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1.4.0-DEV-81899bf99e.log
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Julia Version 1.4.0-DEV.634
Commit 81899bf99e (2019-12-18 10:13 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
Resolving package versions...
Installed InplaceOps ───────── v0.3.0
Installed ProgressMeter ────── v1.2.0
Installed AdvancedHMC ──────── v0.2.14
Installed OrderedCollections ─ v1.1.0
Installed Parameters ───────── v0.12.0
Installed SpecialFunctions ─── v0.9.0
Installed StatsFuns ────────── v0.9.3
Installed StatsBase ────────── v0.32.0
Installed ArrayLayouts ─────── v0.1.5
Installed FillArrays ───────── v0.8.2
Installed DataStructures ───── v0.17.6
Installed OpenSpecFun_jll ──── v0.5.3+1
Installed Missings ─────────── v0.4.3
Installed SortingAlgorithms ── v0.3.1
Installed Rmath ────────────── v0.6.0
Installed StaticArrays ─────── v0.12.1
Installed MacroTools ───────── v0.5.3
Installed ArgCheck ─────────── v1.0.1
Installed LazyArrays ───────── v0.14.10
Installed DataAPI ──────────── v1.1.0
Installed BinaryProvider ───── v0.5.8
Updating `~/.julia/environments/v1.4/Project.toml`
[0bf59076] + AdvancedHMC v0.2.14
Updating `~/.julia/environments/v1.4/Manifest.toml`
[0bf59076] + AdvancedHMC v0.2.14
[dce04be8] + ArgCheck v1.0.1
[4c555306] + ArrayLayouts v0.1.5
[b99e7846] + BinaryProvider v0.5.8
[9a962f9c] + DataAPI v1.1.0
[864edb3b] + DataStructures v0.17.6
[1a297f60] + FillArrays v0.8.2
[505f98c9] + InplaceOps v0.3.0
[5078a376] + LazyArrays v0.14.10
[1914dd2f] + MacroTools v0.5.3
[e1d29d7a] + Missings v0.4.3
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[d96e819e] + Parameters v0.12.0
[92933f4c] + ProgressMeter v1.2.0
[79098fc4] + Rmath v0.6.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[90137ffa] + StaticArrays v0.12.1
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.3
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Rmath → `~/.julia/packages/Rmath/BoBag/deps/build.log`
Path `/home/pkgeval/.julia/packages/Rmath/BoBag` exists and looks like the correct package. Using existing path.
Updating `/tmp/jl_MYtGJu/Project.toml`
[79098fc4] + Rmath v0.6.0 [`~/.julia/packages/Rmath/BoBag`]
Updating `/tmp/jl_MYtGJu/Manifest.toml`
[79098fc4] ~ Rmath v0.6.0 ⇒ v0.6.0 [`~/.julia/packages/Rmath/BoBag`]
Testing AdvancedHMC
Path `/home/pkgeval/.julia/packages/AdvancedHMC/1ngch` exists and looks like the correct package. Using existing path.
Installed NLSolversBase ─────────────── v7.5.0
Installed AxisAlgorithms ────────────── v1.0.0
Installed DiffResults ───────────────── v1.0.1
Installed Polynomials ───────────────── v0.6.0
Installed PDMats ────────────────────── v0.9.10
Installed MKL_jll ───────────────────── v2019.0.117+0
Installed Bijectors ─────────────────── v0.4.0
Installed ForwardDiff ───────────────── v0.10.8
Installed Distributions ─────────────── v0.21.11
Installed UnicodePlots ──────────────── v1.1.0
Installed LineSearches ──────────────── v7.0.1
Installed DataFrames ────────────────── v0.20.0
Installed Turing ────────────────────── v0.7.1
Installed FFTW_jll ──────────────────── v3.3.9+3
Installed RecipesBase ───────────────── v0.7.0
Installed Calculus ──────────────────── v0.5.1
Installed CommonSubexpressions ──────── v0.2.0
Installed FiniteDifferences ─────────── v0.9.0
Installed Tables ────────────────────── v0.2.11
Installed AbstractFFTs ──────────────── v0.5.0
Installed Interpolations ────────────── v0.12.5
Installed PositiveFactorizations ────── v0.2.3
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed InvertedIndices ───────────── v1.0.0
Installed MCMCChains ────────────────── v0.4.1
Installed Combinatorics ─────────────── v1.0.0
Installed QuadGK ────────────────────── v2.3.1
Installed DistributionsAD ───────────── v0.1.1
Installed Optim ─────────────────────── v0.19.7
Installed MappedArrays ──────────────── v0.2.2
Installed Parsers ───────────────────── v0.3.10
Installed Reexport ──────────────────── v0.2.0
Installed Libtask ───────────────────── v0.3.1
Installed Requires ──────────────────── v1.0.0
Installed Ratios ────────────────────── v0.3.1
Installed RangeArrays ───────────────── v0.3.1
Installed AxisArrays ────────────────── v0.3.3
Installed AbstractMCMC ──────────────── v0.1.0
Installed IntelOpenMP_jll ───────────── v2018.0.3+0
Installed IntervalSets ──────────────── v0.3.2
Installed ArrayInterface ────────────── v2.1.0
Installed DiffEqDiffTools ───────────── v1.6.0
Installed Arpack_jll ────────────────── v3.5.0+2
Installed Compat ────────────────────── v2.2.0
Installed Showoff ───────────────────── v0.3.1
Installed CategoricalArrays ─────────── v0.7.4
Installed Arpack ────────────────────── v0.4.0
Installed IterTools ─────────────────── v1.3.0
Installed OpenBLAS_jll ──────────────── v0.3.7+1
Installed PooledArrays ──────────────── v0.5.2
Installed Zygote ────────────────────── v0.3.4
Installed Roots ─────────────────────── v0.8.4
Installed DataValueInterfaces ───────── v1.0.0
Installed NNlib ─────────────────────── v0.6.0
Installed KernelDensity ─────────────── v0.5.1
Installed Adapt ─────────────────────── v1.0.0
Installed Tracker ───────────────────── v0.2.3
Installed TimerOutputs ──────────────── v0.5.3
Installed NaNMath ───────────────────── v0.3.3
Installed WoodburyMatrices ──────────── v0.4.1
Installed IRTools ───────────────────── v0.2.3
Installed JSON ──────────────────────── v0.21.0
Installed OffsetArrays ──────────────── v0.11.4
Installed TableTraits ───────────────── v1.0.0
Installed ZygoteRules ───────────────── v0.1.0
Installed DiffRules ─────────────────── v1.0.0
Installed FFTW ──────────────────────── v1.2.0
Updating `/tmp/jl_DDHZ6D/Project.toml`
[0bf59076] + AdvancedHMC v0.2.14 [`~/.julia/packages/AdvancedHMC/1ngch`]
[163ba53b] + DiffResults v1.0.1
[31c24e10] + Distributions v0.21.11
[f6369f11] + ForwardDiff v0.10.8
[fce5fe82] + Turing v0.7.1
[b8865327] + UnicodePlots v1.1.0
Updating `/tmp/jl_DDHZ6D/Manifest.toml`
[621f4979] + AbstractFFTs v0.5.0
[80f14c24] + AbstractMCMC v0.1.0
[79e6a3ab] + Adapt v1.0.0
[0bf59076] ~ AdvancedHMC v0.2.14 ⇒ v0.2.14 [`~/.julia/packages/AdvancedHMC/1ngch`]
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+2
[4fba245c] + ArrayInterface v2.1.0
[13072b0f] + AxisAlgorithms v1.0.0
[39de3d68] + AxisArrays v0.3.3
[76274a88] + Bijectors v0.4.0
[49dc2e85] + Calculus v0.5.1
[324d7699] + CategoricalArrays v0.7.4
[861a8166] + Combinatorics v1.0.0
[bbf7d656] + CommonSubexpressions v0.2.0
[34da2185] + Compat v2.2.0
[a93c6f00] + DataFrames v0.20.0
[e2d170a0] + DataValueInterfaces v1.0.0
[01453d9d] + DiffEqDiffTools v1.6.0
[163ba53b] + DiffResults v1.0.1
[b552c78f] + DiffRules v1.0.0
[31c24e10] + Distributions v0.21.11
[ced4e74d] + DistributionsAD v0.1.1
[7a1cc6ca] + FFTW v1.2.0
[f5851436] + FFTW_jll v3.3.9+3
[26cc04aa] + FiniteDifferences v0.9.0
[f6369f11] + ForwardDiff v0.10.8
[7869d1d1] + IRTools v0.2.3
[1d5cc7b8] + IntelOpenMP_jll v2018.0.3+0
[a98d9a8b] + Interpolations v0.12.5
[8197267c] + IntervalSets v0.3.2
[41ab1584] + InvertedIndices v1.0.0
[c8e1da08] + IterTools v1.3.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[5ab0869b] + KernelDensity v0.5.1
[6f1fad26] + Libtask v0.3.1
[d3d80556] + LineSearches v7.0.1
[c7f686f2] + MCMCChains v0.4.1
[856f044c] + MKL_jll v2019.0.117+0
[dbb5928d] + MappedArrays v0.2.2
[d41bc354] + NLSolversBase v7.5.0
[872c559c] + NNlib v0.6.0
[77ba4419] + NaNMath v0.3.3
[6fe1bfb0] + OffsetArrays v0.11.4
[4536629a] + OpenBLAS_jll v0.3.7+1
[429524aa] + Optim v0.19.7
[90014a1f] + PDMats v0.9.10
[69de0a69] + Parsers v0.3.10
[f27b6e38] + Polynomials v0.6.0
[2dfb63ee] + PooledArrays v0.5.2
[85a6dd25] + PositiveFactorizations v0.2.3
[1fd47b50] + QuadGK v2.3.1
[b3c3ace0] + RangeArrays v0.3.1
[c84ed2f1] + Ratios v0.3.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[ae029012] + Requires v1.0.0
[f2b01f46] + Roots v0.8.4
[992d4aef] + Showoff v0.3.1
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[a759f4b9] + TimerOutputs v0.5.3
[9f7883ad] + Tracker v0.2.3
[fce5fe82] + Turing v0.7.1
[b8865327] + UnicodePlots v1.1.0
[efce3f68] + WoodburyMatrices v0.4.1
[e88e6eb3] + Zygote v0.3.4
[700de1a5] + ZygoteRules v0.1.0
[8bb1440f] + DelimitedFiles
[9fa8497b] + Future
[a63ad114] + Mmap
[1a1011a3] + SharedArrays
[4607b0f0] + SuiteSparse
Building Libtask → `~/.julia/packages/Libtask/RjRkK/deps/build.log`
Path `/home/pkgeval/.julia/packages/Libtask/RjRkK` exists and looks like the correct package. Using existing path.
Updating `/tmp/jl_vPcgIc/Project.toml`
[6f1fad26] + Libtask v0.3.1 [`~/.julia/packages/Libtask/RjRkK`]
Updating `/tmp/jl_vPcgIc/Manifest.toml`
[6f1fad26] ~ Libtask v0.3.1 ⇒ v0.3.1 [`~/.julia/packages/Libtask/RjRkK`]
Building FFTW ───→ `~/.julia/packages/FFTW/qqcBj/deps/build.log`
Path `/home/pkgeval/.julia/packages/FFTW/qqcBj` exists and looks like the correct package. Using existing path.
Updating `/tmp/jl_uD348k/Project.toml`
[7a1cc6ca] + FFTW v1.2.0 [`~/.julia/packages/FFTW/qqcBj`]
Updating `/tmp/jl_uD348k/Manifest.toml`
[7a1cc6ca] ~ FFTW v1.2.0 ⇒ v1.2.0 [`~/.julia/packages/FFTW/qqcBj`]
Running sandbox
Status `/tmp/jl_DDHZ6D/Project.toml`
[0bf59076] AdvancedHMC v0.2.14 [`~/.julia/packages/AdvancedHMC/1ngch`]
[dce04be8] ArgCheck v1.0.1
[163ba53b] DiffResults v1.0.1
[31c24e10] Distributions v0.21.11
[f6369f11] ForwardDiff v0.10.8
[505f98c9] InplaceOps v0.3.0
[5078a376] LazyArrays v0.14.10
[d96e819e] Parameters v0.12.0
[92933f4c] ProgressMeter v1.2.0
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.3
[fce5fe82] Turing v0.7.1
[b8865327] UnicodePlots v1.1.0
[8ba89e20] Distributed
[37e2e46d] LinearAlgebra
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
┌ Warning: The current proposal will be rejected due to numerical error(s).
│ isfinite.((θ, r, ℓπ, ℓκ)) = (false, false, true, true)
└ @ AdvancedHMC ~/.julia/packages/AdvancedHMC/1ngch/src/hamiltonian.jl:45
┌ Warning: The current proposal will be rejected due to numerical error(s).
│ isfinite.((θ, r, ℓπ, ℓκ)) = (false, false, true, true)
└ @ AdvancedHMC ~/.julia/packages/AdvancedHMC/1ngch/src/hamiltonian.jl:45
┌ Info: Performance of step() v.s. steps()
│ n_steps = 10
│ t_step = 0.155086058
│ t_steps = 0.006510049
└ t_step / t_steps = 23.822563854742107
┌ Info: Finished 1000 adapation steps
│ adaptor = StanHMCAdaptor(n_adapts=1000, pc=DiagPreconditioner, ssa=NesterovDualAveraging(γ=0.05, t_0=10.0, κ=0.75, δ=0.8, state.ϵ=0.5499099388381461), init_buffer=75, term_buffer=50)
│ τ.integrator = Leapfrog(ϵ=0.55)
└ h.metric = DiagEuclideanMetric([0.35950404177463346, 0.757 ...])
┌ Info: Finished 5000 sampling steps for 1 chains in 1.148003007 (s)
│ h = Hamiltonian(metric=DiagEuclideanMetric([0.35950404177463346, 0.757 ...]))
│ τ = NUTS{MultinomialTS,Generalised}(integrator=Leapfrog(ϵ=0.55), max_depth=10), Δ_max=1000.0)
│ EBFMI_est = 4855.7927642314535
└ average_acceptance_rate = 0.9138340808533925
[ Info: Adaptation tests for NUTS{MultinomialTS, Original} with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for HMCDA with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Generalised} with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{MultinomialTS, Generalised} with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for HMC with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Original} with TemperedLeapfrog on DiagEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{MultinomialTS, Original} with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for HMCDA with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Generalised} with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{MultinomialTS, Generalised} with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for HMC with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Original} with TemperedLeapfrog on DenseEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{MultinomialTS, Original} with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for HMCDA with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Generalised} with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{MultinomialTS, Generalised} with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for HMC with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for NUTS{SliceTS, Original} with TemperedLeapfrog on UnitEuclideanMetric are skipped
[ Info: Adaptation tests for HMCDA with NesterovDualAveraging are skipped
Scalabiliry of multiple chains
┌────────────────────────────────────────┐
5 │⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡎⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│ matrix parallism
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢰⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│ seperate
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⢆⠀│
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⠤⠊⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢸⢣⠀⢀⠎⠈⢆│
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡸⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡎⠀⢣⡜⠀⠀⠈│
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡜⢇⠀⢰⠁⠀⠀⠁⠀⠀⠀│
│⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡎⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡜⠀⠈⢆⡎⠀⠀⠀⠀⠀⠀⠀│
Time (s) │⠀⠀⠀⠀⠀⠀⠀⠀⠀⡸⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⢆⠀⠀⡠⠔⠊⠀⠀⠀⠘⠃⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⠀⠀⠀⠀⠀⠀⢠⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⠃⠀⠑⠎⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⠀⠀⠀⠀⠀⠀⡎⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡠⠇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⠀⠀⠀⠀⠀⡸⠀⠀⠀⠀⠀⡠⠒⠒⠒⠒⠊⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⠀⠀⠀⠀⢰⠁⠀⡠⠢⠤⠎⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⢆⠀⠀⢠⠇⠀⡰⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
│⠀⠀⢌⢆⢠⡣⠒⠊⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
1 │⠀⠀⠀⠙⠏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀│
└────────────────────────────────────────┘
0 20
Num of chains
Test Summary: | Pass Total
AdvancedHMC | 2269 2269
Testing AdvancedHMC tests passed