SciML / DifferentialEquations.jl

Multi-language suite for high-performance solvers of differential equations and scientific machine learning (SciML) components. Ordinary differential equations (ODEs), stochastic differential equations (SDEs), delay differential equations (DDEs), differential-algebraic equations (DAEs), and more in Julia.
https://docs.sciml.ai/DiffEqDocs/stable/
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Documentation Serialization Example No Longer Works #1053

Open rconnorjohnstone opened 1 week ago

rconnorjohnstone commented 1 week ago

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):

Status `~/.julia/environments/v1.10/Project.toml`
  [9db2cae5] Gtk4 v0.6.9
  [033835bb] JLD2 v0.5.2
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  [1dea7af3] OrdinaryDiffEq v6.89.0
  [f0f68f2c] PlotlyJS v0.18.14
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Status `~/.julia/environments/v1.10/Manifest.toml`
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  [fa646aed] OrdinaryDiffEqSymplecticRK v1.1.0
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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`
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 commented 6 days ago

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