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SciML / Sundials.jl

Julia interface to Sundials, including a nonlinear solver (KINSOL), ODE's (CVODE and ARKODE), and DAE's (IDA) in a SciML scientific machine learning enabled manner
https://diffeq.sciml.ai
BSD 2-Clause "Simplified" License
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Cannot build v3.7 in Julia 1.3 #239

Closed jacob-roth closed 4 years ago

jacob-roth commented 4 years ago

I'm on julia 1.3 on a Mac, and I can't build Sundials:

versioninfo()
Julia Version 1.3.1
Commit 2d5741174c (2019-12-30 21:36 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin18.6.0)
  CPU: Intel(R) Core(TM) i7-7820HQ CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)
Environment:
  JULIA_LOAD_PATH = :/Users/jakeroth/Desktop/cascades/lorenz/src:/Users/jakeroth/Desktop/planning-large-deviation/code/JuPower/src:/Users/jakeroth/Desktop/planning-large-deviation/code/juthree:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/src:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/test:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyFlow/src

and here's my attempt:

(v1.3) pkg> add Sundials
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — /Users/jakeroth/.julia/registries/General — failed to fetch from repo
└ @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1199
 Resolving package versions...
  Updating `~/.julia/environments/v1.3/Project.toml`
  [c3572dad] + Sundials v3.7.0
  Updating `~/.julia/environments/v1.3/Manifest.toml`
 [no changes]

(v1.3) pkg> build Sundials
  Building Sundials → `~/.julia/packages/Sundials/CRi5j/deps/build.log`
┌ Error: Error building `Sundials`:
│ ┌ Warning: platform_key() is deprecated, use platform_key_abi() from now on
│ │   caller = ip:0x0
│ └ @ Core :-1
│ ERROR: LoadError: LibraryProduct(nothing, ["libbtf"], :libbtf, "Prefix(/Users/jakeroth/.julia/packages/Sundials/CRi5j/deps/usr)") is not satisfied, cannot generate deps.jl!
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] #write_deps_file#152(::Bool, ::typeof(write_deps_file), ::String, ::Array{LibraryProduct,1}) at /Users/jakeroth/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:414
│  [3] write_deps_file(::String, ::Array{LibraryProduct,1}) at /Users/jakeroth/.julia/packages/BinaryProvider/TcAwt/src/Products.jl:395
│  [4] top-level scope at /Users/jakeroth/.julia/packages/Sundials/CRi5j/deps/build.jl:63
│  [5] include at ./boot.jl:328 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1105
│  [7] include(::Module, ::String) at ./Base.jl:31
│  [8] include(::String) at ./client.jl:424
│  [9] top-level scope at none:5
│ in expression starting at /Users/jakeroth/.julia/packages/Sundials/CRi5j/deps/build.jl:63
└ @ Pkg.Operations /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649

I still have to manually click through the "Allow" in the "Security and Privacy" window on Mac.

ChrisRackauckas commented 4 years ago

@staticfloat do you know what this could be?

jacob-roth commented 4 years ago

I just tried this with a fresh julia-1.4 and the latest Sundials, and after manually opening up all of the lib/ files and right-clicking and saying "OK" on the privacy prompt, I was able to build the package. However, when I run a test case that I believe should work, I get an error:

using Sundials

p=[2,1.2,3]

function f(res,du,u,p,t)
  res[1] = du[1] - p[1] * u[1] + p[2] * u[1]*u[2]
  res[2] = du[2] -p[3] * u[2] - u[1]*u[2]
  res[3]=  u[2] + u[1] - u[3]
end

function g(J,du,u,p,gamma,t)
  J[1,1] = gamma - p[1] + p[2] * u[2]
  J[1,2] = p[2]* u[1]
  J[1,3] = 0
  J[2,1] = - 1 * u[2]
  J[2,2] = gamma - p[3] - u[1]
  J[2,3] = 0
  J[3,1] = 1
  J[3,2] = 1
  J[3,3] = -1
  nothing
end

fg = DAEFunction(f;jac=g)

dIC=[-0.8,-4]
IC =[1.0,1.0,2.0]
tspan=(0.0,10.0)
diff_vars = [true,true, false]

testProb2 = DAEProblem(fg,dIC,IC,tspan,p,differential_vars=diff_vars)
julia> sol = solve(testProb2,IDA())

[IDAS ERROR]  IDASolve
  The value tstop = 10 is behind current t = 0, in the direction of integration.

retcode: Failure
Interpolation: 3rd order Hermite
t: 1-element Array{Float64,1}:
 0.0
u: 1-element Array{Array{Float64,1},1}:
 [1.0, 1.0, 2.0]
ChrisRackauckas commented 4 years ago

Interesting, it's working just fine for me. Are the tests passing for you?

jacob-roth commented 4 years ago

No...good place to start :) I'm getting an odd message that it's missing the Test package. I looked in the Project.toml file, but it seems that Test is included there

julia> using Sundials
julia> Pkg.add("Test")
   Updating registry at `~/.julia/registries/General`
   Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — /Users/jakeroth/.julia/registries/General — failed to fetch from repo
└ @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Types.jl:1122
  Resolving package versions...
   Updating `~/.julia/environments/v1.4/Project.toml`
  [8dfed614] + Test
   Updating `~/.julia/environments/v1.4/Manifest.toml`
 [no changes]

julia> Pkg.test("Sundials")
    Testing Sundials
Status `/private/var/folders/10/y7z26t512kbbfrsj12fx3wkr0000gn/T/jl_TupkyI/Manifest.toml`
  [4fba245c] ArrayInterface v1.2.1
  [aae01518] BandedMatrices v0.12.3
  [9e28174c] BinDeps v0.8.10
  [b99e7846] BinaryProvider v0.5.6
  [00ebfdb7] CSTParser v0.6.2
  [a603d957] CanonicalTraits v0.1.0
  [bbf7d656] CommonSubexpressions v0.2.0
  [34da2185] Compat v2.2.0
  [a8cc5b0e] Crayons v4.0.0
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.2
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.3.5
  [eb300fae] DiffEqBiological v4.0.1
  [01453d9d] DiffEqDiffTools v1.3.0
  [c894b116] DiffEqJump v6.2.2
  [9fdde737] DiffEqOperators v4.1.0
  [a077e3f3] DiffEqProblemLibrary v4.5.1
  [163ba53b] DiffResults v0.0.4
  [b552c78f] DiffRules v0.0.10
  [ffbed154] DocStringExtensions v0.8.1
  [497a8b3b] DoubleFloats v0.9.11
  [7c1d4256] DynamicPolynomials v0.3.3
  [fdbdab4c] ElasticArrays v0.4.0
  [1a297f60] FillArrays v0.7.2
  [3dd14ad9] FixedPolynomials v0.4.0
  [59287772] Formatting v0.4.1
  [f6369f11] ForwardDiff v0.10.3
  [069b7b12] FunctionWrappers v1.0.0
  [6b9d7cbe] GeneralizedGenerated v0.1.3
  [01680d73] GenericSVD v0.2.2
  [c145ed77] GenericSchur v0.3.0
  [f213a82b] HomotopyContinuation v1.1.2
  [42fd0dbc] IterativeSolvers v0.8.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [b14d175d] JuliaVariables v0.1.3
  [b964fa9f] LaTeXStrings v1.0.3
  [23fbe1c1] Latexify v0.11.0
  [5078a376] LazyArrays v0.12.2
  [f1f30506] LegibleLambdas v0.2.0
  [d8e11817] MLStyle v0.3.1
  [1914dd2f] MacroTools v0.5.1
  [a3b82374] MatrixFactorizations v0.2.0
  [291d046c] MixedSubdivisions v0.3.2
  [961ee093] ModelingToolkit v0.8.0
  [46d2c3a1] MuladdMacro v0.2.1
  [102ac46a] MultivariatePolynomials v0.3.2
  [872c559c] NNlib v0.6.0
  [77ba4419] NaNMath v0.3.2
  [71a1bf82] NameResolution v0.1.2
  [bac558e1] OrderedCollections v1.1.0
  [d96e819e] Parameters v0.12.0
  [e409e4f3] PoissonRandom v0.4.0
  [f27b6e38] Polynomials v0.5.3
  [8162dcfd] PrettyPrint v0.1.0
  [08abe8d2] PrettyTables v0.5.1
  [92933f4c] ProgressMeter v1.1.0
  [01f381cc] ProjectiveVectors v0.2.2
  [be4d8f0f] Quadmath v0.5.2
  [e6cf234a] RandomNumbers v1.3.0
  [3cdcf5f2] RecipesBase v0.7.0
  [731186ca] RecursiveArrayTools v1.0.2
  [f2c3362d] RecursiveFactorization v0.1.0
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v0.5.2
  [f2b01f46] Roots v0.8.3
  [276daf66] SpecialFunctions v0.8.0
  [90137ffa] StaticArrays v0.11.0
  [62e018b1] StaticPolynomials v1.3.2
  [c3572dad] Sundials v3.7.0
  [123dc426] SymEngine v0.7.0
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v0.2.11
  [a759f4b9] TimerOutputs v0.5.0
  [0796e94c] Tokenize v0.5.6
  [a2a6695c] TreeViews v0.3.0
  [30578b45] URIParser v0.4.0
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4607b0f0] SuiteSparse
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
ERROR: LoadError: ArgumentError: Package Test not found in current path:
- Run `import Pkg; Pkg.add("Test")` to install the Test package.

Stacktrace:
 [1] require(::Module, ::Symbol) at ./loading.jl:892
 [2] include(::String) at ./client.jl:439
 [3] top-level scope at none:6
in expression starting at /Users/jakeroth/.julia/packages/Sundials/CRi5j/test/runtests.jl:2
ERROR: Package Sundials errored during testing
Stacktrace:
 [1] pkgerror(::String, ::Vararg{String,N} where N) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Types.jl:53
 [2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/Operations.jl:1503
 [3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:316
 [4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:303
 [5] #test#68 at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:297 [inlined]
 [6] test at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:297 [inlined]
 [7] #test#67 at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:296 [inlined]
 [8] test at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:296 [inlined]
 [9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:295
 [10] test(::String) at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.4/Pkg/src/API.jl:295
 [11] top-level scope at REPL[15]:1
ChrisRackauckas commented 4 years ago

Is it fine on Julia 1.3? Are you on a non-standard architecture or something?

jacob-roth commented 4 years ago

Weird, it seemed to work for julia 1.3 (or at least return success).

julia> sol = solve(testProb2,IDA())
retcode: Success
Interpolation: 3rd order Hermite
t: 777-element Array{Float64,1}:
  0.0
  5.995585571103871e-154
  1.1991171142207742e-153
  2.3982342284415483e-153
  4.796468456883097e-153
  9.592936913766193e-153
  1.9185873827532386e-152
  3.837174765506477e-152
  7.674349531012955e-152
  1.534869906202591e-151
  ⋮
  9.687785328967703
  9.734936457864725
  9.774941685514284
  9.810946390398886
  9.846951095283488
  9.88295580016809
  9.918960505052693
  9.954965209937296
  9.978246705107482
 10.0
u: 777-element Array{Array{Float64,1},1}:
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 [1.0, 1.0, 2.0]
 ⋮
 [9.76585955303694e-7, 7.026924544694885e12, 7.026924544694885e12]
 [5.499775773830733e-13, 8.095424822498138e12, 8.095424822498138e12]
 [-7.222158850564414e-9, 9.128181292060805e12, 9.128181292060805e12]
 [2.053523722820283e-8, 1.016964066299692e13, 1.016964066299692e13]
 [9.292718801527348e-8, 1.1330162233948816e13, 1.1330162233948818e13]
 [-7.845458998884417e-8, 1.2623148190191896e13, 1.2623148190191895e13]
 [3.931668778070256e-7, 1.4063771175961207e13, 1.4063771175961205e13]
 [-1.6209613503217882e-6, 1.5668801867781602e13, 1.5668801867781605e13]
 [-1.466669741425574e-7, 1.6803109476513234e13, 1.6803109476513234e13]
 [8.696292270819889e-8, 1.7937261901712203e13, 1.7937261901712203e13]

I downloaded prebuilt 1.4 maybe a few days ago, didn't think there was anything non-standard:

julia> versioninfo()
Julia Version 1.4.0
Commit b8e9a9ecc6 (2020-03-21 16:36 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin18.6.0)
  CPU: Intel(R) Core(TM) i7-7820HQ CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
  JULIA_LOAD_PATH = :/Users/jakeroth/Desktop/cascades/lorenz/src:/Users/jakeroth/Desktop/planning-large-deviation/code/JuPower/src:/Users/jakeroth/Desktop/planning-large-deviation/code/juthree:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/src:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/test:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/:/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyFlow/src
ChrisRackauckas commented 4 years ago

I'll open a PR to run the tests on v1.4 CI.

ChrisRackauckas commented 4 years ago

https://github.com/SciML/Sundials.jl/pull/240

Tests seem to pass here. Peculiar...

jacob-roth commented 4 years ago

Hm, thanks for checking. I just downloaded v1.4 (3-21-2020 version) and had the same error where it couldn't find the Test package. I have aliased my calls to different versions of julia as julia-1.X, so I wonder if it's somehow not finding the right path to the julia binaries/application? I tried modifying the runtests.jl file to have import Pkg; Pkg.add("Test"); using Test, but now it's saying it can't find the package Pkg, so something's strange...

StefanKarpinski commented 4 years ago

What's the value of LOAD_PATH?

jacob-roth commented 4 years ago 
julia> LOAD_PATH
11-element Array{String,1}:
 "@"
 "@v#.#"
 "@stdlib"
 "/Users/jakeroth/Desktop/cascades/lorenz/src"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/JuPower/src"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/juthree"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/src"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/test"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyModeling/"
 "/Users/jakeroth/Desktop/planning-large-deviation/code/EnergyFlow/src"
 "/Users/jakeroth/Development/Julia"
StefanKarpinski commented 4 years ago

The build failure appears to be because the build script is using an outdated API. The Test failure is because the project file for version 3.7.0 didn't include Test in the dependencies of its test target. Not sure how that ever worked. Seems like upgrading to the current Sundials version (3.9.0) would likely fix both issues.

jacob-roth commented 4 years ago

Oh interesting, thanks, I thought that I had the latest version when I was in REPL. Doing ] up Sundials only gave me v3.7. I'll get the latest and retry

jacob-roth commented 4 years ago

Tried getting v3.9 but it doens't seem registered? Or I'm doing somethign wrong, because I'm running into dependency issues:


(v1.3) pkg> status
    Status `~/.julia/environments/v1.3/Project.toml`
  [6e4b80f9] BenchmarkTools v0.4.3
  [7a1cc6ca] FFTW v1.0.1
  [f6369f11] ForwardDiff v0.10.3
  [a98d9a8b] Interpolations v0.12.2
  [b6b21f68] Ipopt v0.6.0
  [4076af6c] JuMP v0.20.0
  [5fb14364] OhMyREPL v0.5.2
  [438e738f] PyCall v1.91.2
  [d330b81b] PyPlot v2.8.2
  [e88e6eb3] Zygote v0.3.4
  [37e2e46d] LinearAlgebra
  [8dfed614] Test

(v1.3) pkg> add https://github.com/SciML/Sundials.jl.git
  Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
┌ Warning: Some registries failed to update:
│     — /Users/jakeroth/.julia/registries/General — failed to fetch from repo
└ @ Pkg.Types /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Types.jl:1199
  Updating git-repo `https://github.com/SciML/Sundials.jl.git`
  Updating git-repo `https://github.com/SciML/Sundials.jl.git`
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package DiffEqBase [2b5f629d]:
 DiffEqBase [2b5f629d] log:
 ├─possible versions are: [3.13.2-3.13.3, 4.0.0-4.0.1, 4.1.0, 4.2.0, 4.3.0-4.3.1, 4.4.0, 4.5.0, 4.6.0, 4.7.0, 4.8.0, 4.9.0, 4.10.0-4.10.1, 4.11.0-4.11.1, 4.12.0, 4.13.0, 4.14.0-4.14.1, 4.15.0, 4.16.0, 4.17.0, 4.18.0, 4.19.0, 4.20.0-4.20.3, 4.21.0, 4.21.2-4.21.3, 4.22.0-4.22.2, 4.23.0, 4.23.2-4.23.4, 4.24.0-4.24.3, 4.25.0-4.25.1, 4.26.0-4.26.3, 4.27.0-4.27.1, 4.28.0-4.28.1, 4.29.0-4.29.2, 4.30.0-4.30.2, 4.31.0-4.31.2, 4.32.0, 5.0.0-5.0.1, 5.1.0, 5.2.0-5.2.3, 5.3.0-5.3.2, 5.4.0-5.4.1, 5.5.0-5.5.2, 5.6.0-5.6.4, 5.7.0, 5.8.0-5.8.1, 5.9.0, 5.10.0-5.10.3, 5.11.0-5.11.1, 5.12.0, 5.13.0, 5.14.0-5.14.2, 5.15.0, 5.16.0-5.16.5, 5.17.0-5.17.1, 5.18.0, 5.19.0, 5.20.0-5.20.1, 6.0.0, 6.1.0, 6.2.0-6.2.4, 6.3.0-6.3.5] or uninstalled
 └─restricted to versions 6.21.0-6 by Sundials [c3572dad] — no versions left
   └─Sundials [c3572dad] log:
     ├─possible versions are: 3.9.0 or uninstalled
     └─Sundials [c3572dad] is fixed to version 3.9.0

(v1.3) pkg> add DiffEqBase@6.21.0
 Resolving package versions...
ERROR: Unsatisfiable requirements detected for package DiffEqBase [2b5f629d]:
 DiffEqBase [2b5f629d] log:
 ├─possible versions are: [3.13.2-3.13.3, 4.0.0-4.0.1, 4.1.0, 4.2.0, 4.3.0-4.3.1, 4.4.0, 4.5.0, 4.6.0, 4.7.0, 4.8.0, 4.9.0, 4.10.0-4.10.1, 4.11.0-4.11.1, 4.12.0, 4.13.0, 4.14.0-4.14.1, 4.15.0, 4.16.0, 4.17.0, 4.18.0, 4.19.0, 4.20.0-4.20.3, 4.21.0, 4.21.2-4.21.3, 4.22.0-4.22.2, 4.23.0, 4.23.2-4.23.4, 4.24.0-4.24.3, 4.25.0-4.25.1, 4.26.0-4.26.3, 4.27.0-4.27.1, 4.28.0-4.28.1, 4.29.0-4.29.2, 4.30.0-4.30.2, 4.31.0-4.31.2, 4.32.0, 5.0.0-5.0.1, 5.1.0, 5.2.0-5.2.3, 5.3.0-5.3.2, 5.4.0-5.4.1, 5.5.0-5.5.2, 5.6.0-5.6.4, 5.7.0, 5.8.0-5.8.1, 5.9.0, 5.10.0-5.10.3, 5.11.0-5.11.1, 5.12.0, 5.13.0, 5.14.0-5.14.2, 5.15.0, 5.16.0-5.16.5, 5.17.0-5.17.1, 5.18.0, 5.19.0, 5.20.0-5.20.1, 6.0.0, 6.1.0, 6.2.0-6.2.4, 6.3.0-6.3.5] or uninstalled
 └─restricted to versions 6.21.0 by an explicit requirement — no versions left
ChrisRackauckas commented 4 years ago

Your registry seems to be missing any recent versions... I don't know why? Is it dirty? Are you on a special branch? Maybe it's worth going nuclear and just deleting ~/.julia.

jacob-roth commented 4 years ago

THANKS, registries issue. Deleting registries/ fixed it. Not sure why...

ulia> import Pkg

julia> Pkg.test("Sundials")
    Testing Sundials
Downloading artifact: OpenSpecFun
######################################################################## 100.0%##O=#  Downloading artifact: CompilerSupportLibraries
######################################################################## 100.0%##O=#  Status `/private/var/folders/10/y7z26t512kbbfrsj12fx3wkr0000gn/T/jl_qt7beU/Manifest.toml`
  [1520ce14] AbstractTrees v0.3.2
  [4fba245c] ArrayInterface v2.6.2
  [4c555306] ArrayLayouts v0.1.5
  [aae01518] BandedMatrices v0.14.3
  [b99e7846] BinaryProvider v0.5.8
  [8e7c35d0] BlockArrays v0.11.1
  [ffab5731] BlockBandedMatrices v0.7.2
  [a603d957] CanonicalTraits v0.2.1
  [d360d2e6] ChainRulesCore v0.7.1
  [bbf7d656] CommonSubexpressions v0.2.0
  [34da2185] Compat v3.8.0
  [e66e0078] CompilerSupportLibraries_jll v0.3.1+0
  [88cd18e8] ConsoleProgressMonitor v0.1.2
  [a8cc5b0e] Crayons v4.0.1
  [9a962f9c] DataAPI v1.1.0
  [864edb3b] DataStructures v0.17.10
  [e2d170a0] DataValueInterfaces v1.0.0
  [2b5f629d] DiffEqBase v6.25.1
  [eb300fae] DiffEqBiological v4.2.0
  [c894b116] DiffEqJump v6.5.0
  [9fdde737] DiffEqOperators v4.8.1
  [a077e3f3] DiffEqProblemLibrary v4.6.4
  [163ba53b] DiffResults v1.0.2
  [b552c78f] DiffRules v1.0.1
  [ffbed154] DocStringExtensions v0.8.1
  [497a8b3b] DoubleFloats v1.1.6
  [7c1d4256] DynamicPolynomials v0.3.9
  [fdbdab4c] ElasticArrays v1.0.0
  [1a297f60] FillArrays v0.8.5
  [3dd14ad9] FixedPolynomials v0.4.0
  [59287772] Formatting v0.4.1
  [f6369f11] ForwardDiff v0.10.9
  [069b7b12] FunctionWrappers v1.1.1
  [6b9d7cbe] GeneralizedGenerated v0.2.2
  [01680d73] GenericSVD v0.3.0
  [c145ed77] GenericSchur v0.4.0
  [f213a82b] HomotopyContinuation v1.4.1
  [42fd0dbc] IterativeSolvers v0.8.3
  [82899510] IteratorInterfaceExtensions v1.0.0
  [b14d175d] JuliaVariables v0.2.0
  [b964fa9f] LaTeXStrings v1.1.0
  [23fbe1c1] Latexify v0.12.0
  [5078a376] LazyArrays v0.15.1
  [1d6d02ad] LeftChildRightSiblingTrees v0.1.2
  [e6f89c97] LoggingExtras v0.4.0
  [d8e11817] MLStyle v0.3.1
  [1914dd2f] MacroTools v0.5.5
  [a3b82374] MatrixFactorizations v0.3.0
  [291d046c] MixedSubdivisions v1.0.0
  [961ee093] ModelingToolkit v1.4.2
  [46d2c3a1] MuladdMacro v0.2.2
  [102ac46a] MultivariatePolynomials v0.3.6
  [d8a4904e] MutableArithmetics v0.2.7
  [872c559c] NNlib v0.6.6
  [77ba4419] NaNMath v0.3.3
  [71a1bf82] NameResolution v0.1.3
  [efe28fd5] OpenSpecFun_jll v0.5.3+3
  [bac558e1] OrderedCollections v1.1.0
  [d96e819e] Parameters v0.12.0
  [e409e4f3] PoissonRandom v0.4.0
  [f27b6e38] Polynomials v0.6.1
  [8162dcfd] PrettyPrint v0.1.0
  [08abe8d2] PrettyTables v0.8.4
  [33c8b6b6] ProgressLogging v0.1.2
  [92933f4c] ProgressMeter v1.2.0
  [01f381cc] ProjectiveVectors v1.1.2
  [be4d8f0f] Quadmath v0.5.4
  [e6cf234a] RandomNumbers v1.4.0
  [3cdcf5f2] RecipesBase v0.8.0
  [731186ca] RecursiveArrayTools v2.1.0
  [f2c3362d] RecursiveFactorization v0.1.0
  [189a3867] Reexport v0.2.0
  [ae029012] Requires v1.0.1
  [f2b01f46] Roots v1.0.1
  [276daf66] SpecialFunctions v0.10.0
  [90137ffa] StaticArrays v0.12.1
  [62e018b1] StaticPolynomials v1.3.3
  [c3572dad] Sundials v3.9.0
  [123dc426] SymEngine v0.7.1
  [3783bdb8] TableTraits v1.0.0
  [bd369af6] Tables v1.0.3
  [5d786b92] TerminalLoggers v0.1.1
  [a2a6695c] TreeViews v0.3.0
  [700de1a5] ZygoteRules v0.2.0
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [8ba89e20] Distributed
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [44cfe95a] Pkg
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics
  [4607b0f0] SuiteSparse
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
T=0.4, Y=[0.9899652943580798, 3.4705641920208314e-5, 0.01]
roots=Int32[0, 1]
T=0.4, Y=[0.9851640909284242, 3.386241704950175e-5, 0.014802046654526432]
T=4.0, Y=[0.9055096703060879, 2.2403378568484244e-5, 0.09446792631534301]
T=40.0, Y=[0.7158025114908454, 9.184971961186271e-6, 0.2841883035371925]
T=400.0, Y=[0.45049625037673735, 3.2225997752630977e-6, 0.5495005270234858]
T=4000.0, Y=[0.18318162739328903, 8.940819373535722e-7, 0.8168174785247727]
T=40000.0, Y=[0.038987918672711896, 1.6219549966603174e-7, 0.9610119191317875]
T=400000.0, Y=[0.004937718504660662, 1.984771908119386e-8, 0.9950622616476194]
T=4.0e6, Y=[0.0005164957707206657, 2.0670370590145256e-9, 0.9994835021622415]
T=4.0e7, Y=[9.999999999999996e-5, 4.000393162978798e-10, 0.9998999995999598]
roots=Int32[-1, 0]
T=4.0e7, Y=[5.203762195676103e-5, 2.081611962477128e-10, 0.999947962169881]
T=4.0e8, Y=[5.21719209390933e-6, 2.086888660177039e-11, 0.9999947827870365]
T=4.0e9, Y=[5.320326328232402e-7, 2.1281317045334404e-12, 0.9999994679652385]
T=4.0e10, Y=[5.471566559787941e-8, 2.1886267858337263e-13, 0.9999999452841147]
Test Summary: |
CVODE         | No tests
T=0.4, Y=[0.9851721138377025, 3.386406120817996e-5, 0.014794022101089307]
T=4.0, Y=[0.9055186785328794, 2.2404781805334787e-5, 0.09445891668531428]
T=40.0, Y=[0.715827068739702, 9.185512472082487e-6, 0.28416374574782616]
T=400.0, Y=[0.45051866843284366, 3.222907159344263e-6, 0.5494781086599967]
T=4000.0, Y=[0.18320225667994575, 8.94230214472978e-7, 0.8167968490898406]
T=40000.0, Y=[0.03898337827880326, 1.621799878073902e-7, 0.96101645954121]
T=400000.0, Y=[0.004938270331418616, 1.985351550862375e-8, 0.9950617098150669]
T=4.0e6, Y=[0.0005168101324260045, 2.068434777531092e-9, 0.9994831877991401]
T=4.0e7, Y=[5.202985953290682e-5, 2.0832525035625152e-10, 0.9999479699321431]
T=4.0e8, Y=[5.207659630111956e-6, 2.0841931899519505e-11, 0.9999947923195291]
T=4.0e9, Y=[5.208321136050987e-7, 2.0828928173656967e-12, 0.9999994791658047]
T=4.0e10, Y=[5.208358902243623e-8, 1.977013868181389e-13, 0.999999947916214]
Test Summary: |
ARK           | No tests
T=0.4, Y=[0.9899652943718806, 3.4705628119662186e-5, 0.010000000000000002]
roots=Int32[0, 1]
T=0.4, Y=[0.9851707623122912, 3.386371656828505e-5, 0.01479537397114059]
T=4.0, Y=[0.905504728443, 2.24030741323827e-5, 0.09447286848286832]
T=40.0, Y=[0.71584189841088, 9.186119502141643e-6, 0.28414891546961785]
T=400.0, Y=[0.450537891284184, 3.2231511100140762e-6, 0.5494588855647063]
T=4000.0, Y=[0.1831996994939642, 8.942143972145097e-7, 0.8167994062916398]
T=40000.0, Y=[0.03898368270471694, 1.6217829385564226e-7, 0.9610161551169892]
T=400000.0, Y=[0.004938675705721228, 1.985155431045523e-8, 0.995061304442724]
T=4.0e6, Y=[0.00051688824532254, 2.0686115064950218e-9, 0.9994831096860671]
T=4.0e7, Y=[9.999999999999957e-5, 4.0003952202291907e-10, 0.9998999995999608]
roots=Int32[-1, 0]
T=4.0e7, Y=[5.204772673760556e-5, 2.0820161918090773e-10, 0.9999479520650573]
T=4.0e8, Y=[5.205357160339493e-6, 2.0821535764088784e-11, 0.9999947946220178]
T=4.0e9, Y=[5.190800205273695e-7, 2.076321146499096e-12, 0.9999994809179031]
T=4.0e10, Y=[5.11777367290652e-8, 2.047109574722673e-13, 0.9999999488220584]
Test Summary: |
IDA           | No tests
Solution: [0.7861540663366059, 0.6180344478352109]
Residual: [4.794728554635697e-6, -3.7681823696900096e-6]
Test Summary: | Pass  Total
Kinsol        |    2      2
Test Summary: | Pass  Total
Handle Tests  |   13     13

[IDAS ERROR]  IDASolve
  At t = 0.0395936 and h = 6.30116e-16, the corrector convergence failed repeatedly or with |h| = hmin.

[IDAS ERROR]  IDASolve
  At t = 0.0317944 and h = 3.07674e-19, the corrector convergence failed repeatedly or with |h| = hmin.

With consistent initial conditions:
With inconsistent initial conditions:
Jacobian vs no Jacobian difference:
8.828493491819245e-13
i.t = 0.04436589458068945
i.t = 0.11976370878673312
i.t = 0.19516152299277678
i.t = 0.27055933719882047
i.t = 0.34595715140486416
i.t = 0.42135496561090785
i.t = 0.5878600458168253
i.t = 0.7543651260227427
i.t = 0.9208702062286602
i.t = 1.0
Test error handling

[CVODES WARNING]  CVode
  Internal t = 0 and h = 0 are such that t + h = t on the next step. The solver will continue anyway.

[CVODES ERROR]  CVode
  At t = 0 and h = 0, the corrector convergence test failed repeatedly or with |h| = hmin.

[IDAS ERROR]  IDACalcIC
  Newton/Linesearch algorithm failed to converge.

Test Summary:    | Pass  Broken  Total
Common Interface |   47       2     49
    Testing Sundials tests passed