Closed FalkoSp closed 2 years ago
Hi, sorry for the delay on this. This is really strange, especially since StructArrays in included as a dependency for SampleChainsDynamicHMC
. Does the package manager otherwise seem happy? Have you tried ]resolve
?
Oh, I guess the error is coming from TupleVectors, but StructArrays is a dependency there too. Can you do status -m
?
Btw, SampleChainsDynamicHMC gives a warning.
julia> using SampleChainsDynamicHMC
[ Info: Precompiling BenchmarkTools [6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf]
┌ Warning: Package Soss does not have SampleChainsDynamicHMC in its dependencies:
│ - If you have Soss checked out for development and have
│ added SampleChainsDynamicHMC as a dependency but haven't updated your primary
│ environment's manifest file, try `Pkg.resolve()`.
│ - Otherwise you may need to report an issue with Soss
└ Loading SampleChainsDynamicHMC into Soss from project dependency, future warnings for Soss are suppressed.
status -m gives
(sosstest) pkg> status -m
Status `C:\projects\sosstest\Manifest.toml`
[c3fe647b] AbstractAlgebra v0.15.1
[398f06c4] AbstractLattices v0.2.1
[1520ce14] AbstractTrees v0.3.4
[7d9f7c33] Accessors v0.1.4
[79e6a3ab] Adapt v3.3.1
[dce04be8] ArgCheck v2.1.0
[4fba245c] ArrayInterface v3.1.17
[4c555306] ArrayLayouts v0.7.3
[65a8f2f4] ArraysOfArrays v0.5.3
[198e06fe] BangBang v0.3.31
[6e4b80f9] BenchmarkTools v0.7.0
[336ed68f] CSV v0.8.5
[49dc2e85] Calculus v0.5.1
[d360d2e6] ChainRulesCore v1.3.0
[35d6a980] ColorSchemes v3.14.0
[3da002f7] ColorTypes v0.11.0
[5ae59095] Colors v0.12.8
[861a8166] Combinatorics v1.0.2
[bbf7d656] CommonSubexpressions v0.3.0
[34da2185] Compat v3.32.0
[a33af91c] CompositionsBase v0.1.1
[2569d6c7] ConcreteStructs v0.2.2
[187b0558] ConstructionBase v1.3.0
[d38c429a] Contour v0.5.7
[a8cc5b0e] Crayons v4.0.4
[9a962f9c] DataAPI v1.7.0
[a93c6f00] DataFrames v1.2.2
[864edb3b] DataStructures v0.18.10
[e2d170a0] DataValueInterfaces v1.0.0
[163ba53b] DiffResults v1.0.3
[b552c78f] DiffRules v1.3.0
[31c24e10] Distributions v0.24.18
[ffbed154] DocStringExtensions v0.8.5
[bbc10e6e] DynamicHMC v3.1.0
[6c76993d] DynamicIterators v0.4.2
[fdbdab4c] ElasticArrays v1.2.9
[e2ba6199] ExprTools v0.1.6
[c87230d0] FFMPEG v0.4.1
[1a297f60] FillArrays v0.11.9
[6a86dc24] FiniteDiff v2.8.1
[53c48c17] FixedPointNumbers v0.8.4
[b67e1e5a] FlexLinearAlgebra v0.1.0
[59287772] Formatting v0.4.2
[f6369f11] ForwardDiff v0.10.19
[28b8d3ca] GR v0.58.1
[6b9d7cbe] GeneralizedGenerated v0.3.2
[5c1252a2] GeometryBasics v0.3.12
[86223c79] Graphs v0.10.3
[42e2da0e] Grisu v1.0.2
[cd3eb016] HTTP v0.9.13
[7869d1d1] IRTools v0.4.3
[615f187c] IfElse v0.1.0
[4858937d] InfiniteArrays v0.11.2
[e1ba4f0e] Infinities v0.1.0
[83e8ac13] IniFile v0.5.0
[22cec73e] InitialValues v0.2.10
[d8418881] Intervals v1.5.0
[41ab1584] InvertedIndices v1.0.0
[92d709cd] IrrationalConstants v0.1.0
[c8e1da08] IterTools v1.3.0
[82899510] IteratorInterfaceExtensions v1.0.0
[692b3bcd] JLLWrappers v1.3.0
[682c06a0] JSON v0.21.2
[b14d175d] JuliaVariables v0.2.4
[4d827475] KeywordCalls v0.2.2
[b964fa9f] LaTeXStrings v1.2.1
[2ee39098] LabelledArrays v1.6.4
[23fbe1c1] Latexify v0.15.6
[5078a376] LazyArrays v0.21.15
[9c8b4983] LightXML v0.9.0
[d3d80556] LineSearches v7.1.1
[9b3f67b0] LinearAlgebraX v0.1.9
[6fdf6af0] LogDensityProblems v0.10.6
[2ab3a3ac] LogExpFunctions v0.3.0
[6e857e4b] MCMCDiagnostics v0.3.0
[d8e11817] MLStyle v0.4.10
[1914dd2f] MacroTools v0.5.7
[dbb5928d] MappedArrays v0.3.0
[a3b82374] MatrixFactorizations v0.8.4
[739be429] MbedTLS v1.0.3
[eadaa1a4] MeasureTheory v0.10.1
[eff96d63] Measurements v2.6.0
[442fdcdd] Measures v0.3.1
[e1d29d7a] Missings v1.0.0
[78c3b35d] Mocking v0.7.2
[7475f97c] Mods v1.3.1
[3b2b4ff1] Multisets v0.4.2
[d41bc354] NLSolversBase v7.8.1
[77ba4419] NaNMath v0.3.5
[71a1bf82] NameResolution v0.1.5
[d9ec5142] NamedTupleTools v0.13.7
[a734d2a7] NestedTuples v0.3.6
[6fe1bfb0] OffsetArrays v1.10.5
[429524aa] Optim v1.4.1
[bac558e1] OrderedCollections v1.4.1
[90014a1f] PDMats v0.11.1
[d96e819e] Parameters v0.12.2
[69de0a69] Parsers v1.1.2
[2ae35dd2] Permutations v0.4.8
[ccf2f8ad] PlotThemes v2.0.1
[995b91a9] PlotUtils v1.0.11
[91a5bcdd] Plots v1.20.1
[f27b6e38] Polynomials v1.2.1
[2dfb63ee] PooledArrays v1.2.1
[85a6dd25] PositiveFactorizations v0.2.4
[21216c6a] Preferences v1.2.2
[8162dcfd] PrettyPrint v0.2.0
[08abe8d2] PrettyTables v1.1.0
[27ebfcd6] Primes v0.5.0
[92933f4c] ProgressMeter v1.7.1
[1fd47b50] QuadGK v2.4.1
[fb686558] RandomExtensions v0.4.3
[3cdcf5f2] RecipesBase v1.1.1
[01d81517] RecipesPipeline v0.3.4
[189a3867] Reexport v1.1.0
[ae029012] Requires v1.1.3
[286e9d63] RingLists v0.2.6
[79098fc4] Rmath v0.7.0
[7e49a35a] RuntimeGeneratedFunctions v0.5.3
[754583d1] SampleChains v0.5.0
[6d9fd711] SampleChainsDynamicHMC v0.3.3
[6c6a2e73] Scratch v1.1.0
[91c51154] SentinelArrays v1.3.6
[efcf1570] Setfield v0.7.1
[992d4aef] Showoff v1.0.3
[55797a34] SimpleGraphs v0.7.9
[ec83eff0] SimplePartitions v0.3.0
[cc47b68c] SimplePolynomials v0.2.7
[b2aef97b] SimplePosets v0.1.4
[a6525b86] SimpleRandom v0.3.1
[a2af1166] SortingAlgorithms v1.0.1
[8ce77f84] Soss v0.20.2
[276daf66] SpecialFunctions v1.6.1
[aedffcd0] Static v0.2.5
[90137ffa] StaticArrays v1.2.12
[82ae8749] StatsAPI v1.0.0
[2913bbd2] StatsBase v0.33.9
[4c63d2b9] StatsFuns v0.9.9
[09ab397b] StructArrays v0.5.1
[fc9b0551] SymbolicCodegen v0.2.2
[d1185830] SymbolicUtils v0.11.0
[3783bdb8] TableTraits v1.0.1
[bd369af6] Tables v1.5.0
[f269a46b] TimeZones v1.5.6
[a759f4b9] TimerOutputs v0.5.12
[2c80a279] Trajectories v0.2.2
[84d833dd] TransformVariables v0.4.1
[410a4b4d] Tricks v0.1.4
[bc48ee85] Tullio v0.3.2
[615932cf] TupleVectors v0.1.0
[5c2747f8] URIs v1.3.0
[3a884ed6] UnPack v1.0.2
[c4a57d5a] UnsafeArrays v1.0.3
[700de1a5] ZygoteRules v0.2.1
[6e34b625] Bzip2_jll v1.0.6+5
[83423d85] Cairo_jll v1.16.0+6
[5ae413db] EarCut_jll v2.1.5+1
[2e619515] Expat_jll v2.2.10+0
[b22a6f82] FFMPEG_jll v4.3.1+4
[a3f928ae] Fontconfig_jll v2.13.1+14
[d7e528f0] FreeType2_jll v2.10.1+5
[559328eb] FriBidi_jll v1.0.10+0
[0656b61e] GLFW_jll v3.3.5+0
[d2c73de3] GR_jll v0.58.1+0
[78b55507] Gettext_jll v0.21.0+0
[7746bdde] Glib_jll v2.68.3+0
[aacddb02] JpegTurbo_jll v2.1.0+0
[c1c5ebd0] LAME_jll v3.100.1+0
[dd4b983a] LZO_jll v2.10.1+0
[dd192d2f] LibVPX_jll v1.10.0+0
[e9f186c6] Libffi_jll v3.2.2+0
[d4300ac3] Libgcrypt_jll v1.8.7+0
[7e76a0d4] Libglvnd_jll v1.3.0+3
[7add5ba3] Libgpg_error_jll v1.42.0+0
[94ce4f54] Libiconv_jll v1.16.1+1
[4b2f31a3] Libmount_jll v2.35.0+0
[89763e89] Libtiff_jll v4.3.0+0
[38a345b3] Libuuid_jll v2.36.0+0
[e7412a2a] Ogg_jll v1.3.5+0
[458c3c95] OpenSSL_jll v1.1.10+0
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[91d4177d] Opus_jll v1.3.2+0
[2f80f16e] PCRE_jll v8.44.0+0
[30392449] Pixman_jll v0.40.1+0
[ea2cea3b] Qt5Base_jll v5.15.3+0
[f50d1b31] Rmath_jll v0.3.0+0
[a2964d1f] Wayland_jll v1.19.0+0
[2381bf8a] Wayland_protocols_jll v1.18.0+4
[02c8fc9c] XML2_jll v2.9.12+0
[aed1982a] XSLT_jll v1.1.34+0
[4f6342f7] Xorg_libX11_jll v1.6.9+4
[0c0b7dd1] Xorg_libXau_jll v1.0.9+4
[935fb764] Xorg_libXcursor_jll v1.2.0+4
[a3789734] Xorg_libXdmcp_jll v1.1.3+4
[1082639a] Xorg_libXext_jll v1.3.4+4
[d091e8ba] Xorg_libXfixes_jll v5.0.3+4
[a51aa0fd] Xorg_libXi_jll v1.7.10+4
[d1454406] Xorg_libXinerama_jll v1.1.4+4
[ec84b674] Xorg_libXrandr_jll v1.5.2+4
[ea2f1a96] Xorg_libXrender_jll v0.9.10+4
[14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
[c7cfdc94] Xorg_libxcb_jll v1.13.0+3
[cc61e674] Xorg_libxkbfile_jll v1.1.0+4
[12413925] Xorg_xcb_util_image_jll v0.4.0+1
[2def613f] Xorg_xcb_util_jll v0.4.0+1
[975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
[0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
[c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
[35661453] Xorg_xkbcomp_jll v1.4.2+4
[33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
[c5fb5394] Xorg_xtrans_jll v1.4.0+3
[3161d3a3] Zstd_jll v1.5.0+0
[0ac62f75] libass_jll v0.14.0+4
[f638f0a6] libfdk_aac_jll v0.1.6+4
[b53b4c65] libpng_jll v1.6.38+0
[f27f6e37] libvorbis_jll v1.3.7+0
[1270edf5] x264_jll v2020.7.14+2
[dfaa095f] x265_jll v3.0.0+3
[d8fb68d0] xkbcommon_jll v0.9.1+5
[0dad84c5] ArgTools
[56f22d72] Artifacts
[2a0f44e3] Base64
[ade2ca70] Dates
[8bb1440f] DelimitedFiles
[8ba89e20] Distributed
[f43a241f] Downloads
[9fa8497b] Future
[b77e0a4c] InteractiveUtils
[4af54fe1] LazyArtifacts
[b27032c2] LibCURL
[76f85450] LibGit2
[8f399da3] Libdl
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[d6f4376e] Markdown
[a63ad114] Mmap
[ca575930] NetworkOptions
[44cfe95a] Pkg
[de0858da] Printf
[3fa0cd96] REPL
[9a3f8284] Random
[ea8e919c] SHA
[9e88b42a] Serialization
[1a1011a3] SharedArrays
[6462fe0b] Sockets
[2f01184e] SparseArrays
[10745b16] Statistics
[4607b0f0] SuiteSparse
[fa267f1f] TOML
[a4e569a6] Tar
[8dfed614] Test
[cf7118a7] UUIDs
[4ec0a83e] Unicode
[e66e0078] CompilerSupportLibraries_jll
[deac9b47] LibCURL_jll
[29816b5a] LibSSH2_jll
[c8ffd9c3] MbedTLS_jll
[14a3606d] MozillaCACerts_jll
[83775a58] Zlib_jll
[8e850ede] nghttp2_jll
[3f19e933] p7zip_jll
(sosstest) pkg>
Ah, and when I directly include the code from https://github.com/cscherrer/Soss.jl/blob/master/src/samplechains/dynamichmc.jl, it works completely fine. Even in Pluto. I don't see why.
begin
using Random
using SampleChainsDynamicHMC:DynamicHMCConfig
function sample(rng::AbstractRNG,
m,#::ConditionalModel,
config::DynamicHMCConfig,
nsamples::Int=1000,
nchains::Int=4)
ℓ(x) = Soss.logdensity(m, x)
tr = xform(m)
chains = newchain(rng, nchains, config, ℓ, tr)
sample!(chains, nsamples - 1)
return chains
end
function sample(
m,#::ConditionalModel,
config::DynamicHMCConfig,
nsamples::Int=1000,
nchains::Int=4)
sample(Random.GLOBAL_RNG, m, config, nsamples, nchains)
end
end
Hi @FalkoSp , I just realized this hasn't been resolved. Could you update your packages and try again? TupleVectors is currently at 0.1.2, so it's best to make sure you can use that release
@sethaxen may have fixed the problem in https://github.com/cscherrer/Soss.jl/pull/300
@FalkoSp @gzagatti could you try again with the latest version please?
Yes, that should fix the problem. I'd seen the error message for a while, but it caused Pluto to completely fail, which is what led me to fix it. Now I'm using Soss in Pluto with no problems.
This is great!!!
@FalkoSp and @gzagatti, if you can confirm when you have a chance, we can close this issue :)
Thank you @sethaxen, thank you @cscherrer - works now!
Hi, I'm slowly following the JuliaCon21 video. The call to sample(..) fails.
(I had another issue before that it wasn't found in a Pluto notebook. I'll try to reproduce that when I have it running without Pluto.)
The call to sample in the last line gives
What am I doing wrong?
Kind greetings, f.