NeuralPDE fail to compile

[naceurCRAAG]

Chris

NeuralPDE refuses to compile I'm using julia 18.5 and trying just to run the tutorial example https://docs.sciml.ai/NeuralPDE/stable/tutorials/pdesystem/

Naceur

Here is the error output [ Info: Precompiling NeuralPDE [315f7962-48a3-4962-8226-d0f33b1235f0] WARNING: Method definition solve(SciMLBase.IntegralProblem{isinplace, P, F, B, K} where K where B where F where P where isinplace) in module Integrals at /home/naceur/.julia/packages/Integrals/9qNWp/src/Integrals.jl:111 overwritten at /home/naceur/.julia/packages/Integrals/9qNWp/src/Integrals.jl:60. incremental compilation may be fatally broken for this module

ERROR: LoadError: UndefVarError: @nograd not defined Stacktrace: [1] include @ ./Base.jl:419 [inlined] [2] 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:1554 [3] top-level scope @ stdin:1 in expression starting at /home/naceur/.julia/packages/NeuralPDE/pmYyp/src/NeuralPDE.jl:1 in expression starting at stdin:1

---

Failed to precompile NeuralPDE [315f7962-48a3-4962-8226-d0f33b1235f0] to /home/naceur/.julia/compiled/v1.8/NeuralPDE/jl_19oxqF.

Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:1707 [3] compilecache @ ./loading.jl:1651 [inlined] [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base ./loading.jl:1200 [6] macro expansion @ ./loading.jl:1180 [inlined] [7] macro expansion @ ./lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144

[ChrisRackauckas]

Share ]st -m?

[naceurCRAAG]

Hi Chris :)

here is my ]st -m I did that in NeuralPDE directory I just activated

(NeuralPde) pkg> st -m Status ~/NeuralPde/Manifest.toml ⌅ [c3fe647b] AbstractAlgebra v0.27.10 [621f4979] AbstractFFTs v1.3.1 [1520ce14] AbstractTrees v0.4.4 [7d9f7c33] Accessors v0.1.28 [79e6a3ab] Adapt v3.6.1 [dce04be8] ArgCheck v2.3.0 [ec485272] ArnoldiMethod v0.2.0 ⌅ [4fba245c] ArrayInterface v6.0.25 [30b0a656] ArrayInterfaceCore v0.1.29 [6ba088a2] ArrayInterfaceGPUArrays v0.2.2 [015c0d05] ArrayInterfaceOffsetArrays v0.1.7 [b0d46f97] ArrayInterfaceStaticArrays v0.1.5 [dd5226c6] ArrayInterfaceStaticArraysCore v0.1.4 [a2b0951a] ArrayInterfaceTracker v0.1.1 [4c555306] ArrayLayouts v0.8.18 [a9b6321e] Atomix v0.1.0 [15f4f7f2] AutoHashEquals v0.2.0 ⌅ [ab4f0b2a] BFloat16s v0.2.0 [aae01518] BandedMatrices v0.17.17 [198e06fe] BangBang v0.3.37 [9718e550] Baselet v0.1.1 [e2ed5e7c] Bijections v0.1.4 [d1d4a3ce] BitFlags v0.1.7 [62783981] BitTwiddlingConvenienceFunctions v0.1.5 [8e7c35d0] BlockArrays v0.16.24 [ffab5731] BlockBandedMatrices v0.11.10 [764a87c0] BoundaryValueDiffEq v2.11.0 [e1450e63] BufferedStreams v1.1.0 [fa961155] CEnum v0.4.2 [2a0fbf3d] CPUSummary v0.2.2 [00ebfdb7] CSTParser v3.3.6 [336ed68f] CSV v0.10.9 ⌅ [052768ef] CUDA v3.13.1 [72cfdca4] CUDAKernels v0.4.7 [49dc2e85] Calculus v0.5.1 [7057c7e9] Cassette v0.3.11 [082447d4] ChainRules v1.48.0 [d360d2e6] ChainRulesCore v1.15.7 [9e997f8a] ChangesOfVariables v0.1.6 [46823bd8] Chemfiles v0.10.31 ⌃ [fb6a15b2] CloseOpenIntervals v0.1.11 [944b1d66] CodecZlib v0.7.1 [35d6a980] ColorSchemes v3.20.0 [3da002f7] ColorTypes v0.11.4 [c3611d14] ColorVectorSpace v0.9.10 [5ae59095] Colors v0.12.10 [861a8166] Combinatorics v1.0.2 [a80b9123] CommonMark v0.8.10 [38540f10] CommonSolve v0.2.3 [bbf7d656] CommonSubexpressions v0.3.0 [34da2185] Compat v4.6.1 ⌃ [b0b7db55] ComponentArrays v0.13.7 [b152e2b5] CompositeTypes v0.1.3 [a33af91c] CompositionsBase v0.1.1 [8f4d0f93] Conda v1.8.0 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.5.1 [6add18c4] ContextVariablesX v0.1.3 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [8a292aeb] Cuba v2.3.0 [667455a9] Cubature v1.5.1 [9a962f9c] DataAPI v1.14.0 [124859b0] DataDeps v0.7.10 [a93c6f00] DataFrames v1.5.0 ⌅ [82cc6244] DataInterpolations v3.12.0 [864edb3b] DataStructures v0.18.13 [e2d170a0] DataValueInterfaces v1.0.0 [244e2a9f] DefineSingletons v0.1.2 ⌃ [bcd4f6db] DelayDiffEq v5.41.1 [b429d917] DensityInterface v0.4.0 ⌃ [2b5f629d] DiffEqBase v6.119.0 [459566f4] DiffEqCallbacks v2.26.0 ⌃ [aae7a2af] DiffEqFlux v1.53.0 [77a26b50] DiffEqNoiseProcess v5.16.0 [9fdde737] DiffEqOperators v4.45.0 [41bf760c] DiffEqSensitivity v6.79.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.13.0 [0c46a032] DifferentialEquations v7.7.0 [b4f34e82] Distances v0.10.8 [31c24e10] Distributions v0.25.86 [ced4e74d] DistributionsAD v0.6.43 [ffbed154] DocStringExtensions v0.9.3 ⌅ [5b8099bc] DomainSets v0.5.15 [fa6b7ba4] DualNumbers v0.6.8 [7c1d4256] DynamicPolynomials v0.4.6 ⌃ [da5c29d0] EllipsisNotation v1.6.0 [4e289a0a] EnumX v1.0.4 [7da242da] Enzyme v0.10.18 ⌅ [f151be2c] EnzymeCore v0.1.0 ⌃ [d4d017d3] ExponentialUtilities v1.23.0 [e2ba6199] ExprTools v0.1.9 [7a1cc6ca] FFTW v1.6.0 [cc61a311] FLoops v0.2.1 [b9860ae5] FLoopsBase v0.1.1 ⌃ [7034ab61] FastBroadcast v0.2.4 [9aa1b823] FastClosures v0.3.2 [29a986be] FastLapackInterface v1.2.9 [5789e2e9] FileIO v1.16.0 [48062228] FilePathsBase v0.9.20 [1a297f60] FillArrays v0.13.10 ⌃ [6a86dc24] FiniteDiff v2.17.0 [53c48c17] FixedPointNumbers v0.8.4 ⌃ [587475ba] Flux v0.13.13 [9c68100b] FoldsThreads v0.1.1 [59287772] Formatting v0.4.2 [f6369f11] ForwardDiff v0.10.35 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 ⌅ [d9f16b24] Functors v0.3.0 [0c68f7d7] GPUArrays v8.6.5 [46192b85] GPUArraysCore v0.1.4 ⌅ [61eb1bfa] GPUCompiler v0.17.3 [92fee26a] GZip v0.5.1 [c145ed77] GenericSchur v0.5.3 [7e08b658] GeometricFlux v0.13.8 [c27321d9] Glob v1.3.0 ⌅ [cffab07f] GraphNeuralNetworks v0.4.5 [3ebe565e] GraphSignals v0.8.5 [a2bd30eb] Graphics v1.1.2 [86223c79] Graphs v1.8.0 ⌅ [0b43b601] Groebner v0.2.11 [d5909c97] GroupsCore v0.4.0 [19dc6840] HCubature v1.5.1 [f67ccb44] HDF5 v0.16.14 [cd3eb016] HTTP v1.7.4 [3e5b6fbb] HostCPUFeatures v0.1.14 [34004b35] HypergeometricFunctions v0.3.11 [7073ff75] IJulia v1.24.0 [7869d1d1] IRTools v0.4.9 [615f187c] IfElse v0.1.1 [c817782e] ImageBase v0.1.5 [a09fc81d] ImageCore v0.9.4 [4e3cecfd] ImageShow v0.3.7 [d25df0c9] Inflate v0.1.3 [83e8ac13] IniFile v0.5.1 [22cec73e] InitialValues v0.3.1 [842dd82b] InlineStrings v1.4.0 [18e54dd8] IntegerMathUtils v0.1.0 [7d512f48] InternedStrings v0.7.0 ⌅ [8197267c] IntervalSets v0.7.3 [3587e190] InverseFunctions v0.1.8 [41ab1584] InvertedIndices v1.3.0 [92d709cd] IrrationalConstants v0.2.2 [42fd0dbc] IterativeSolvers v0.9.2 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.4.31 [692b3bcd] JLLWrappers v1.4.1 [682c06a0] JSON v0.21.3 [0f8b85d8] JSON3 v1.12.0 [98e50ef6] JuliaFormatter v1.0.25 [b14d175d] JuliaVariables v0.2.4 ⌃ [ccbc3e58] JumpProcesses v9.5.1 [ef3ab10e] KLU v0.4.0 ⌅ [63c18a36] KernelAbstractions v0.8.6 [ba0b0d4f] Krylov v0.9.0 ⌅ [0b1a1467] KrylovKit v0.5.4 [929cbde3] LLVM v4.17.1 [b964fa9f] LaTeXStrings v1.3.0 ⌃ [2ee39098] LabelledArrays v1.13.0 [984bce1d] LambertW v0.4.6 [23fbe1c1] Latexify v0.15.18 [a5e1c1ea] LatinHypercubeSampling v1.8.0 [73f95e8e] LatticeRules v0.0.1 ⌃ [10f19ff3] LayoutPointers v0.1.13 [50d2b5c4] Lazy v0.15.1 [5078a376] LazyArrays v0.22.18 ⌅ [d7e5e226] LazyBandedMatrices v0.7.17 [8cdb02fc] LazyModules v0.3.1 [0fc2ff8b] LeastSquaresOptim v0.8.4 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [2d8b4e74] LevyArea v1.0.0 [d3d80556] LineSearches v7.2.0 ⌃ [7ed4a6bd] LinearSolve v1.37.0 [2ab3a3ac] LogExpFunctions v0.3.23 [e6f89c97] LoggingExtras v1.0.0 ⌃ [bdcacae8] LoopVectorization v0.12.150 ⌃ [b2108857] Lux v0.4.37 [bb33d45b] LuxCore v0.1.3 [82251201] LuxLib v0.1.12 [23992714] MAT v0.10.4 [eb30cadb] MLDatasets v0.7.9 [d8e11817] MLStyle v0.4.17 ⌅ [f1d291b0] MLUtils v0.2.11 [1914dd2f] MacroTools v0.5.10 [d125e4d3] ManualMemory v0.1.8 [dbb5928d] MappedArrays v0.4.1 [a3b82374] MatrixFactorizations v0.9.6 [739be429] MbedTLS v1.1.7 [c03570c3] Memoize v0.4.4 ⌅ [e9d8d322] Metatheory v1.3.5 [128add7d] MicroCollections v0.1.4 [e1d29d7a] Missings v1.1.0 ⌃ [961ee093] ModelingToolkit v8.46.1 ⌅ [4886b29c] MonteCarloIntegration v0.0.3 [e94cdb99] MosaicViews v0.3.4 [46d2c3a1] MuladdMacro v0.2.4 [102ac46a] MultivariatePolynomials v0.4.7 [d8a4904e] MutableArithmetics v1.2.3 [d41bc354] NLSolversBase v7.8.3 [2774e3e8] NLsolve v4.5.1 [872c559c] NNlib v0.8.19 ⌃ [a00861dc] NNlibCUDA v0.2.6 [15e1cf62] NPZ v0.4.3 [77ba4419] NaNMath v1.0.2 [71a1bf82] NameResolution v0.1.5 [b8a86587] NearestNeighbors v0.4.13 [dc0c328b] NeuralGraphPDE v0.1.9 [ea5c82af] NeuralOperators v0.4.5 ⌅ [315f7962] NeuralPDE v4.11.0 [7c138fc3] NeuralPDELogging v0.1.0 [8913a72c] NonlinearSolve v1.5.1 [d8793406] ObjectFile v0.3.7 [6fe1bfb0] OffsetArrays v1.12.9 [0b1bfda6] OneHotArrays v0.2.3 [4d8831e6] OpenSSL v1.3.3 [429524aa] Optim v1.7.4 [3bd65402] Optimisers v0.2.15 [7f7a1694] Optimization v3.12.1 [253f991c] OptimizationFlux v0.1.2 [36348300] OptimizationOptimJL v0.1.5 [42dfb2eb] OptimizationOptimisers v0.1.2 [500b13db] OptimizationPolyalgorithms v0.1.1 [bac558e1] OrderedCollections v1.4.1 ⌃ [1dea7af3] OrdinaryDiffEq v6.44.1 [90014a1f] PDMats v0.11.17 [5432bcbf] PaddedViews v0.5.11 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.5.8 [fbb45041] Pickle v0.3.2 [e409e4f3] PoissonRandom v0.4.4 ⌃ [f517fe37] Polyester v0.7.2 [1d0040c9] PolyesterWeave v0.2.1 [2dfb63ee] PooledArrays v1.4.2 [85a6dd25] PositiveFactorizations v0.2.4 ⌃ [d236fae5] PreallocationTools v0.4.11 [21216c6a] Preferences v1.3.0 [8162dcfd] PrettyPrint v0.2.0 [08abe8d2] PrettyTables v2.2.3 [27ebfcd6] Primes v0.5.3 [33c8b6b6] ProgressLogging v0.1.4 [92933f4c] ProgressMeter v1.7.2 ⌅ [3349acd9] ProtoBuf v0.11.5 [1fd47b50] QuadGK v2.8.2 [67601950] Quadrature v2.1.0 [e0ec9b62] QuadratureCubature v0.1.1 [8a4e6c94] QuasiMonteCarlo v0.2.19 [74087812] Random123 v1.6.0 [fb686558] 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TermInterface v0.2.3 [5d786b92] TerminalLoggers v0.1.6 [8290d209] ThreadingUtilities v0.5.1 [ac1d9e8a] ThreadsX v0.1.11 [a759f4b9] TimerOutputs v0.5.22 [0796e94c] Tokenize v0.5.25 [9f7883ad] Tracker v0.2.23 [3bb67fe8] TranscodingStreams v0.9.11 [28d57a85] Transducers v0.4.75 [a2a6695c] TreeViews v0.3.0 [d5829a12] TriangularSolve v0.1.19 [410a4b4d] Tricks v0.1.6 [781d530d] TruncatedStacktraces v1.3.0 [bc48ee85] Tullio v0.3.5 [9d95972d] TupleTools v1.3.0 [5c2747f8] URIs v1.4.2 [3a884ed6] UnPack v1.0.2 [d9a01c3f] Underscores v3.0.0 [1986cc42] Unitful v1.12.4 [013be700] UnsafeAtomics v0.2.1 [d80eeb9a] UnsafeAtomicsLLVM v0.1.0 ⌃ [3d5dd08c] VectorizationBase v0.21.58 [81def892] VersionParsing v1.3.0 [19fa3120] VertexSafeGraphs v0.2.0 [ea10d353] WeakRefStrings v1.4.2 [c64b6f0f] Word2Vec v0.5.3 [76eceee3] WorkerUtilities v1.6.1 [c2297ded] ZMQ v1.2.2 [a5390f91] ZipFile v0.10.1 [e88e6eb3] Zygote v0.6.59 [700de1a5] ZygoteRules v0.2.3 [78a364fa] Chemfiles_jll v0.10.3+0 [3bed1096] Cuba_jll v4.2.2+1 [7bc98958] Cubature_jll v1.0.5+0 ⌅ [7cc45869] Enzyme_jll v0.0.48+1 [f5851436] FFTW_jll v3.3.10+0 [0234f1f7] HDF5_jll v1.12.2+2 [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2 ⌅ [dad2f222] LLVMExtra_jll v0.0.18+0 [94ce4f54] Libiconv_jll v1.16.1+2 [856f044c] MKL_jll v2022.2.0+0 [458c3c95] OpenSSL_jll v1.1.20+0 [efe28fd5] OpenSpecFun_jll v0.5.5+0 [f50d1b31] Rmath_jll v0.4.0+0 [fb77eaff] Sundials_jll v5.2.1+0 [9fbe4022] Word2Vec_jll v0.1.0+0 [8f1865be] ZeroMQ_jll v4.3.4+0 [a9144af2] libsodium_jll v1.0.20+0 [c7845625] protoc_jll v3.21.12+1 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [8bf52ea8] CRC32c [ade2ca70] Dates [8bb1440f] DelimitedFiles [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.3 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.8.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [1a1011a3] SharedArrays [6462fe0b] Sockets [2f01184e] SparseArrays [10745b16] Statistics [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.0 [a4e569a6] Tar v1.10.1 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.0.1+0 [deac9b47] LibCURL_jll v7.84.0+0 [29816b5a] LibSSH2_jll v1.10.2+0 [c8ffd9c3] MbedTLS_jll v2.28.0+0 [14a3606d] MozillaCACerts_jll v2022.2.1 [4536629a] OpenBLAS_jll v0.3.20+0 [05823500] OpenLibm_jll v0.8.1+0 [bea87d4a] SuiteSparse_jll v5.10.1+0 [83775a58] Zlib_jll v1.2.12+3 [8e850b90] libblastrampoline_jll v5.1.1+0 [8e850ede] nghttp2_jll v1.48.0+0 [3f19e933] p7zip_jll v17.4.0+0 Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use status --outdated -m

[naceurCRAAG]

Chris ! It's huge Am'I working cleanly ? Naceur

[ChrisRackauckas]

Share ]st?

[naceurCRAAG]

Here it is

(NeuralPde) pkg> st Status ~/NeuralPde/Project.toml [7073ff75] IJulia v1.24.0 [dc0c328b] NeuralGraphPDE v0.1.9 [ea5c82af] NeuralOperators v0.4.5 ⌅ [315f7962] NeuralPDE v4.11.0 [7c138fc3] NeuralPDELogging v0.1.0 [0bca4576] SciMLBase v1.91.3 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use status --outdated

[ChrisRackauckas]

NeuralGraphPDE looks like it might be behind, missing CUDA v4. Try ]rm NeuralGraphPDE and then ]up and see if things rejigger.

[naceurCRAAG]

Will do that I even do not know why I installed NeuralGraphPDE :(

[naceurCRAAG]

Chris

I did ]rm NeuralGraphPDE and ]rm NeuralPDELogging and then ]up It works Chris :1st_place_medal: :+1: I am very happy :) . This is my first run of NeuralPDE :) It's absolutely magical :) As I progress, I'll tell you about a little work in planetary science that could illustrates (if we succeeds) once again the fruitfulness of your approach... as soon as I'm close I'll tell you more by email.

Have A Nice Day

Many Thanks Chris

Naceur

[xtalax]

@naceurCRAAG If you have a system related to planetery science, please submit it to https://github.com/SciML/PDESystemLibrary.jl, we need more physical systems!

[naceurCRAAG]

Dear Alex Yes ! I have a student who is trying to rewrite what I did using the Fortran code from netlib. He is rewriting this code in julia and using both MethodOfLines and NeuralPDE and he is going to compare the two outputs (performance results and others) on an application in the field of planetary science (comet nucleus process). I think he will need your expertise Could I tell him not to hesitate to ask you when he or I are stuck because we are new in julia?

Have A Nice Day

Naceur

Le sam. 25 mars 2023 à 01:27, Alex Jones @.***> a écrit :

@naceurCRAAG https://github.com/naceurCRAAG If you have a system related to planetery science, please submit it to https://github.com/SciML/PDESystemLibrary.jl, we need more physical systems!

— Reply to this email directly, view it on GitHub https://github.com/SciML/NeuralPDE.jl/issues/660#issuecomment-1483631900, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMXQQP3TAVGCSDQ4ODYXI3W5Y3WVANCNFSM6AAAAAAWGSMZ24 . You are receiving this because you were mentioned.Message ID: @.***>

[xtalax]

Yes, by all means reach out in an issue, on the slack, or discourse, if a few seconds for me saves hours of yours it is worth it!

[naceurCRAAG]

Thank you so much Alex. Naceur

Le dim. 26 mars 2023, 22:30, Alex Jones @.***> a écrit :

Yes, by all means reach out in an issue, on the slack, or discourse, if a few seconds for me saves hours of yours it is worth it!

— Reply to this email directly, view it on GitHub https://github.com/SciML/NeuralPDE.jl/issues/660#issuecomment-1484229754, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACMXQQOYL2MUHGMIHNACAEDW6C7OTANCNFSM6AAAAAAWGSMZ24 . You are receiving this because you were mentioned.Message ID: @.***>