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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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Precompilation issue on 1.7.2 #872

Closed arnold-c closed 2 years ago

arnold-c commented 2 years ago

I seem to be running into a similar problem to others wrt precompilations of DifferentialEquations.jl. I'm afraid that I'm brand new to Julia so don't have a lot of experience dealing with these kinds of issues. I tried removing and re-installing packages, including ArrayInterface.jl, but that didn't seem to work; sorry about that.

If you had any suggestions it'd be very much appreciated.

julia> versioninfo()
Julia Version 1.7.2
Commit bf53498635 (2022-02-06 15:21 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.2.0)
  CPU: Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, cyclone)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS =
`Pkg.precompile()` error ``` julia> import Pkg; Pkg.precompile() Precompiling project... ✗ OrdinaryDiffEq ✗ DelayDiffEq ✗ StochasticDiffEq ✗ MultiScaleArrays ✗ DifferentialEquations 0 dependencies successfully precompiled in 127 seconds (383 already precompiled) ERROR: The following 1 direct dependency failed to precompile: DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] to /Users/cfa5228/.julia/compiled/v1.7/DifferentialEquations/jl_gSh9Kx. WARNING: Method definition setindex(AbstractArray{T, 2} where T, Any, Int64, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:163 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:129. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, 1} where T, Any, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:158 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:124. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, N} where N where T, Any, Any...) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:152 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:118. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, 2} where T, Any, Int64, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:163 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:129. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, 1} where T, Any, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:158 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:124. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, N} where N where T, Any, Any...) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:152 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:118. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, 2} where T, Any, Int64, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:163 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:129. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, 1} where T, Any, Int64) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:158 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:124. ** incremental compilation may be fatally broken for this module ** WARNING: Method definition setindex(AbstractArray{T, N} where N where T, Any, Any...) in module ArrayInterface at /Users/cfa5228/.julia/packages/ArrayInterface/TCj9U/src/ArrayInterface.jl:152 overwritten in module ArrayInterfaceCore at /Users/cfa5228/.julia/packages/ArrayInterfaceCore/wwYvJ/src/ArrayInterfaceCore.jl:118. ** incremental compilation may be fatally broken for this module ** ERROR: LoadError: UndefVarError: DEFAULT_LINSOLVE not defined Stacktrace: [1] OrdinaryDiffEq.Rosenbrock23() @ OrdinaryDiffEq ~/.julia/packages/OrdinaryDiffEq/4BjSL/src/algorithms.jl:3626 [2] top-level scope @ ~/.julia/packages/OrdinaryDiffEq/4BjSL/src/OrdinaryDiffEq.jl:189 [3] include @ ./Base.jl:418 [inlined] [4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String) @ Base ./loading.jl:1318 [5] top-level scope @ none:1 [6] eval @ ./boot.jl:373 [inlined] [7] eval(x::Expr) @ Base.MainInclude ./client.jl:453 [8] top-level scope @ none:1 in expression starting at /Users/cfa5228/.julia/packages/OrdinaryDiffEq/4BjSL/src/OrdinaryDiffEq.jl:1 ERROR: LoadError: Failed to precompile OrdinaryDiffEq [1dea7af3-3e70-54e6-95c3-0bf5283fa5ed] to /Users/cfa5228/.julia/compiled/v1.7/OrdinaryDiffEq/jl_fNPW2D. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool) @ Base ./loading.jl:1466 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1410 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1120 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:1013 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:997 [7] include @ ./Base.jl:418 [inlined] [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String) @ Base ./loading.jl:1318 [9] top-level scope @ none:1 [10] eval @ ./boot.jl:373 [inlined] [11] eval(x::Expr) @ Base.MainInclude ./client.jl:453 [12] top-level scope @ none:1 in expression starting at /Users/cfa5228/.julia/packages/StochasticDiffEq/ls8gH/src/StochasticDiffEq.jl:1 ERROR: LoadError: Failed to precompile StochasticDiffEq [789caeaf-c7a9-5a7d-9973-96adeb23e2a0] to /Users/cfa5228/.julia/compiled/v1.7/StochasticDiffEq/jl_BEkGeh. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool) @ Base ./loading.jl:1466 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1410 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1120 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:1013 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:997 [7] include @ ./Base.jl:418 [inlined] [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing) @ Base ./loading.jl:1318 [9] top-level scope @ none:1 [10] eval @ ./boot.jl:373 [inlined] [11] eval(x::Expr) @ Base.MainInclude ./client.jl:453 [12] top-level scope @ none:1 in expression starting at /Users/cfa5228/.julia/packages/DifferentialEquations/7WPQg/src/DifferentialEquations.jl:1 Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68 [2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:1362 [3] precompile @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:1013 [inlined] [4] #precompile#220 @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:1011 [inlined] [5] precompile() @ Pkg.API /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Pkg/src/API.jl:1011 [6] top-level scope @ REPL[17]:1 ```
`] st -m` ``` julia> ] st -m Status `~/Documents/Repos/Data4Action/Manifest.toml` [c3fe647b] AbstractAlgebra v0.26.0 [621f4979] AbstractFFTs v1.1.0 [537997a7] AbstractPlotting v0.15.27 [1520ce14] AbstractTrees v0.3.4 [79e6a3ab] Adapt v2.4.0 [cbdf2221] AlgebraOfGraphics v0.2.4 [27a7e980] Animations v0.4.1 [dce04be8] ArgCheck v2.3.0 [ec485272] ArnoldiMethod v0.1.0 [7d9fca2a] Arpack v0.5.3 [4fba245c] ArrayInterface v3.2.2 [30b0a656] ArrayInterfaceCore v0.1.10 [4c555306] ArrayLayouts v0.7.5 [69666777] Arrow v2.3.0 [31f734f8] ArrowTypes v1.2.1 [bf4720bc] AssetRegistry v0.1.0 [15f4f7f2] AutoHashEquals v0.2.0 [13072b0f] AxisAlgorithms v1.0.1 [aae01518] BandedMatrices v0.16.13 [198e06fe] BangBang v0.3.36 [9718e550] Baselet v0.1.1 [e2ed5e7c] Bijections v0.1.4 [c3b6d118] BitIntegers v0.2.6 [62783981] BitTwiddlingConvenienceFunctions v0.1.3 [764a87c0] BoundaryValueDiffEq v2.8.0 [fa961155] CEnum v0.4.2 [2a0fbf3d] CPUSummary v0.1.22 [70588ee8] CSSUtil v0.1.1 [00ebfdb7] CSTParser v3.3.3 [336ed68f] 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DataAPI v1.10.0 [a93c6f00] DataFrames v1.3.4 [1313f7d8] DataFramesMeta v0.11.0 [864edb3b] DataStructures v0.18.13 [e2d170a0] DataValueInterfaces v1.0.0 [e7dc6d0d] DataValues v0.4.13 [244e2a9f] DefineSingletons v0.1.2 [bcd4f6db] DelayDiffEq v5.33.0 [2b5f629d] DiffEqBase v6.89.5 [459566f4] DiffEqCallbacks v2.23.0 [5a0ffddc] DiffEqFinancial v2.4.0 [c894b116] DiffEqJump v7.3.1 [77a26b50] DiffEqNoiseProcess v5.11.1 [055956cb] DiffEqPhysics v3.9.0 [163ba53b] DiffResults v1.0.3 [b552c78f] DiffRules v1.11.0 [0c46a032] DifferentialEquations v6.19.0 [c619ae07] DimensionalPlotRecipes v1.2.0 [b4f34e82] Distances v0.10.7 [31c24e10] Distributions v0.24.18 [ffbed154] DocStringExtensions v0.8.6 [5b8099bc] DomainSets v0.5.10 [7c1d4256] DynamicPolynomials v0.4.5 [da5c29d0] EllipsisNotation v1.6.0 [d4d017d3] ExponentialUtilities v1.17.1 [e2ba6199] ExprTools v0.1.8 [c87230d0] FFMPEG v0.4.1 [7a1cc6ca] FFTW v1.4.6 [7034ab61] FastBroadcast v0.1.16 [9aa1b823] FastClosures v0.3.2 [5789e2e9] FileIO v1.14.0 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arnold-c commented 2 years ago

I'm going to close this for now as I removed all packages and reinstalled starting with DifferentialEquations.jl and it seems to be working fine. I have been using the JuliaConnectoR R package, and that has had issues finding some of my installed Julia packages, so I suspect there may have been some issues introduced there.

ChrisRackauckas commented 2 years ago

https://github.com/JuliaRegistries/General/pull/62170 should stop that combination of packages from existing in the future.