I’m trying to get up and running with the DifferentialEquations.jl package. It seems that there is some problem when installing due to a soname bump in the libklu library which is part of SuiteSparse. My system has SuiteSparse 7.2.1. Or perhaps I’m doing something wrong. Can anyone advise on what the best approach is to get going with this package?
$ julia
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.9.3 (2023-08-24)
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|__/ |
(@v1.9) pkg> add DifferentialEquations
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Installed TreeViews ──────────────────────── v0.3.0
Installed Calculus ───────────────────────── v0.5.1
Installed NonlinearSolve ─────────────────── v2.3.0
Installed OffsetArrays ───────────────────── v1.12.10
Installed Preferences ────────────────────── v1.4.1
Installed DifferentialEquations ──────────── v7.11.0
Installed StatsFuns ──────────────────────── v1.3.0
Installed PDMats ─────────────────────────── v0.11.28
Installed Polyester ──────────────────────── v0.7.8
Installed HypergeometricFunctions ────────── v0.3.23
Installed Sundials_jll ───────────────────── v5.2.1+0
Installed EnumX ──────────────────────────── v1.0.4
Installed StaticArrays ───────────────────── v1.6.5
Installed CEnum ──────────────────────────── v0.4.2
Installed FunctionWrappers ───────────────── v1.1.3
Installed TriangularSolve ────────────────── v0.1.19
Installed RecursiveArrayTools ────────────── v2.38.10
Installed RandomNumbers ──────────────────── v1.5.3
Installed IntelOpenMP_jll ────────────────── v2023.2.0+0
Installed ZygoteRules ────────────────────── v0.2.3
Installed Static ─────────────────────────── v0.8.8
Installed BoundaryValueDiffEq ────────────── v5.1.0
Installed SteadyStateDiffEq ──────────────── v1.16.1
Installed Distances ──────────────────────── v0.10.10
Installed Missings ───────────────────────── v1.1.0
Installed Tricks ─────────────────────────── v0.1.8
Installed SLEEFPirates ───────────────────── v0.6.39
Installed FiniteDiff ─────────────────────── v2.21.1
Installed MuladdMacro ────────────────────── v0.2.4
Installed IrrationalConstants ────────────── v0.2.2
Installed SIMDTypes ──────────────────────── v0.1.0
Installed Functors ───────────────────────── v0.4.5
Installed CpuId ──────────────────────────── v0.3.1
Installed ArnoldiMethod ──────────────────── v0.2.0
Installed SimpleUnPack ───────────────────── v1.1.0
Installed DiffEqBase ─────────────────────── v6.133.1
Installed SciMLBase ──────────────────────── v2.4.2
Installed NLsolve ────────────────────────── v4.5.1
Installed SciMLNLSolve ───────────────────── v0.1.9
Installed LinearSolve ────────────────────── v2.11.0
Installed ADTypes ────────────────────────── v0.2.4
Installed IfElse ─────────────────────────── v0.1.1
Installed SimpleNonlinearSolve ───────────── v0.1.22
Installed SpecialFunctions ───────────────── v2.3.1
Installed StaticArraysCore ───────────────── v1.4.2
Installed NaNMath ────────────────────────── v1.0.2
Installed DiffEqNoiseProcess ─────────────── v5.19.0
Installed OrdinaryDiffEq ─────────────────── v6.58.0
Installed ArrayInterfaceCore ─────────────── v0.1.29
Installed ThreadingUtilities ─────────────── v0.5.2
Installed Graphs ─────────────────────────── v1.9.0
Installed ManualMemory ───────────────────── v0.1.8
Installed SnoopPrecompile ────────────────── v1.0.3
Installed JumpProcesses ──────────────────── v9.8.0
Installed Rmath_jll ──────────────────────── v0.4.0+0
Installed NLSolversBase ──────────────────── v7.8.3
Installed Random123 ──────────────────────── v1.6.1
Installed LevyArea ───────────────────────── v1.0.0
Installed StatsAPI ───────────────────────── v1.7.0
Installed DataStructures ─────────────────── v0.18.15
Installed CommonSubexpressions ───────────── v0.3.0
Installed ExprTools ──────────────────────── v0.1.10
Installed Lazy ───────────────────────────── v0.15.1
Installed Compat ─────────────────────────── v4.10.0
Installed StatsBase ──────────────────────── v0.34.2
Installed StaticArrayInterface ───────────── v1.4.1
Installed DiffRules ──────────────────────── v1.15.1
Installed BitTwiddlingConvenienceFunctions ─ v0.1.5
Installed GenericSchur ───────────────────── v0.5.3
Installed FunctionWrappersWrappers ───────── v0.1.3
Installed TableTraits ────────────────────── v1.0.1
Installed LayoutPointers ─────────────────── v0.1.14
Installed StochasticDiffEq ───────────────── v6.63.0
Installed Inflate ────────────────────────── v0.1.4
Installed DiffResults ────────────────────── v1.1.0
Installed Sundials ───────────────────────── v4.20.0
Installed PositiveFactorizations ─────────── v0.2.4
Installed SciMLOperators ─────────────────── v0.3.6
Installed MKL_jll ────────────────────────── v2023.2.0+0
Installed JLLWrappers ────────────────────── v1.5.0
Installed DelayDiffEq ────────────────────── v5.43.1
Installed EnzymeCore ─────────────────────── v0.6.2
Installed ConstructionBase ───────────────── v1.5.4
Installed DiffEqCallbacks ────────────────── v2.33.1
Installed Setfield ───────────────────────── v1.1.1
Installed LoopVectorization ──────────────── v0.12.165
Installed DataValueInterfaces ────────────── v1.0.0
Installed FastClosures ───────────────────── v0.3.2
Installed OrderedCollections ─────────────── v1.6.2
Installed LineSearches ───────────────────── v7.2.0
Installed ChainRulesCore ─────────────────── v1.18.0
Installed Reexport ───────────────────────── v1.2.2
Installed PolyesterWeave ─────────────────── v0.2.1
Installed FastLapackInterface ────────────── v2.0.0
Installed ArrayInterface ─────────────────── v7.4.11
Installed KLU ────────────────────────────── v0.4.1
Installed PreallocationTools ─────────────── v0.4.12
Installed LogExpFunctions ────────────────── v0.3.26
Installed CloseOpenIntervals ─────────────── v0.1.12
Installed OpenSpecFun_jll ────────────────── v0.5.5+0
Installed UnPack ─────────────────────────── v1.0.2
Installed MacroTools ─────────────────────── v0.5.11
Installed CommonSolve ────────────────────── v0.2.4
Installed PackageExtensionCompat ─────────── v1.0.2
Installed Krylov ─────────────────────────── v0.9.4
Installed SimpleTraits ───────────────────── v0.9.4
Installed GPUArraysCore ──────────────────── v0.1.5
Installed Adapt ──────────────────────────── v3.6.2
Installed DualNumbers ────────────────────── v0.6.8
Installed StrideArraysCore ───────────────── v0.4.17
Installed DocStringExtensions ────────────── v0.9.3
Installed ExponentialUtilities ───────────── v1.25.0
Installed Rmath ──────────────────────────── v0.7.1
Installed VectorizationBase ──────────────── v0.21.64
Installed RuntimeGeneratedFunctions ──────── v0.5.12
Installed CPUSummary ─────────────────────── v0.2.4
Installed RecipesBase ────────────────────── v1.3.4
Installed VertexSafeGraphs ───────────────── v0.2.0
Installed DataAPI ────────────────────────── v1.15.0
Installed Tables ─────────────────────────── v1.11.0
Installed ConcreteStructs ────────────────── v0.2.3
Installed Optim ──────────────────────────── v1.7.8
Installed TruncatedStacktraces ───────────── v1.4.0
Installed IteratorInterfaceExtensions ────── v1.0.0
Installed HostCPUFeatures ────────────────── v0.1.16
Installed SymbolicIndexingInterface ──────── v0.2.2
Installed PrecompileTools ────────────────── v1.2.0
Installed ResettableStacks ───────────────── v1.1.1
Installed PoissonRandom ──────────────────── v0.4.4
Installed FillArrays ─────────────────────── v1.7.0
Installed QuadGK ─────────────────────────── v2.9.1
Installed ForwardDiff ────────────────────── v0.10.36
Installed Requires ───────────────────────── v1.3.0
Installed FastBroadcast ──────────────────── v0.2.7
Installed Distributions ──────────────────── v0.25.102
Installed SortingAlgorithms ──────────────── v1.2.0
Installed Parameters ─────────────────────── v0.12.3
Installed SparseDiffTools ────────────────── v2.8.0
Installed RecursiveFactorization ─────────── v0.2.20
Installed Sparspak ───────────────────────── v0.3.9
Downloaded artifact: Sundials
Downloaded artifact: IntelOpenMP
Downloaded artifact: Rmath
Downloaded artifact: OpenSpecFun
Updating `~/.julia/environments/v1.9/Project.toml`
[0c46a032] + DifferentialEquations v7.11.0
Updating `~/.julia/environments/v1.9/Manifest.toml`
[47edcb42] + ADTypes v0.2.4
[79e6a3ab] + Adapt v3.6.2
[ec485272] + ArnoldiMethod v0.2.0
[4fba245c] + ArrayInterface v7.4.11
[30b0a656] + ArrayInterfaceCore v0.1.29
[62783981] + BitTwiddlingConvenienceFunctions v0.1.5
[764a87c0] + BoundaryValueDiffEq v5.1.0
⌅ [fa961155] + CEnum v0.4.2
[2a0fbf3d] + CPUSummary v0.2.4
[49dc2e85] + Calculus v0.5.1
[d360d2e6] + ChainRulesCore v1.18.0
[fb6a15b2] + CloseOpenIntervals v0.1.12
[38540f10] + CommonSolve v0.2.4
[bbf7d656] + CommonSubexpressions v0.3.0
[34da2185] + Compat v4.10.0
[2569d6c7] + ConcreteStructs v0.2.3
[187b0558] + ConstructionBase v1.5.4
[adafc99b] + CpuId v0.3.1
[9a962f9c] + DataAPI v1.15.0
[864edb3b] + DataStructures v0.18.15
[e2d170a0] + DataValueInterfaces v1.0.0
[bcd4f6db] + DelayDiffEq v5.43.1
[2b5f629d] + DiffEqBase v6.133.1
[459566f4] + DiffEqCallbacks v2.33.1
[77a26b50] + DiffEqNoiseProcess v5.19.0
[163ba53b] + DiffResults v1.1.0
[b552c78f] + DiffRules v1.15.1
[0c46a032] + DifferentialEquations v7.11.0
[b4f34e82] + Distances v0.10.10
[31c24e10] + Distributions v0.25.102
[ffbed154] + DocStringExtensions v0.9.3
[fa6b7ba4] + DualNumbers v0.6.8
[4e289a0a] + EnumX v1.0.4
[f151be2c] + EnzymeCore v0.6.2
[d4d017d3] + ExponentialUtilities v1.25.0
[e2ba6199] + ExprTools v0.1.10
[7034ab61] + FastBroadcast v0.2.7
[9aa1b823] + FastClosures v0.3.2
[29a986be] + FastLapackInterface v2.0.0
[1a297f60] + FillArrays v1.7.0
[6a86dc24] + FiniteDiff v2.21.1
[f6369f11] + ForwardDiff v0.10.36
[069b7b12] + FunctionWrappers v1.1.3
[77dc65aa] + FunctionWrappersWrappers v0.1.3
[d9f16b24] + Functors v0.4.5
[46192b85] + GPUArraysCore v0.1.5
[c145ed77] + GenericSchur v0.5.3
[86223c79] + Graphs v1.9.0
[3e5b6fbb] + HostCPUFeatures v0.1.16
[34004b35] + HypergeometricFunctions v0.3.23
[615f187c] + IfElse v0.1.1
[d25df0c9] + Inflate v0.1.4
[92d709cd] + IrrationalConstants v0.2.2
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.5.0
[ccbc3e58] + JumpProcesses v9.8.0
[ef3ab10e] + KLU v0.4.1
[ba0b0d4f] + Krylov v0.9.4
[10f19ff3] + LayoutPointers v0.1.14
[50d2b5c4] + Lazy v0.15.1
[2d8b4e74] + LevyArea v1.0.0
[d3d80556] + LineSearches v7.2.0
[7ed4a6bd] + LinearSolve v2.11.0
[2ab3a3ac] + LogExpFunctions v0.3.26
[bdcacae8] + LoopVectorization v0.12.165
[1914dd2f] + MacroTools v0.5.11
[d125e4d3] + ManualMemory v0.1.8
[e1d29d7a] + Missings v1.1.0
[46d2c3a1] + MuladdMacro v0.2.4
[d41bc354] + NLSolversBase v7.8.3
[2774e3e8] + NLsolve v4.5.1
[77ba4419] + NaNMath v1.0.2
[8913a72c] + NonlinearSolve v2.3.0
[6fe1bfb0] + OffsetArrays v1.12.10
[429524aa] + Optim v1.7.8
[bac558e1] + OrderedCollections v1.6.2
[1dea7af3] + OrdinaryDiffEq v6.58.0
[90014a1f] + PDMats v0.11.28
[65ce6f38] + PackageExtensionCompat v1.0.2
[d96e819e] + Parameters v0.12.3
[e409e4f3] + PoissonRandom v0.4.4
[f517fe37] + Polyester v0.7.8
[1d0040c9] + PolyesterWeave v0.2.1
[85a6dd25] + PositiveFactorizations v0.2.4
[d236fae5] + PreallocationTools v0.4.12
[aea7be01] + PrecompileTools v1.2.0
[21216c6a] + Preferences v1.4.1
[1fd47b50] + QuadGK v2.9.1
[74087812] + Random123 v1.6.1
[e6cf234a] + RandomNumbers v1.5.3
[3cdcf5f2] + RecipesBase v1.3.4
[731186ca] + RecursiveArrayTools v2.38.10
[f2c3362d] + RecursiveFactorization v0.2.20
[189a3867] + Reexport v1.2.2
[ae029012] + Requires v1.3.0
[ae5879a3] + ResettableStacks v1.1.1
[79098fc4] + Rmath v0.7.1
[7e49a35a] + RuntimeGeneratedFunctions v0.5.12
[94e857df] + SIMDTypes v0.1.0
[476501e8] + SLEEFPirates v0.6.39
[0bca4576] + SciMLBase v2.4.2
[e9a6253c] + SciMLNLSolve v0.1.9
[c0aeaf25] + SciMLOperators v0.3.6
[efcf1570] + Setfield v1.1.1
[727e6d20] + SimpleNonlinearSolve v0.1.22
[699a6c99] + SimpleTraits v0.9.4
[ce78b400] + SimpleUnPack v1.1.0
[66db9d55] + SnoopPrecompile v1.0.3
[a2af1166] + SortingAlgorithms v1.2.0
[47a9eef4] + SparseDiffTools v2.8.0
[e56a9233] + Sparspak v0.3.9
[276daf66] + SpecialFunctions v2.3.1
[aedffcd0] + Static v0.8.8
[0d7ed370] + StaticArrayInterface v1.4.1
[90137ffa] + StaticArrays v1.6.5
[1e83bf80] + StaticArraysCore v1.4.2
[82ae8749] + StatsAPI v1.7.0
[2913bbd2] + StatsBase v0.34.2
[4c63d2b9] + StatsFuns v1.3.0
[9672c7b4] + SteadyStateDiffEq v1.16.1
[789caeaf] + StochasticDiffEq v6.63.0
⌅ [7792a7ef] + StrideArraysCore v0.4.17
[c3572dad] + Sundials v4.20.0
[2efcf032] + SymbolicIndexingInterface v0.2.2
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.11.0
[8290d209] + ThreadingUtilities v0.5.2
[a2a6695c] + TreeViews v0.3.0
[d5829a12] + TriangularSolve v0.1.19
[410a4b4d] + Tricks v0.1.8
[781d530d] + TruncatedStacktraces v1.4.0
[3a884ed6] + UnPack v1.0.2
[3d5dd08c] + VectorizationBase v0.21.64
[19fa3120] + VertexSafeGraphs v0.2.0
[700de1a5] + ZygoteRules v0.2.3
[1d5cc7b8] + IntelOpenMP_jll v2023.2.0+0
[856f044c] + MKL_jll v2023.2.0+0
[efe28fd5] + OpenSpecFun_jll v0.5.5+0
[f50d1b31] + Rmath_jll v0.4.0+0
⌅ [fb77eaff] + Sundials_jll v5.2.1+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 v0.6.3
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.9.2
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics v1.9.0
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.5+0
[deac9b47] + LibCURL_jll v7.84.0+0
[29816b5a] + LibSSH2_jll v1.10.2+0
[c8ffd9c3] + MbedTLS_jll v2.28.2+0
[14a3606d] + MozillaCACerts_jll v2022.10.11
[4536629a] + OpenBLAS_jll v0.3.21+4
[05823500] + OpenLibm_jll v0.8.1+0
[bea87d4a] + SuiteSparse_jll v5.10.1+6
[83775a58] + Zlib_jll v1.2.13+0
[8e850b90] + libblastrampoline_jll v5.8.0+0
[8e850ede] + nghttp2_jll v1.48.0+0
[3f19e933] + p7zip_jll v17.4.0+0
Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Precompiling project...
✗ Sundials
✗ DifferentialEquations
162 dependencies successfully precompiled in 243 seconds. 8 already precompiled.
2 dependencies errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the packages
1 dependency had warnings during precompilation:
┌ MKL_jll [856f044c-d86e-5d09-b602-aeab76dc8ba7]
│ Downloading artifact: MKL
└
(@v1.9) pkg> precompile
Precompiling project...
✗ Sundials
✗ DifferentialEquations
0 dependencies successfully precompiled in 12 seconds. 170 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 "/home/lund/.julia/compiled/v1.9/DifferentialEquations/jl_IcFzKp".
ERROR: LoadError: InitError: could not load library "/home/lund/.julia/artifacts/cb7fc2801ca0133a5bdea4bc4585d07c08284cfa/lib/libsundials_sunlinsolklu.so"
libklu.so.1: cannot open shared object file: No such file or directory
Stacktrace:
[1] macro expansion
@ ~/.julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
[2] __init__()
@ Sundials_jll ~/.julia/packages/Sundials_jll/rXn1i/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:93
[3] top-level scope
@ stdin:3
during initialization of module Sundials_jll
in expression starting at /home/lund/.julia/packages/Sundials/G2RH1/src/Sundials.jl:3
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile Sundials [c3572dad-4567-51f8-b174-8c6c989267f4] to "/home/lund/.julia/compiled/v1.9/Sundials/jl_m0CYKI".
Stacktrace:
[1] top-level scope
@ stdin:3
in expression starting at /home/lund/.julia/packages/DifferentialEquations/Tu7HS/src/DifferentialEquations.jl:1
in expression starting at stdin:3