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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Unable to get full matrix whose columns is the solution to an ODE with newer version of RecursiveArrayTools. #1021

Closed DanielHolleufer closed 3 months ago

DanielHolleufer commented 3 months ago

Describe the bug 🐞

In newer version of DifferentialEquations.jl and RecursiveArrayTools.jl I am unable to get the matrix whose columns correspond to the solution at certain time steps using sol[:, :], where sol is the output of solve(ODEProblem). Instead it throws an AssertionError (written below). I am still able to get specific columns out with sol[:, 1] or sol[:, end]. I only get an error when trying to get the full matrix sol[:, :].

Expected behavior

Here is an example that works in DifferentialEquations.jl v7.12.0 and RecursiveArrayTools.jl v3.10.0 on a Windows 11 PC with Julia 1.10.1.

using DifferentialEquations

function f!(du, u, p, t)
    du[1] = u[2]
    du[2] = -u[1]
end

u0 = [1.0; 0.0]
tspan = (0.0, 10.0)
prob = ODEProblem(f!, u0, tspan)
sol = solve(prob)
u = sol[:, :]

The output is

2×22 Matrix{Float64}:
 1.0   1.0           0.99994     0.996813    0.971246   0.886414   0.70578    0.383645  -0.0594364  …  0.549492  0.959565   0.874642   0.33484   -0.469997  -0.943144  -0.870614  -0.839023
 0.0  -0.000999001  -0.0109888  -0.0797744  -0.23808   -0.462893  -0.708431  -0.923481  -0.998232      0.835517  0.281561  -0.484848  -0.942323  -0.882749  -0.332628   0.4922     0.544306

Minimal Reproducible Example 👇

Running the same example again, this time with DifferentialEquations.jl v7.13.0 and RecursiveArrayTools.jl v3.10.1 on a MacOs 14.3.1 also with Julia 1.10.1 I get an AssertionError from RecursiveArrayTools.jl

using DifferentialEquations

function f!(du, u, p, t)
    du[1] = u[2]
    du[2] = -u[1]
end

u0 = [1.0; 0.0]
tspan = (0.0, 10.0)
prob = ODEProblem(f!, u0, tspan)
sol = solve(prob)
u = sol[:, :]

Error & Stacktrace ⚠️

ERROR: AssertionError: length(I) == ndims(A.u)
Stacktrace:
 [1] _getindex
   @ ~/.julia/packages/RecursiveArrayTools/dzBRE/src/vector_of_array.jl:309 [inlined]
 [2] getindex(A::ODESolution{…}, _arg::Function, args::Function)
   @ RecursiveArrayTools ~/.julia/packages/RecursiveArrayTools/dzBRE/src/vector_of_array.jl:435
 [3] top-level scope
   @ REPL[9]:1
Some type information was truncated. Use `show(err)` to see complete types.

Environment (please complete the following information): Here is the environment info in the case where i get an AssertionError. Below all this, I provide equivalent info for when I get the expected output.

`~/.julia/environments/v1.10/Project.toml`
  [6e4b80f9] BenchmarkTools v1.5.0
  [336ed68f] CSV v0.10.13
  [13f3f980] CairoMakie v0.11.9
  [a93c6f00] DataFrames v1.6.1
  [8bb1440f] DelimitedFiles v1.9.1
⌅ [459566f4] DiffEqCallbacks v2.37.0
  [0c46a032] DifferentialEquations v7.13.0
  [31c24e10] Distributions v0.25.107
  [e9467ef8] GLMakie v0.9.9
  [b964fa9f] LaTeXStrings v1.3.1
  [5fb14364] OhMyREPL v0.5.24
  [91a5bcdd] Plots v1.40.1
  [6e0679c1] QuantumOptics v1.0.15
  [bd369af6] Tables v1.11.1
  [10745b16] Statistics v1.10.0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated`
`~/.julia/environments/v1.10/Manifest.toml`
  [47edcb42] ADTypes v0.2.6
  [621f4979] AbstractFFTs v1.5.0
  [398f06c4] AbstractLattices v0.3.0
  [1520ce14] AbstractTrees v0.4.5
⌅ [79e6a3ab] Adapt v3.7.2
  [27a7e980] Animations v0.4.1
⌅ [ec485272] ArnoldiMethod v0.2.0
⌅ [7d9fca2a] Arpack v0.5.3
⌃ [4fba245c] ArrayInterface v7.7.1
  [4c555306] ArrayLayouts v1.6.1
  [67c07d97] Automa v1.0.3
  [13072b0f] AxisAlgorithms v1.1.0
  [39de3d68] AxisArrays v0.4.7
  [aae01518] BandedMatrices v1.5.0
  [6e4b80f9] BenchmarkTools v1.5.0
  [d1d4a3ce] BitFlags v0.1.8
  [62783981] BitTwiddlingConvenienceFunctions v0.1.5
  [764a87c0] BoundaryValueDiffEq v5.6.3
  [fa961155] CEnum v0.5.0
  [2a0fbf3d] CPUSummary v0.2.4
  [336ed68f] CSV v0.10.13
  [159f3aea] Cairo v1.0.5
  [13f3f980] CairoMakie v0.11.9
  [49dc2e85] Calculus v0.5.1
  [d360d2e6] ChainRulesCore v1.23.0
  [fb6a15b2] CloseOpenIntervals v0.1.12
  [523fee87] CodecBzip2 v0.8.2
  [944b1d66] CodecZlib v0.7.4
  [a2cac450] ColorBrewer v0.4.0
  [35d6a980] ColorSchemes v3.24.0
  [3da002f7] ColorTypes v0.11.4
  [c3611d14] ColorVectorSpace v0.10.0
  [5ae59095] Colors v0.12.10
  [861a8166] Combinatorics v1.0.2
  [38540f10] CommonSolve v0.2.4
  [bbf7d656] CommonSubexpressions v0.3.0
  [34da2185] Compat v4.14.0
  [2569d6c7] ConcreteStructs v0.2.3
  [f0e56b4a] ConcurrentUtilities v2.3.1
  [187b0558] ConstructionBase v1.5.4
  [d38c429a] Contour v0.6.2
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.6.1
  [864edb3b] DataStructures v0.18.18
  [e2d170a0] DataValueInterfaces v1.0.0
  [927a84f5] DelaunayTriangulation v0.8.12
  [bcd4f6db] DelayDiffEq v5.47.1
  [8bb1440f] DelimitedFiles v1.9.1
⌃ [2b5f629d] DiffEqBase v6.147.3
⌅ [459566f4] DiffEqCallbacks v2.37.0
  [77a26b50] DiffEqNoiseProcess v5.21.0
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [0c46a032] DifferentialEquations v7.13.0
  [b4f34e82] Distances v0.10.11
  [31c24e10] Distributions v0.25.107
  [ffbed154] DocStringExtensions v0.9.3
  [fa6b7ba4] DualNumbers v0.6.8
  [4e289a0a] EnumX v1.0.4
⌃ [f151be2c] EnzymeCore v0.6.5
  [429591f6] ExactPredicates v2.2.8
  [460bff9d] ExceptionUnwrapping v0.1.10
  [d4d017d3] ExponentialUtilities v1.26.1
  [e2ba6199] ExprTools v0.1.10
  [411431e0] Extents v0.1.2
  [c87230d0] FFMPEG v0.4.1
  [7a1cc6ca] FFTW v1.8.0
  [9d29842c] FastAlmostBandedMatrices v0.1.0
  [7034ab61] FastBroadcast v0.2.8
  [9aa1b823] FastClosures v0.3.2
  [7868e603] FastExpm v1.1.0
  [442a2c76] FastGaussQuadrature v1.0.2
  [29a986be] FastLapackInterface v2.0.2
  [5789e2e9] FileIO v1.16.2
  [8fc22ac5] FilePaths v0.8.3
  [48062228] FilePathsBase v0.9.21
  [1a297f60] FillArrays v1.9.3
  [6a86dc24] FiniteDiff v2.22.0
  [53c48c17] FixedPointNumbers v0.8.4
  [1fa38f19] Format v1.3.6
  [f6369f11] ForwardDiff v0.10.36
  [b38be410] FreeType v4.1.1
  [663a7486] FreeTypeAbstraction v0.10.1
  [069b7b12] FunctionWrappers v1.1.3
  [77dc65aa] FunctionWrappersWrappers v0.1.3
  [d9f16b24] Functors v0.4.7
  [f7f18e0c] GLFW v3.4.1
  [e9467ef8] GLMakie v0.9.9
⌃ [46192b85] GPUArraysCore v0.1.5
  [28b8d3ca] GR v0.73.2
  [92c85e6c] GSL v1.0.1
  [c145ed77] GenericSchur v0.5.3
  [cf35fbd7] GeoInterface v1.3.3
  [5c1252a2] GeometryBasics v0.4.10
  [a2bd30eb] Graphics v1.1.2
  [86223c79] Graphs v1.9.0
  [3955a311] GridLayoutBase v0.10.0
  [42e2da0e] Grisu v1.0.2
  [cd3eb016] HTTP v1.10.3
  [f0d1745a] HalfIntegers v1.5.1
  [3e5b6fbb] HostCPUFeatures v0.1.16
  [34004b35] HypergeometricFunctions v0.3.23
  [615f187c] IfElse v0.1.1
  [2803e5a7] ImageAxes v0.6.11
  [c817782e] ImageBase v0.1.7
  [a09fc81d] ImageCore v0.10.2
  [82e4d734] ImageIO v0.6.7
  [bc367c6b] ImageMetadata v0.9.9
  [9b13fd28] IndirectArrays v1.0.0
  [d25df0c9] Inflate v0.1.4
  [842dd82b] InlineStrings v1.4.0
  [18e54dd8] IntegerMathUtils v0.1.2
  [a98d9a8b] Interpolations v0.15.1
  [d1acc4aa] IntervalArithmetic v0.22.8
  [8197267c] IntervalSets v0.7.10
  [41ab1584] InvertedIndices v1.3.0
  [92d709cd] IrrationalConstants v0.2.2
  [f1662d9f] Isoband v0.1.1
  [c8e1da08] IterTools v1.10.0
  [42fd0dbc] IterativeSolvers v0.9.4
  [82899510] IteratorInterfaceExtensions v1.0.0
  [1019f520] JLFzf v0.1.7
  [692b3bcd] JLLWrappers v1.5.0
  [682c06a0] JSON v0.21.4
  [b835a17e] JpegTurbo v0.1.5
  [70703baa] JuliaSyntax v0.4.8
  [ccbc3e58] JumpProcesses v9.10.1
⌅ [ef3ab10e] KLU v0.4.1
  [5ab0869b] KernelDensity v0.6.8
  [ba0b0d4f] Krylov v0.9.5
  [0b1a1467] KrylovKit v0.6.1
  [8ac3fa9e] LRUCache v1.6.1
  [b964fa9f] LaTeXStrings v1.3.1
  [23fbe1c1] Latexify v0.16.2
  [10f19ff3] LayoutPointers v0.1.15
  [5078a376] LazyArrays v1.8.3
  [8cdb02fc] LazyModules v0.3.1
  [2d8b4e74] LevyArea v1.0.0
  [9c8b4983] LightXML v0.9.1
  [d3d80556] LineSearches v7.2.0
  [9b3f67b0] LinearAlgebraX v0.2.7
  [7a12625a] LinearMaps v3.11.2
⌃ [7ed4a6bd] LinearSolve v2.22.1
  [2ab3a3ac] LogExpFunctions v0.3.27
  [e6f89c97] LoggingExtras v1.0.3
  [bdcacae8] LoopVectorization v0.12.166
  [1914dd2f] MacroTools v0.5.13
  [ee78f7c6] Makie v0.20.8
  [20f20a25] MakieCore v0.7.3
  [d125e4d3] ManualMemory v0.1.8
  [dbb5928d] MappedArrays v0.4.2
  [b8f27783] MathOptInterface v1.27.0
  [0a4f8689] MathTeXEngine v0.5.7
  [a3b82374] MatrixFactorizations v2.1.0
  [bb5d69b7] MaybeInplace v0.1.1
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [7269a6da] MeshIO v0.4.11
  [e1d29d7a] Missings v1.1.0
  [66fc600b] ModernGL v1.1.7
  [7475f97c] Mods v2.2.4
  [e94cdb99] MosaicViews v0.3.4
  [46d2c3a1] MuladdMacro v0.2.4
  [3b2b4ff1] Multisets v0.4.4
  [d8a4904e] MutableArithmetics v1.4.1
  [d41bc354] NLSolversBase v7.8.3
  [2774e3e8] NLsolve v4.5.1
  [77ba4419] NaNMath v1.0.2
  [f09324ee] Netpbm v1.1.1
  [8913a72c] NonlinearSolve v3.7.3
  [510215fc] Observables v0.5.5
  [6fe1bfb0] OffsetArrays v1.13.0
  [5fb14364] OhMyREPL v0.5.24
  [52e1d378] OpenEXR v0.3.2
  [4d8831e6] OpenSSL v1.4.2
  [429524aa] Optim v1.9.2
  [bac558e1] OrderedCollections v1.6.3
  [1dea7af3] OrdinaryDiffEq v6.74.0
  [90014a1f] PDMats v0.11.31
  [f57f5aa1] PNGFiles v0.4.3
  [65ce6f38] PackageExtensionCompat v1.0.2
  [19eb6ba3] Packing v0.5.0
  [5432bcbf] PaddedViews v0.5.12
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.1
  [2ae35dd2] Permutations v0.4.20
  [3bbf5609] PikaParser v0.6.1
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.1.0
  [995b91a9] PlotUtils v1.4.1
  [91a5bcdd] Plots v1.40.1
  [e409e4f3] PoissonRandom v0.4.4
  [f517fe37] Polyester v0.7.9
  [1d0040c9] PolyesterWeave v0.2.1
  [647866c9] PolygonOps v0.1.2
  [f27b6e38] Polynomials v4.0.6
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [d236fae5] PreallocationTools v0.4.20
  [aea7be01] PrecompileTools v1.2.0
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.3.1
  [27ebfcd6] Primes v0.5.6
  [92933f4c] ProgressMeter v1.10.0
  [4b34888f] QOI v1.0.0
  [1fd47b50] QuadGK v2.9.4
  [5717a53b] QuantumInterface v0.3.4
  [6e0679c1] QuantumOptics v1.0.15
  [4f57444f] QuantumOpticsBase v0.4.21
  [74087812] Random123 v1.7.0
  [2576dda1] RandomMatrices v0.5.4
  [e6cf234a] RandomNumbers v1.5.3
  [b3c3ace0] RangeArrays v0.3.2
  [308eb6b3] RationalRoots v0.2.1
  [c84ed2f1] Ratios v0.4.5
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [731186ca] RecursiveArrayTools v3.10.1
  [f2c3362d] RecursiveFactorization v0.2.21
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [ae5879a3] ResettableStacks v1.1.1
  [286e9d63] RingLists v0.2.8
  [79098fc4] Rmath v0.7.1
  [5eaf0fd0] RoundingEmulator v0.2.1
  [7e49a35a] RuntimeGeneratedFunctions v0.5.12
  [94e857df] SIMDTypes v0.1.0
  [476501e8] SLEEFPirates v0.6.42
  [0bca4576] SciMLBase v2.29.0
  [c0aeaf25] SciMLOperators v0.3.8
  [6c6a2e73] Scratch v1.2.1
  [91c51154] SentinelArrays v1.4.1
  [efcf1570] Setfield v1.1.1
  [65257c39] ShaderAbstractions v0.4.1
  [992d4aef] Showoff v1.0.3
  [73760f76] SignedDistanceFields v0.4.0
  [777ac1f9] SimpleBufferStream v1.1.0
  [55797a34] SimpleGraphs v0.8.6
  [727e6d20] SimpleNonlinearSolve v1.5.0
  [ec83eff0] SimplePartitions v0.3.2
  [cc47b68c] SimplePolynomials v0.2.17
  [a6525b86] SimpleRandom v0.3.1
  [699a6c99] SimpleTraits v0.9.4
  [ce78b400] SimpleUnPack v1.1.0
  [45858cf5] Sixel v0.1.3
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.17.0
  [e56a9233] Sparspak v0.3.9
  [276daf66] SpecialFunctions v2.3.1
  [c5dd0088] StableHashTraits v1.1.8
  [cae243ae] StackViews v0.1.1
  [aedffcd0] Static v0.8.10
  [0d7ed370] StaticArrayInterface v1.5.0
  [90137ffa] StaticArrays v1.9.3
  [1e83bf80] StaticArraysCore v1.4.2
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.2
  [4c63d2b9] StatsFuns v1.3.1
⌃ [9672c7b4] SteadyStateDiffEq v2.0.1
  [789caeaf] StochasticDiffEq v6.65.1
  [7792a7ef] StrideArraysCore v0.5.2
  [5e0ebb24] Strided v2.0.4
  [4db3bf67] StridedViews v0.2.2
  [892a3eda] StringManipulation v0.3.4
  [09ab397b] StructArrays v0.6.18
  [c3572dad] Sundials v4.24.0
  [2efcf032] SymbolicIndexingInterface v0.3.8
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.11.1
  [62fd8b95] TensorCore v0.1.1
  [8290d209] ThreadingUtilities v0.5.2
⌅ [731e570b] TiffImages v0.6.8
  [a759f4b9] TimerOutputs v0.5.23
  [3bb67fe8] TranscodingStreams v0.10.4
  [d5829a12] TriangularSolve v0.1.20
  [410a4b4d] Tricks v0.1.8
  [981d1d27] TriplotBase v0.1.0
  [781d530d] TruncatedStacktraces v1.4.0
  [9d95972d] TupleTools v1.5.0
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [1986cc42] Unitful v1.19.0
  [45397f5d] UnitfulLatexify v1.6.3
  [c4a57d5a] UnsafeArrays v1.0.5
  [41fe7b60] Unzip v0.2.0
  [3d5dd08c] VectorizationBase v0.21.65
  [19fa3120] VertexSafeGraphs v0.2.0
  [ea10d353] WeakRefStrings v1.4.2
  [9f57e263] WignerSymbols v2.0.0
  [efce3f68] WoodburyMatrices v1.0.0
  [76eceee3] WorkerUtilities v1.6.1
⌅ [68821587] Arpack_jll v3.5.1+1
  [6e34b625] Bzip2_jll v1.0.8+1
  [4e9b3aee] CRlibm_jll v1.0.1+0
  [83423d85] Cairo_jll v1.16.1+1
  [5ae413db] EarCut_jll v2.2.4+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.5.0+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [f5851436] FFTW_jll v3.3.10+0
  [a3f928ae] Fontconfig_jll v2.13.93+0
  [d7e528f0] FreeType2_jll v2.13.1+0
  [559328eb] FriBidi_jll v1.0.10+0
  [0656b61e] GLFW_jll v3.3.9+0
  [d2c73de3] GR_jll v0.73.2+0
  [1b77fbbe] GSL_jll v2.7.2+0
  [78b55507] Gettext_jll v0.21.0+0
  [7746bdde] Glib_jll v2.76.5+0
  [3b182d85] Graphite2_jll v1.3.14+0
  [2e76f6c2] HarfBuzz_jll v2.8.1+1
  [905a6f67] Imath_jll v3.1.7+0
  [1d5cc7b8] IntelOpenMP_jll v2024.0.2+0
  [aacddb02] JpegTurbo_jll v3.0.2+0
  [c1c5ebd0] LAME_jll v3.100.1+0
  [88015f11] LERC_jll v3.0.0+1
  [1d63c593] LLVMOpenMP_jll v15.0.7+0
  [dd4b983a] LZO_jll v2.10.1+0
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.8.7+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.42.0+0
  [94ce4f54] Libiconv_jll v1.17.0+0
  [4b2f31a3] Libmount_jll v2.35.0+0
⌅ [89763e89] Libtiff_jll v4.5.1+1
  [38a345b3] Libuuid_jll v2.39.3+0
  [856f044c] MKL_jll v2024.0.0+0
  [e7412a2a] Ogg_jll v1.3.5+1
  [18a262bb] OpenEXR_jll v3.1.4+0
  [458c3c95] OpenSSL_jll v3.0.13+0
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.2+0
  [36c8627f] Pango_jll v1.50.14+0
  [30392449] Pixman_jll v0.42.2+0
  [c0090381] Qt6Base_jll v6.5.3+1
  [f50d1b31] Rmath_jll v0.4.0+0
⌅ [fb77eaff] Sundials_jll v5.2.2+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 1.10.1
Commit 7790d6f0641 (2024-02-13 20:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 10 × Apple M2 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 6 virtual cores)

Environment info in which I get the expected behaviour:

Additional context

The code that gives the AssertionError was added to RecursiveArrayTools.jl just a few days ago, but I do not know how DifferentialEquations.jl actually uses RecursiveArrayTools.jl, so I decided to post the problem here.

ChrisRackauckas commented 3 months ago

Interesting that worked. It was always Array(sol)

DanielHolleufer commented 3 months ago

Ahh, I was not aware that I wasn't using the standard way to get the solution. I tested Array(sol) and that does indeed work in both versions. Thank you for clarifying.