deserialization, though) where it seems to be trying to access an undefined reference, but it doesn't tell me much more than that, so I'm not sure where to look.

[jClugstor]

Yes, this needs to be updated to use the new strip_solution functionality. I'll be updating it soon.