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v3.2.0 precompiles fail with "Method definition overwritten" #306

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sjdaines opened this issue Dec 20, 2023 · 5 comments
Closed

v3.2.0 precompiles fail with "Method definition overwritten" #306

sjdaines opened this issue Dec 20, 2023 · 5 comments
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@sjdaines
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sjdaines commented Dec 20, 2023 •
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Describe the bug 🐞
Many SciML packages fail to precompile following a pkg> update that updates to:

  • DiffEqBase v6.144.0 -> v6.144.1
  • SciMLBase v2.11.1 -> v2.11.3
  • RecursiveArrayTools v3.1.0 -> v3.2.0
  • OffsetArrays v1.12.10 -> v1.13.0

Pinning RecursiveArrayTools to v3.1.0 [edit: not v3.2.1 !] allows precompile to work normally

Expected behavior

A clear and concise description of what you expected to happen.

Minimal Reproducible Example 👇

] update

Error & Stacktrace ⚠️

┌ SciMLBase
│  WARNING: Method definition ldiv!(T, RecursiveArrayTools.ArrayPartition{T, S} where S<:Tuple where T) where {T<:Union{}} in module RecursiveArrayTools at /home/sd336/.julia/packages/RecursiveArrayTools/aXSjX/src/array_partition.jl:431 overwritten on the same line (check for duplicate calls to `include`).
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└

and many other examples from SciML packages

Environment (please complete the following information):

  • Output of using Pkg; Pkg.status()


    

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



julia> Pkg.status(;mode=Pkg.PKGMODE_MANIFEST)
Project PALEOreactions v0.21.10
Status `~/PALEO/PALEOdev.jl/PALEOreactions/Manifest.toml`
  [47edcb42] ADTypes v0.2.5
⌅ [79e6a3ab] Adapt v3.7.2
  [ec485272] ArnoldiMethod v0.2.0
  [4fba245c] ArrayInterface v7.7.0
  [4c555306] ArrayLayouts v1.4.5
⌃ [13072b0f] AxisAlgorithms v1.0.1
  [6e4b80f9] BenchmarkTools v1.4.0
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [e1450e63] BufferedStreams v1.2.1
  [179af706] CFTime v0.1.2
  [2a0fbf3d] CPUSummary v0.2.4
  [336ed68f] CSV v0.10.11
  [d360d2e6] ChainRulesCore v1.19.0
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [da1fd8a2] CodeTracking v1.3.5
  [944b1d66] CodecZlib v0.7.3
⌅ [1fbeeb36] CommonDataModel v0.2.5
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.10.1
  [2569d6c7] ConcreteStructs v0.2.3
  [187b0558] ConstructionBase v1.5.4
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.15.0
  [a93c6f00] DataFrames v1.6.1
  [864edb3b] DataStructures v0.18.15
  [e2d170a0] DataValueInterfaces v1.0.0
  [8bb1440f] DelimitedFiles v1.9.1
  [2b5f629d] DiffEqBase v6.144.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [b4f34e82] Distances v0.10.11
  [ffbed154] DocStringExtensions v0.9.3
  [4e289a0a] EnumX v1.0.4
  [f151be2c] EnzymeCore v0.6.4
  [d4d017d3] ExponentialUtilities v1.25.0
  [e2ba6199] ExprTools v0.1.10
  [8f5d6c58] EzXML v1.2.0
  [7034ab61] FastBroadcast v0.2.8
  [9aa1b823] FastClosures v0.3.2
  [29a986be] FastLapackInterface v2.0.0
  [48062228] FilePathsBase v0.9.21
  [1a297f60] FillArrays v1.9.3
  [6a86dc24] FiniteDiff v2.21.1
  [f6369f11] ForwardDiff v0.10.36
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
⌃ [46192b85] GPUArraysCore v0.1.5
  [c145ed77] GenericSchur v0.5.3
  [86223c79] Graphs v1.9.0
  [f67ccb44] HDF5 v0.17.1
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [615f187c] IfElse v0.1.1
  [5903a43b] Infiltrator v1.6.4
  [d25df0c9] Inflate v0.1.4
  [842dd82b] InlineStrings v1.4.0
⌅ [a98d9a8b] Interpolations v0.14.7
  [41ab1584] InvertedIndices v1.3.0
  [92d709cd] IrrationalConstants v0.2.2
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [aa1ae85d] JuliaInterpreter v0.9.27
  [ef3ab10e] KLU v0.4.1
  [ba0b0d4f] Krylov v0.9.5
  [b964fa9f] LaTeXStrings v1.3.1
  [10f19ff3] LayoutPointers v0.1.15
  [50d2b5c4] Lazy v0.15.1
  [5078a376] LazyArrays v1.8.3
  [d3d80556] LineSearches v7.2.0
  [7ed4a6bd] LinearSolve v2.21.1
  [2ab3a3ac] LogExpFunctions v0.3.26
  [bdcacae8] LoopVectorization v0.12.166
  [6f1432cf] LoweredCodeUtils v2.3.2
  [23992714] MAT v0.10.6
  [3da0fdf6] MPIPreferences v0.1.10
  [1914dd2f] MacroTools v0.5.12
  [d125e4d3] ManualMemory v0.1.8
  [a3b82374] MatrixFactorizations v2.1.0
  [bb5d69b7] MaybeInplace v0.1.1
  [e1d29d7a] Missings v1.1.0
  [46d2c3a1] MuladdMacro v0.2.4
⌅ [85f8d34a] NCDatasets v0.12.17
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1 `https://github.com/PALEOtoolkit/NLsolve.jl#project_region`
  [77ba4419] NaNMath v1.0.2
  [8913a72c] NonlinearSolve v3.1.1
  [6fe1bfb0] OffsetArrays v1.13.0
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.63.0
  [673cec3b] PALEOaqchem v0.3.1
  [804b410e] PALEOboxes v0.21.20
  [41de04b1] PALEOocean v0.4.3
  [65ce6f38] PackageExtensionCompat v1.0.2
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.0
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [2dfb63ee] PooledArrays v1.4.3
  [d236fae5] PreallocationTools v0.4.13
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.1
  [08abe8d2] PrettyTables v2.3.1
  [c84ed2f1] Ratios v0.4.5
  [3cdcf5f2] RecipesBase v1.3.4
  [731186ca] RecursiveArrayTools v3.2.0
  [f2c3362d] RecursiveFactorization v0.2.21
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.0
  [295af30f] Revise v3.5.10
  [f2b01f46] Roots v2.0.22
  [7e49a35a] RuntimeGeneratedFunctions v0.5.12
  [fdea26ae] SIMD v3.4.6
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.42
  [0bca4576] SciMLBase v2.11.3
  [c0aeaf25] SciMLOperators v0.3.7
  [91c51154] SentinelArrays v1.4.1
  [efcf1570] Setfield v1.1.1
  [727e6d20] SimpleNonlinearSolve v1.0.3
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [66db9d55] SnoopPrecompile v1.0.3
  [a2af1166] SortingAlgorithms v1.2.0
  [47a9eef4] SparseDiffTools v2.15.0
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.3.1
  [aedffcd0] Static v0.8.8
  [0d7ed370] StaticArrayInterface v1.5.0
  [90137ffa] StaticArrays v1.8.1
  [1e83bf80] StaticArraysCore v1.4.2
  [82ae8749] StatsAPI v1.7.0
  [7792a7ef] StrideArraysCore v0.5.2
  [69024149] StringEncodings v0.3.7
  [892a3eda] StringManipulation v0.3.4
  [09ab397b] StructArrays v0.6.16
  [2efcf032] SymbolicIndexingInterface v0.3.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [1e6cf692] TestEnv v1.101.1
  [8290d209] ThreadingUtilities v0.5.2
  [a759f4b9] TimerOutputs v0.5.23
  [3bb67fe8] TranscodingStreams v0.10.2
  [d5829a12] TriangularSolve v0.1.20
  [410a4b4d] Tricks v0.1.8
  [781d530d] TruncatedStacktraces v1.4.0
  [3a884ed6] UnPack v1.0.2
  [3d5dd08c] VectorizationBase v0.21.65
  [19fa3120] VertexSafeGraphs v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
⌅ [efce3f68] WoodburyMatrices v0.5.6
  [76eceee3] WorkerUtilities v1.6.1
  [fdbf4ff8] XLSX v0.10.0
  [ddb6d928] YAML v0.4.9
  [a5390f91] ZipFile v0.10.1
⌅ [0234f1f7] HDF5_jll v1.12.2+2
  [1d5cc7b8] IntelOpenMP_jll v2024.0.0+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [856f044c] MKL_jll v2024.0.0+0
⌃ [7243133f] NetCDF_jll v400.902.5+1
⌅ [458c3c95] OpenSSL_jll v1.1.23+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [63e82ce6] SLEEF_jll v3.5.2+0
  [02c8fc9c] XML2_jll v2.12.2+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
  [9abbd945] Profile
  [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 v1.0.5+1
  [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
  [3a97d323] MPFR_jll v4.2.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+2
  [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
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> versioninfo()
Julia Version 1.10.0-rc3
Commit ed79752b939 (2023-12-18 09:57 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 12 × AMD Ryzen 5 7600 6-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
  Threads: 1 on 12 virtual cores


Additional context


Not sure if this is actually a problem in RecursiveArrayTools or a symptom of an issue somewhere else, but pinning to v3.1.0 does allow other packages to precompile normally

      		
    

      
  





        



            

              
            

        

      


      
    








      

    



      

  
            

    

      
    

    


      

          @sjdaines
sjdaines




          added
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      Dec 20, 2023

    

  








      

  
      



  

  @ChrisRackauckas





  


    

      

  

    

        
    
    

  


      
          
  
      
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Pinning RecursiveArrayTools to v3.2.1 allows precompile to work normally




Doesn't the already released patch fix this?

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @sjdaines





  


    

      

  

    

        
    
    

  


      
          
  
      
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Is this a patch in RecursiveArrayTools or in a different package ?

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @sjdaines





  


    

      

  

    

        
    
    

  


      
          
  
      
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Apologies, typo in the original report:  Pinning RecursiveArrayTools to v3.1.0 allows precompile to work normally.

(and v3.2.0 appears to break precompiles)

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @ChrisRackauckas





  


    

      

  

    

        
    
    

  


      
          
  
      
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Try updating, new hotfix.

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
      



  

  @ChrisRackauckas





  


    

      

  

    

        
    
    

  


      
          
  
      
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Testing locally, this was fixed by the hotfix, so closing. Please feel free to comment if it's not working on your end.

      		
    

  





        


            

            

              
            

        

      


      

            
  

    
  
    
    

  

  



    












      

  
            

    











  
  

    

      

  





  




  
  

              

  
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      2 participants
    

    

        
          @sjdaines 
        
          @ChrisRackauckas