Hi everyone,
I am getting a precompilation error when trying to using Optimization.
Any help would be appreciated.
P.S.: I am not sure how this precompilation error affects the rest of the code. My script runs as it should after I get the error message. Should I assume that it is not as optimized as it could? Or maybe I am just not using the parts of the package that are not precompiled?
(PulsarPinn3D) pkg> st
Project PulsarPinn3D v0.1.0
Status `~/phys/ml_pde/PulsarPinn3D/Project.toml`
[6e4b80f9] BenchmarkTools v1.5.0
[b0b7db55] ComponentArrays v0.15.13
[5218b696] Configurations v0.17.6
[31c24e10] Distributions v0.25.108
[615f187c] IfElse v0.1.1
⌃ [c3a54625] JET v0.9.1
[033835bb] JLD2 v0.4.48
[3db4a2ba] LegendrePolynomials v0.4.4
[d3d80556] LineSearches v7.2.0
[b2108857] Lux v0.5.51
[d0bbae9a] LuxCUDA v0.3.2
[961ee093] ModelingToolkit v9.15.0
[315f7962] NeuralPDE v5.16.0
[429524aa] Optim v1.9.4
[7f7a1694] Optimization v3.25.1
[36348300] OptimizationOptimJL v0.3.1
[42dfb2eb] OptimizationOptimisers v0.2.1
[91a5bcdd] Plots v1.40.4
[8162dcfd] PrettyPrint v0.2.0
[92933f4c] ProgressMeter v1.10.0
[438e738f] PyCall v1.96.4
[d330b81b] PyPlot v2.11.2
[8a4e6c94] QuasiMonteCarlo v0.3.3
[295af30f] Revise v3.5.14
[f2b01f46] Roots v2.1.5
[e88e6eb3] Zygote v0.6.70
[de0858da] Printf
[9a3f8284] Random
[fa267f1f] TOML v1.0.3
Error message
Precompiling PulsarPinn3D
? OptimizationBase → OptimizationMTKExt
536 dependencies successfully precompiled in 812 seconds. 16 already precompiled.
1 dependency failed but may be precompilable after restarting julia
2 dependencies had output during precompilation:
┌ NeuralPDE
│ WARNING: Method definition AutoModelingToolkit() in module ADTypes at deprecated.jl:103 overwritten in module OptimizationMTKExt at /home/petros/.julia/packages/OptimizationBase/QZlI6/ext/OptimizationMTKExt.jl:9.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
│ ┌ Error: Error during loading of extension OptimizationMTKExt of OptimizationBase, use `Base.retry_load_extensions()` to retry.
│ │ exception =
│ │ 1-element ExceptionStack:
│ │ Declaring __precompile__(false) is not allowed in files that are being precompiled.
│ │ Stacktrace:
│ │ [1] _require(pkg::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1999
│ │ [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│ │ @ Base ./loading.jl:1812
│ │ [3] #invoke_in_world#3
│ │ @ ./essentials.jl:926 [inlined]
│ │ [4] invoke_in_world
│ │ @ ./essentials.jl:923 [inlined]
│ │ [5] _require_prelocked
│ │ @ ./loading.jl:1803 [inlined]
│ │ [6] _require_prelocked
│ │ @ ./loading.jl:1802 [inlined]
│ │ [7] run_extension_callbacks(extid::Base.ExtensionId)
│ │ @ Base ./loading.jl:1295
│ │ [8] run_extension_callbacks(pkgid::Base.PkgId)
│ │ @ Base ./loading.jl:1330
│ │ [9] run_package_callbacks(modkey::Base.PkgId)
│ │ @ Base ./loading.jl:1164
│ │ [10] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
│ │ @ Base ./loading.jl:1487
│ │ [11] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
│ │ @ Base ./loading.jl:1574
│ │ [12] _require(pkg::Base.PkgId, env::String)
│ │ @ Base ./loading.jl:1938
│ │ [13] __require_prelocked(uuidkey::Base.PkgId, env::String)
│ │ @ Base ./loading.jl:1812
│ │ [14] #invoke_in_world#3
│ │ @ ./essentials.jl:926 [inlined]
│ │ [15] invoke_in_world
│ │ @ ./essentials.jl:923 [inlined]
│ │ [16] _require_prelocked(uuidkey::Base.PkgId, env::String)
│ │ @ Base ./loading.jl:1803
│ │ [17] macro expansion
│ │ @ ./loading.jl:1790 [inlined]
│ │ [18] macro expansion
│ │ @ ./lock.jl:267 [inlined]
│ │ [19] __require(into::Module, mod::Symbol)
│ │ @ Base ./loading.jl:1753
│ │ [20] #invoke_in_world#3
│ │ @ ./essentials.jl:926 [inlined]
│ │ [21] invoke_in_world
│ │ @ ./essentials.jl:923 [inlined]
│ │ [22] require(into::Module, mod::Symbol)
│ │ @ Base ./loading.jl:1746
│ │ [23] include
│ │ @ ./Base.jl:495 [inlined]
│ │ [24] 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, UInt128}}, source::Nothing)
│ │ @ Base ./loading.jl:2222
│ │ [25] top-level scope
│ │ @ stdin:3
│ │ [26] eval
│ │ @ ./boot.jl:385 [inlined]
│ │ [27] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│ │ @ Base ./loading.jl:2076
│ │ [28] include_string
│ │ @ ./loading.jl:2086 [inlined]
│ │ [29] exec_options(opts::Base.JLOptions)
│ │ @ Base ./client.jl:316
│ │ [30] _start()
│ │ @ Base ./client.jl:552
│ └ @ Base loading.jl:1301
└
┌ OptimizationBase → OptimizationMTKExt
│ WARNING: Method definition AutoModelingToolkit() in module ADTypes at deprecated.jl:103 overwritten in module OptimizationMTKExt at /home/petros/.julia/packages/OptimizationBase/QZlI6/ext/OptimizationMTKExt.jl:9.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└
Can you print the result of pkg> st -m in that environment? Wanna see if it’s related to some changes @Vaibhavdixit02 and I made recently
1 Like
Hi @gdalle and thanks for the reply.
Here is the output of ]st -m
(PulsarPinn3D) pkg> st -m
Project PulsarPinn3D v0.1.0
Status `~/phys/ml_pde/PulsarPinn3D/Manifest.toml`
[47edcb42] ADTypes v1.2.1
[621f4979] AbstractFFTs v1.5.0
[80f14c24] AbstractMCMC v5.2.0
[1520ce14] AbstractTrees v0.4.5
[7d9f7c33] Accessors v0.1.36
[79e6a3ab] Adapt v4.0.4
[0bf59076] AdvancedHMC v0.6.1
[66dad0bd] AliasTables v1.1.3
[dce04be8] ArgCheck v2.3.0
[ec485272] ArnoldiMethod v0.4.0
[4fba245c] ArrayInterface v7.10.0
[4c555306] ArrayLayouts v1.9.3
[a9b6321e] Atomix v0.1.0
[13072b0f] AxisAlgorithms v1.1.0
[39de3d68] AxisArrays v0.4.7
[ab4f0b2a] BFloat16s v0.5.0
[198e06fe] BangBang v0.4.2
[9718e550] Baselet v0.1.1
[6e4b80f9] BenchmarkTools v1.5.0
[e2ed5e7c] Bijections v0.1.6
[d1d4a3ce] BitFlags v0.1.8
[62783981] BitTwiddlingConvenienceFunctions v0.1.5
[fa961155] CEnum v0.5.0
[2a0fbf3d] CPUSummary v0.2.5
[00ebfdb7] CSTParser v3.4.3
[052768ef] CUDA v5.3.4
⌅ [1af6417a] CUDA_Runtime_Discovery v0.2.4
[49dc2e85] Calculus v0.5.1
[082447d4] ChainRules v1.66.0
[d360d2e6] ChainRulesCore v1.23.0
[ae650224] ChunkSplitters v2.4.2
[fb6a15b2] CloseOpenIntervals v0.1.12
[da1fd8a2] CodeTracking v1.3.5
[944b1d66] CodecZlib v0.7.4
[35d6a980] ColorSchemes v3.25.0
[3da002f7] ColorTypes v0.11.5
[c3611d14] ColorVectorSpace v0.10.0
[5ae59095] Colors v0.12.11
[861a8166] Combinatorics v1.0.2
[a80b9123] CommonMark v0.8.12
[38540f10] CommonSolve v0.2.4
[bbf7d656] CommonSubexpressions v0.3.0
[34da2185] Compat v4.15.0
[b0b7db55] ComponentArrays v0.15.13
[b152e2b5] CompositeTypes v0.1.4
[a33af91c] CompositionsBase v0.1.2
[2569d6c7] ConcreteStructs v0.2.3
[f0e56b4a] ConcurrentUtilities v2.4.1
[8f4d0f93] Conda v1.10.0
[5218b696] Configurations v0.17.6
[88cd18e8] ConsoleProgressMonitor v0.1.2
[187b0558] ConstructionBase v1.5.5
[d38c429a] Contour v0.6.3
[adafc99b] CpuId v0.3.1
[a8cc5b0e] Crayons v4.1.1
[667455a9] Cubature v1.5.1
[9a962f9c] DataAPI v1.16.0
[a93c6f00] DataFrames v1.6.1
[864edb3b] DataStructures v0.18.20
[e2d170a0] DataValueInterfaces v1.0.0
[244e2a9f] DefineSingletons v0.1.2
[8bb1440f] DelimitedFiles v1.9.1
[2b5f629d] DiffEqBase v6.151.1
[459566f4] DiffEqCallbacks v3.6.2
[77a26b50] DiffEqNoiseProcess v5.21.0
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.15.1
[31c24e10] Distributions v0.25.108
[ffbed154] DocStringExtensions v0.9.3
[5b8099bc] DomainSets v0.7.14
[fa6b7ba4] DualNumbers v0.6.8
[7c1d4256] DynamicPolynomials v0.5.7
⌅ [06fc5a27] DynamicQuantities v0.13.2
[4e289a0a] EnumX v1.0.4
[f151be2c] EnzymeCore v0.7.2
[460bff9d] ExceptionUnwrapping v0.1.10
[d4d017d3] ExponentialUtilities v1.26.1
[e2ba6199] ExprTools v0.1.10
[55351af7] ExproniconLite v0.10.8
[c87230d0] FFMPEG v0.4.1
[7a1cc6ca] FFTW v1.8.0
[7034ab61] FastBroadcast v0.2.8
[9aa1b823] FastClosures v0.3.2
[29a986be] FastLapackInterface v2.0.4
[5789e2e9] FileIO v1.16.3
[1a297f60] FillArrays v1.11.0
[64ca27bc] FindFirstFunctions v1.2.0
[6a86dc24] FiniteDiff v2.23.1
[53c48c17] FixedPointNumbers v0.8.5
[1fa38f19] Format v1.3.7
[f6369f11] ForwardDiff v0.10.36
[069b7b12] FunctionWrappers v1.1.3
[77dc65aa] FunctionWrappersWrappers v0.1.3
[d9f16b24] Functors v0.4.10
[0c68f7d7] GPUArrays v10.1.1
[46192b85] GPUArraysCore v0.1.6
⌃ [61eb1bfa] GPUCompiler v0.26.4
[28b8d3ca] GR v0.73.5
[c145ed77] GenericSchur v0.5.4
[c27321d9] Glob v1.3.1
[86223c79] Graphs v1.11.0
[42e2da0e] Grisu v1.0.2
[19dc6840] HCubature v1.6.0
[cd3eb016] HTTP v1.10.8
[3e5b6fbb] HostCPUFeatures v0.1.16
[34004b35] HypergeometricFunctions v0.3.23
[7869d1d1] IRTools v0.4.14
[615f187c] IfElse v0.1.1
[d25df0c9] Inflate v0.1.4
[22cec73e] InitialValues v0.3.1
[842dd82b] InlineStrings v1.4.0
[505f98c9] InplaceOps v0.3.0
[18e54dd8] IntegerMathUtils v0.1.2
[de52edbc] Integrals v4.4.1
[a98d9a8b] Interpolations v0.15.1
[8197267c] IntervalSets v0.7.10
[3587e190] InverseFunctions v0.1.14
[41ab1584] InvertedIndices v1.3.0
[92d709cd] IrrationalConstants v0.2.2
[c8e1da08] IterTools v1.10.0
[82899510] IteratorInterfaceExtensions v1.0.0
⌃ [c3a54625] JET v0.9.1
[033835bb] JLD2 v0.4.48
[1019f520] JLFzf v0.1.7
[692b3bcd] JLLWrappers v1.5.0
[682c06a0] JSON v0.21.4
[98e50ef6] JuliaFormatter v1.0.56
[aa1ae85d] JuliaInterpreter v0.9.31
[ccbc3e58] JumpProcesses v9.11.1
[ef3ab10e] KLU v0.6.0
[63c18a36] KernelAbstractions v0.9.19
[5ab0869b] KernelDensity v0.6.9
[ba0b0d4f] Krylov v0.9.6
[5be7bae1] LBFGSB v0.4.1
⌅ [929cbde3] LLVM v6.6.3
[8b046642] LLVMLoopInfo v1.0.0
[b964fa9f] LaTeXStrings v1.3.1
[2ee39098] LabelledArrays v1.16.0
[984bce1d] LambertW v0.4.6
[23fbe1c1] Latexify v0.16.3
[73f95e8e] LatticeRules v0.0.1
[10f19ff3] LayoutPointers v0.1.15
⌅ [5078a376] LazyArrays v1.10.0
[1d6d02ad] LeftChildRightSiblingTrees v0.2.0
[3db4a2ba] LegendrePolynomials v0.4.4
[d3d80556] LineSearches v7.2.0
[7ed4a6bd] LinearSolve v2.30.0
[6fdf6af0] LogDensityProblems v2.1.1
[996a588d] LogDensityProblemsAD v1.9.0
[2ab3a3ac] LogExpFunctions v0.3.27
[e6f89c97] LoggingExtras v1.0.3
[bdcacae8] LoopVectorization v0.12.170
[6f1432cf] LoweredCodeUtils v2.4.6
[b2108857] Lux v0.5.51
[d0bbae9a] LuxCUDA v0.3.2
[bb33d45b] LuxCore v0.1.15
[34f89e08] LuxDeviceUtils v0.1.20
[82251201] LuxLib v0.3.26
[c7f686f2] MCMCChains v6.0.6
[be115224] MCMCDiagnosticTools v0.3.10
[e80e1ace] MLJModelInterface v1.9.6
[d8e11817] MLStyle v0.4.17
[1914dd2f] MacroTools v0.5.13
[d125e4d3] ManualMemory v0.1.8
⌅ [a3b82374] MatrixFactorizations v2.2.0
[bb5d69b7] MaybeInplace v0.1.2
[739be429] MbedTLS v1.1.9
[442fdcdd] Measures v0.3.2
[128add7d] MicroCollections v0.2.0
[e1d29d7a] Missings v1.2.0
[961ee093] ModelingToolkit v9.15.0
[4886b29c] MonteCarloIntegration v0.2.0
[0987c9cc] MonteCarloMeasurements v1.1.6
[46d2c3a1] MuladdMacro v0.2.4
[102ac46a] MultivariatePolynomials v0.5.5
[d8a4904e] MutableArithmetics v1.4.4
[d41bc354] NLSolversBase v7.8.3
[872c559c] NNlib v0.9.17
[5da4648a] NVTX v0.3.4
[77ba4419] NaNMath v1.0.2
[c020b1a1] NaturalSort v1.0.0
[315f7962] NeuralPDE v5.16.0
[8913a72c] NonlinearSolve v3.12.0
[6fe1bfb0] OffsetArrays v1.14.0
[67456a42] OhMyThreads v0.5.2
[4d8831e6] OpenSSL v1.4.3
[429524aa] Optim v1.9.4
[3bd65402] Optimisers v0.3.3
[7f7a1694] Optimization v3.25.1
[bca83a33] OptimizationBase v1.0.2
[36348300] OptimizationOptimJL v0.3.1
[42dfb2eb] OptimizationOptimisers v0.2.1
[bac558e1] OrderedCollections v1.6.3
[1dea7af3] OrdinaryDiffEq v6.79.0
[90014a1f] PDMats v0.11.31
[65ce6f38] PackageExtensionCompat v1.0.2
[d96e819e] Parameters v0.12.3
[69de0a69] Parsers v2.8.1
[570af359] PartialFunctions v1.2.0
[b98c9c47] Pipe v1.3.0
[ccf2f8ad] PlotThemes v3.1.0
[995b91a9] PlotUtils v1.4.1
[91a5bcdd] Plots v1.40.4
[e409e4f3] PoissonRandom v0.4.4
[f517fe37] Polyester v0.7.14
[1d0040c9] PolyesterWeave v0.2.1
[2dfb63ee] PooledArrays v1.4.3
[85a6dd25] PositiveFactorizations v0.2.4
[d236fae5] PreallocationTools v0.4.21
[aea7be01] PrecompileTools v1.2.1
[21216c6a] Preferences v1.4.3
[8162dcfd] PrettyPrint v0.2.0
[08abe8d2] PrettyTables v2.3.1
[27ebfcd6] Primes v0.5.6
[33c8b6b6] ProgressLogging v0.1.4
[92933f4c] ProgressMeter v1.10.0
[43287f4e] PtrArrays v1.2.0
[438e738f] PyCall v1.96.4
[d330b81b] PyPlot v2.11.2
[1fd47b50] QuadGK v2.9.4
[8a4e6c94] QuasiMonteCarlo v0.3.3
[74087812] Random123 v1.7.0
[e6cf234a] RandomNumbers v1.5.3
[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 v3.19.0
[f2c3362d] RecursiveFactorization v0.2.23
[189a3867] Reexport v1.2.2
[05181044] RelocatableFolders v1.0.1
[ae029012] Requires v1.3.0
[ae5879a3] ResettableStacks v1.1.1
[295af30f] Revise v3.5.14
[79098fc4] Rmath v0.7.1
[f2b01f46] Roots v2.1.5
[7e49a35a] RuntimeGeneratedFunctions v0.5.13
[94e857df] SIMDTypes v0.1.0
[476501e8] SLEEFPirates v0.6.42
[0bca4576] SciMLBase v2.38.0
[c0aeaf25] SciMLOperators v0.3.8
[53ae85a6] SciMLStructures v1.2.0
[30f210dd] ScientificTypesBase v3.0.0
[6c6a2e73] Scratch v1.2.1
[91c51154] SentinelArrays v1.4.3
[efcf1570] Setfield v1.1.1
[992d4aef] Showoff v1.0.3
[777ac1f9] SimpleBufferStream v1.1.0
[727e6d20] SimpleNonlinearSolve v1.8.0
[699a6c99] SimpleTraits v0.9.4
[ce78b400] SimpleUnPack v1.1.0
[ed01d8cd] Sobol v1.5.0
[a2af1166] SortingAlgorithms v1.2.1
[47a9eef4] SparseDiffTools v2.19.0
[dc90abb0] SparseInverseSubset v0.1.2
[e56a9233] Sparspak v0.3.9
[276daf66] SpecialFunctions v2.4.0
[171d559e] SplittablesBase v0.1.15
[91464d47] StableTasks v0.1.5
[aedffcd0] Static v0.8.10
[0d7ed370] StaticArrayInterface v1.5.0
[90137ffa] StaticArrays v1.9.4
[1e83bf80] StaticArraysCore v1.4.2
[64bff920] StatisticalTraits v3.2.0
[82ae8749] StatsAPI v1.7.0
[2913bbd2] StatsBase v0.34.3
[4c63d2b9] StatsFuns v1.3.1
[7792a7ef] StrideArraysCore v0.5.6
[892a3eda] StringManipulation v0.3.4
[09ab397b] StructArrays v0.6.18
[2efcf032] SymbolicIndexingInterface v0.3.21
[19f23fe9] SymbolicLimits v0.2.0
[d1185830] SymbolicUtils v1.6.0
[0c5d862f] Symbolics v5.28.0
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.11.1
[ed4db957] TaskLocalValues v0.1.1
[62fd8b95] TensorCore v0.1.1
[8ea1fca8] TermInterface v0.4.1
[5d786b92] TerminalLoggers v0.1.7
[1c621080] TestItems v0.1.1
[8290d209] ThreadingUtilities v0.5.2
[a759f4b9] TimerOutputs v0.5.24
[0796e94c] Tokenize v0.5.29
[3bb67fe8] TranscodingStreams v0.10.8
[28d57a85] Transducers v0.4.82
[d5829a12] TriangularSolve v0.2.0
[410a4b4d] Tricks v0.1.8
[781d530d] TruncatedStacktraces v1.4.0
[5c2747f8] URIs v1.5.1
[3a884ed6] UnPack v1.0.2
[1cfade01] UnicodeFun v0.4.1
[1986cc42] Unitful v1.20.0
[45397f5d] UnitfulLatexify v1.6.3
[a7c27f48] Unityper v0.1.6
[013be700] UnsafeAtomics v0.2.1
[d80eeb9a] UnsafeAtomicsLLVM v0.1.4
[41fe7b60] Unzip v0.2.0
[3d5dd08c] VectorizationBase v0.21.67
[81def892] VersionParsing v1.3.0
[19fa3120] VertexSafeGraphs v0.2.0
[d49dbf32] WeightInitializers v0.1.7
[efce3f68] WoodburyMatrices v1.0.0
[e88e6eb3] Zygote v0.6.70
[700de1a5] ZygoteRules v0.2.5
[02a925ec] cuDNN v1.3.1
[6e34b625] Bzip2_jll v1.0.8+1
⌅ [4ee394cb] CUDA_Driver_jll v0.8.1+0
⌅ [76a88914] CUDA_Runtime_jll v0.12.1+0
⌅ [62b44479] CUDNN_jll v9.0.0+1
[83423d85] Cairo_jll v1.18.0+2
[7bc98958] Cubature_jll v1.0.5+0
[2702e6a9] EpollShim_jll v0.0.20230411+0
[2e619515] Expat_jll v2.6.2+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
[f5851436] FFTW_jll v3.3.10+0
[a3f928ae] Fontconfig_jll v2.13.96+0
[d7e528f0] FreeType2_jll v2.13.2+0
[559328eb] FriBidi_jll v1.0.14+0
[0656b61e] GLFW_jll v3.3.9+0
[d2c73de3] GR_jll v0.73.5+0
[78b55507] Gettext_jll v0.21.0+0
[7746bdde] Glib_jll v2.80.2+0
[3b182d85] Graphite2_jll v1.3.14+0
[2e76f6c2] HarfBuzz_jll v2.8.1+1
[1d5cc7b8] IntelOpenMP_jll v2024.1.0+0
[aacddb02] JpegTurbo_jll v3.0.3+0
[9c1d0b0a] JuliaNVTXCallbacks_jll v0.2.1+0
[c1c5ebd0] LAME_jll v3.100.2+0
⌅ [88015f11] LERC_jll v3.0.0+1
[dad2f222] LLVMExtra_jll v0.0.29+0
[1d63c593] LLVMOpenMP_jll v15.0.7+0
[dd4b983a] LZO_jll v2.10.2+0
[81d17ec3] L_BFGS_B_jll v3.0.1+0
⌅ [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
⌅ [89763e89] Libtiff_jll v4.5.1+1
[38a345b3] Libuuid_jll v2.40.1+0
[856f044c] MKL_jll v2024.1.0+0
[e98f9f5b] NVTX_jll v3.1.0+2
[e7412a2a] Ogg_jll v1.3.5+1
[458c3c95] OpenSSL_jll v3.0.13+1
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[91d4177d] Opus_jll v1.3.2+0
[30392449] Pixman_jll v0.43.4+0
⌅ [c0090381] Qt6Base_jll v6.5.3+1
[f50d1b31] Rmath_jll v0.4.2+0
[a44049a8] Vulkan_Loader_jll v1.3.243+0
[a2964d1f] Wayland_jll v1.21.0+1
[2381bf8a] Wayland_protocols_jll v1.31.0+0
[02c8fc9c] XML2_jll v2.12.7+0
[aed1982a] XSLT_jll v1.1.34+0
[ffd25f8a] XZ_jll v5.4.6+0
[f67eecfb] Xorg_libICE_jll v1.1.1+0
[c834827a] Xorg_libSM_jll v1.2.4+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
[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 v1.15.0+0
[cc61e674] Xorg_libxkbfile_jll v1.1.2+0
[e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
[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+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
[35ca27e7] eudev_jll v3.2.9+0
⌅ [214eeab7] fzf_jll v0.43.0+0
[1a1c6b14] gperf_jll v3.1.1+0
[a4ae2306] libaom_jll v3.9.0+0
[0ac62f75] libass_jll v0.15.1+0
[2db6ffa8] libevdev_jll v1.11.0+0
[f638f0a6] libfdk_aac_jll v2.0.2+0
[36db933b] libinput_jll v1.18.0+0
[b53b4c65] libpng_jll v1.6.43+1
[f27f6e37] libvorbis_jll v1.3.7+1
[009596ad] mtdev_jll v1.1.6+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+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
[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 v1.1.0+0
[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 v5.8.0+1
[8e850ede] nghttp2_jll v1.52.0+1
[3f19e933] p7zip_jll v17.4.0+2
Let me know if I can provide any more info that could be helpful.
@Vaibhavdixit02 I think it might be due to this part of the extension:
import OptimizationBase.ADTypes: AutoModelingToolkit, AutoSymbolics, AutoSparse
isdefined(Base, :get_extension) ? (using ModelingToolkit) : (using ..ModelingToolkit)
function OptimizationBase.ADTypes.AutoModelingToolkit(sparse = false, cons_sparse = false)
if sparse || cons_sparse
return AutoSparse(AutoSymbolics())
else
return AutoSymbolics()
end
end
Since AutoModelingToolkit doesn’t exist anymore, I don’t see how you can extend the constructor?
I am unable to recreate the issue. @gdalle did you get the failure to precompile?
AutoModelingToolkit still exists since @deprecate defines a new method for the deprecated one Essentials · The Julia Language
defining a new method old with the specified signature in the process.
1 Like
I can reproduce indeed, fresh REPL, temporary environment, updated registry:
Precompiling project...
? OptimizationBase → OptimizationMTKExt
61 dependencies successfully precompiled in 221 seconds. 177 already precompiled.
1 dependency failed but may be precompilable after restarting julia
1 dependency had output during precompilation:
┌ OptimizationBase → OptimizationMTKExt
│ WARNING: Method definition AutoModelingToolkit() in module ADTypes at deprecated.jl:103 overwritten in module OptimizationMTKExt at /home/guillaume/.julia/packages/OptimizationBase/QZlI6/ext/OptimizationMTKExt.jl:9.
│ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└
(jl_0WQIHS) pkg> st
Status `/tmp/jl_0WQIHS/Project.toml`
[961ee093] ModelingToolkit v9.15.0
[bca83a33] OptimizationBase v1.0.2
@Vaibhavdixit02 , @gdalle
I am also running into this issue, but can successfully compile when I use julia version “1.11.0-beta2” with the following package versions.
[336ed68f] CSV v0.10.14
[a93c6f00] DataFrames v1.6.1
[0c46a032] DifferentialEquations v7.13.0
[9aa1b823] FastClosures v0.3.2
[f6369f11] ForwardDiff v0.10.36
[c27321d9] Glob v1.3.1
[a5e1c1ea] LatinHypercubeSampling v1.9.0
[961ee093] ModelingToolkit v9.13.0
[7f7a1694] Optimization v3.25.0
⌃ [1ed8b502] SciMLSensitivity v7.56.2
⌃ [90137ffa] StaticArrays v1.9.3
[37e2e46d] LinearAlgebra v1.11.0
[9a3f8284] Random v1.11.0
Is it possible to get version 3.25.0? I need to install on cluster and want to replicate successful local installation, but cannot seem to get it with Pkg.add(Pkg.PackageSpec(;name=“Optimization”, version=“3.25.0”))
When I try: Pkg.add(Pkg.PackageSpec(;name=“Optimization”, version=“3.25.0”))
I get the error:
**ERROR:** Unsatisfiable requirements detected for package OptimizationBase [bca83a33]:
OptimizationBase [bca83a33] log:
├─possible versions are: 0.0.1 - 1.0.2 or uninstalled
└─found to have no compatible versions left with Optimization [7f7a1694]
└─Optimization [7f7a1694] log:
├─possible versions are: 3.5.0 - 3.25.1 or uninstalled
└─restricted to versions 3.25.0 by an explicit requirement, leaving only versions: 3.25.0
Stacktrace:
[1] **propagate_constraints!(**graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool**)**
@ Pkg.Resolve ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1072
[2] **propagate_constraints!** (repeats 2 times)
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1008 [inlined]
[3] **simplify_graph!(**graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool**)**
@ Pkg.Resolve ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1533
[4] **simplify_graph!** (repeats 2 times)
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1532 [inlined]
[5] **resolve_versions!(**env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, julia_version::VersionNumber, installed_only::Bool**)**
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:423
[6] **targeted_resolve(**env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber**)**
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1384
[7] **tiered_resolve(**env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, julia_version::VersionNumber, try_all_installed::Bool**)**
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1373
[8] **_resolve(**io::IOContext{…}, env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber**)**
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1394
[9] **add(**ctx::Pkg.Types.Context, pkgs::Vector{…}, new_git::Set{…}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol**)**
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1427
[10] **add**
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1400 [inlined]
[11] **add(**ctx::Pkg.Types.Context, pkgs::Vector{…}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{…}**)**
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:306
[12] **add(**pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{}**)**
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
[13] **add(**pkgs::Vector{Pkg.Types.PackageSpec}**)**
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
[14] **add(**pkg::Pkg.Types.PackageSpec**)**
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:146
[15] top-level scope
@ REPL[6]:1
Some type information was truncated. Use `show(err)` to see complete types.
I think @Vaibhavdixit02 you just need to tag a new release of Optimization.jl with the right compat bounds for OptimizationBase.jl
1 Like
I think this has to do with incompatibility with some other packages in the OP and @cefitzg ’s environment I have not been able to reproduce this. @gdalle why is the MTK extension precompiling for you in your environment without loading MTK, or did you have to load it to get an error?
Even with MTK, I tried both MTK first and the Optimization and the other way around in a fresh environment (and actually a fresh computer that I just installed julia on) and was unable to recreate any error, the MTK warning showed up but that should be fine for the purposes here
gdalle
June 5, 2024, 2:35pm
12
It was a fresh install in a temporary environment, and I possibly didn’t have that version of MTK on my computer prior to that, so it might have precompiled upon install?
Also started over on this side (Pkg.rm all packages and delete all compiled files). I am using version “1.11.0-beta2" through juliaup.
Then I do Pkg.add(“Optimization”). No issues here. I can get 3.25.1.
Then I try Pkg.add(“SciMLSensitivity”) and I get
Precompiling project...
✗ Enzyme
✗ Enzyme → EnzymeSpecialFunctionsExt
✗ Enzyme → EnzymeStaticArraysExt
✗ Enzyme → EnzymeChainRulesCoreExt
✗ DifferentiationInterface → DifferentiationInterfaceEnzymeExt
✗ OptimizationBase → OptimizationEnzymeExt
✗ LinearSolve → LinearSolveEnzymeExt
✗ DiffEqBase → DiffEqBaseEnzymeExt
✗ SparseDiffTools → SparseDiffToolsEnzymeExt
✗ SciMLSensitivity
214 dependencies successfully precompiled in 679 seconds. 88 already precompiled.
10 dependencies errored.
For a report of the errors see `julia> err`. To retry use `pkg> precompile`
@Vaibhavdixit02 is possible to get Optimization 3.25.0 anymore? When I Pkg.rm Optimization 3.25.1 and the failed SciMLSensitivity 7.60.1 and restart with
Pkg.add(Pkg.PackageSpec(;name=“Optimization”, version=“3.25.0”))
I get the error which involves OptimizationBase
ERROR: Unsatisfiable requirements detected for package OptimizationBase [bca83a33]:
OptimizationBase [bca83a33] log:
├─possible versions are: 0.0.1 - 1.0.2 or uninstalled
└─found to have no compatible versions left with Optimization [7f7a1694]
└─Optimization [7f7a1694] log:
├─possible versions are: 3.5.0 - 3.25.1 or uninstalled
└─restricted to versions 3.25.0 by an explicit requirement, leaving only versions: 3.25.0
Stacktrace:
[1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool)
@ Pkg.Resolve ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1072
[2] propagate_constraints! (repeats 2 times)
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1008 [inlined]
[3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool)
@ Pkg.Resolve ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1533
[4] simplify_graph! (repeats 2 times)
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Resolve/graphtype.jl:1532 [inlined]
[5] resolve_versions!(env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, julia_version::VersionNumber, installed_only::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:423
[6] targeted_resolve(env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1384
[7] tiered_resolve(env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, julia_version::VersionNumber, try_all_installed::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1373
[8] _resolve(io::IOContext{…}, env::Pkg.Types.EnvCache, registries::Vector{…}, pkgs::Vector{…}, preserve::Pkg.Types.PreserveLevel, julia_version::VersionNumber)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1394
[9] add(ctx::Pkg.Types.Context, pkgs::Vector{…}, new_git::Set{…}; allow_autoprecomp::Bool, preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol)
@ Pkg.Operations ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1427
[10] add
@ ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1400 [inlined]
[11] add(ctx::Pkg.Types.Context, pkgs::Vector{…}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{…})
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:306
[12] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{})
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
[13] add(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
[14] add(pkg::Pkg.Types.PackageSpec)
@ Pkg.API ~/.julia/juliaup/julia-1.11.0-beta2+0.x64.linux.gnu/share/julia/stdlib/v1.11/Pkg/src/API.jl:146
[15] top-level scope
@ REPL[11]:1
Some type information was truncated. Use `show(err)` to see complete types.
gdalle
June 5, 2024, 2:51pm
15
I think it has to do with the versions of OptimizationBase that we yanked from the general registry
1 Like
yeah that’s it, one option I can see is to yank 3.25.0
@cefitzg why do you want that specific release and not the latest 3.25.1?
@Vaibhavdixit02 , if 3.25.1 can become compatible that is also OK!
I just need to be able to use the following packages for a computing job with version v"1.11.0-beta2":
[336ed68f] CSV v0.10.14
[a93c6f00] DataFrames v1.6.1
[0c46a032] DifferentialEquations v7.13.0
[9aa1b823] FastClosures v0.3.2
[f6369f11] ForwardDiff v0.10.36
[c27321d9] Glob v1.3.1
[a5e1c1ea] LatinHypercubeSampling v1.9.0
[961ee093] ModelingToolkit v9.13.0
[7f7a1694] Optimization v3.25.0
⌃ [1ed8b502] SciMLSensitivity v7.56.2
⌃ [90137ffa] StaticArrays v1.9.3
[37e2e46d] LinearAlgebra v1.11.0
[9a3f8284] Random v1.11.0
The goal is to use LBFGSB algo through Optimization.LBFGS() don’t care if it’s 3.25.1 or 3.25.0. Would prefer 3.25.1.
@Vaibhavdixit02 could you let me know when this is good to go so I can install on cluster?
Have you tried ]up to update the packages since there seem to be a couple that can be updated from your snippet