Extensions: pre-compilation fails if more than one extension

[omlins]

MWE: https://github.com/omlins/ParallelStencil.jl/pull/130/files#diff-4fd906dc9bd8d9fc59a9eab475a5119bbd4505ba46a091bede7d8cec6cabe8b8 In brief this MWE contains:

name = "Diffusion3D_minimal"
uuid = "91637811-9d05-4227-81a2-fe1d069b6ecb"
authors = ["Samuel Omlin <samuel.omlin@cscs.ch>"]
version = "0.1.0"

[deps]
ParallelStencil = "94395366-693c-11ea-3b26-d9b7aac5d958"

[compat]
ParallelStencil = ">= 0.4.0"

[weakdeps]
AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"

[extensions]
D3D_AMDGPUExt = "AMDGPU"
D3D_CUDAExt = "CUDA"

and:

module Diffusion3D_minimal
    using ParallelStencil
    f() = return
end

module D3D_CUDAExt
    import Diffusion3D_minimal
    g() = return
end

module D3D_AMDGPUExt
    import Diffusion3D_minimal
    h() = return
end

The error is the following:

julia> Base.compilecache(Base.PkgId(Base.UUID("94395366-693c-11ea-3b26-d9b7aac5d958"), "ParallelStencil")); Base.compilecache(Base.PkgId(Base.UUID("91637811-9d05-4227-81a2-fe1d069b6ecb"), "Diffusion3D_minimal")); Base.compilecache(Base.PkgId(Base.UUID("38fae68b-b861-5d3c-b423-1a3f5200d4e2"), "D3D_CUDAExt"))
[ Info: Precompiling ParallelStencil [94395366-693c-11ea-3b26-d9b7aac5d958]
[ Info: Precompiling Diffusion3D_minimal [91637811-9d05-4227-81a2-fe1d069b6ecb]
[ Info: Precompiling D3D_CUDAExt [38fae68b-b861-5d3c-b423-1a3f5200d4e2]
┌ Warning: Module D3D_CUDAExt with build ID ffffffff-ffff-ffff-000e-c267534cc71f is missing from the cache.
│ This may mean D3D_CUDAExt [38fae68b-b861-5d3c-b423-1a3f5200d4e2] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1942
┌ Error: Error during loading of extension D3D_CUDAExt of Diffusion3D_minimal, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│    Stacktrace:
│      [1] _require(pkg::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1946
│      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1806
│      [3] #invoke_in_world#3
│        @ Base ./essentials.jl:921 [inlined]
│      [4] invoke_in_world
│        @ Base ./essentials.jl:918 [inlined]
│      [5] _require_prelocked
│        @ Base ./loading.jl:1797 [inlined]
│      [6] _require_prelocked
│        @ Base ./loading.jl:1796 [inlined]
│      [7] run_extension_callbacks(extid::Base.ExtensionId)
│        @ Base ./loading.jl:1289
│      [8] run_extension_callbacks(pkgid::Base.PkgId)
│        @ Base ./loading.jl:1324
│      [9] run_package_callbacks(modkey::Base.PkgId)
│        @ Base ./loading.jl:1158
│     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1813
│     [11] #invoke_in_world#3
│        @ Base ./essentials.jl:921 [inlined]
│     [12] invoke_in_world
│        @ Base ./essentials.jl:918 [inlined]
│     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1797
│     [14] macro expansion
│        @ Base ./loading.jl:1784 [inlined]
│     [15] macro expansion
│        @ Base ./lock.jl:267 [inlined]
│     [16] __require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1747
│     [17] #invoke_in_world#3
│        @ Base ./essentials.jl:921 [inlined]
│     [18] invoke_in_world
│        @ Base ./essentials.jl:918 [inlined]
│     [19] require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1740
│     [20] include
│        @ Base ./Base.jl:489 [inlined]
│     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│        @ Base ./loading.jl:2216
│     [22] top-level scope
│        @ stdin:3
│     [23] eval
│        @ Core ./boot.jl:383 [inlined]
│     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│        @ Base ./loading.jl:2070
│     [25] include_string
│        @ Base ./loading.jl:2080 [inlined]
│     [26] exec_options(opts::Base.JLOptions)
│        @ Base ./client.jl:316
│     [27] _start()
│        @ Base ./client.jl:552
└ @ Base loading.jl:1295
("/scratch/snx3000tds/julia/omlins/daint-gpu/compiled/v1.10/D3D_CUDAExt/owmDu_K34O8.ji", "/scratch/snx3000tds/julia/omlins/daint-gpu/compiled/v1.10/D3D_CUDAExt/owmDu_K34O8.so")

If one of the two extensions is deactivated by commenting the corresponding line in the project.toml (e.g. #D3D_AMDGPUExt = "AMDGPU" to deactivate the AMDGPU extension), then the problem disappears, e.g.:

julia> Base.compilecache(Base.PkgId(Base.UUID("94395366-693c-11ea-3b26-d9b7aac5d958"), "ParallelStencil")); Base.compilecache(Base.PkgId(Base.UUID("91637811-9d05-4227-81a2-fe1d069b6ecb"), "Diffusion3D_minimal")); Base.compilecache(Base.PkgId(Base.UUID("38fae68b-b861-5d3c-b423-1a3f5200d4e2"), "D3D_CUDAExt"))
[ Info: Precompiling ParallelStencil [94395366-693c-11ea-3b26-d9b7aac5d958]
[ Info: Precompiling Diffusion3D_minimal [91637811-9d05-4227-81a2-fe1d069b6ecb]
[ Info: Precompiling D3D_CUDAExt [38fae68b-b861-5d3c-b423-1a3f5200d4e2]
("/scratch/snx3000tds/julia/omlins/daint-gpu/compiled/v1.10/D3D_CUDAExt/owmDu_K34O8.ji", "/scratch/snx3000tds/julia/omlins/daint-gpu/compiled/v1.10/D3D_CUDAExt/owmDu_K34O8.so")

Note that ParallelStencil does not contain any module __init__ definition.

The problem appears with both tested julia versions, 1.9.4 and 1.10.

[omlins]

@KristofferC

[omlins]

Opening instead an issue on Pkg.jl: https://github.com/JuliaLang/Pkg.jl/issues/3728

[KristofferC]

There is not really any Pkg code being executed here so this repo is actually probably better.

[omlins]

@KristofferC Do you have any idea what is wrong here?

[omlins]

@KristofferC : could the reason for the failure be that ParallelStencil itself does not yet use extensions and has both GPU packages as normal dependencies? (This will change shortly and ParallelStencil will have the GPU packages as week dependencies)

[KristofferC]

I have not looked into this one yet.

[lassepe]

Duplicate of https://github.com/JuliaLang/julia/issues/52132?

[KristofferC]

I don't think so. That's related to stdlibs in the sysimage.

[ViralBShah]

I ran into this when just doing Pkg.test("Sundials").

[aplavin]

Also, see more examples in https://github.com/JuliaLang/julia/issues/52132 (closed as a duplicate). At least in those cases, everything loads and works correctly – but big "errors"/warnings look scary to users.

[alecloudenback]

I'm also running into this on 1.10.2 on Mac Arm64 and Ubutunu x_86_64

[alecloudenback]

Update: I deleted my packages and compiled subfolders in my .julia and I don't see the issue anymore.

[KristofferC]

I looked at this now and this is identical to https://github.com/JuliaLang/julia/issues/53081. The issue is the following:

• ParallelStencil depends on AMDGPU and CUDA.
• The package depends on ParallelStencil and has extensions that gets loaded from AMDGPU and CUDA:

So what happens when the package loads:

• Package starts loading
• It loads ParallelStencil
• ParallelStencil loads AMDGPU
• Our extension for AMDGPU starts loading
  • The extension loads the package
  • The package loads ParallelStencil
  • ParallelStencil loads CUDA
  • The extension for CUDA starts loading
  • The extension loads the package
  • The package loads ParallelStencil
  • ParallelStencil loads AMDGPU
  • Our extension for AMDGPU starts loading

As you see, we are now in a cycle where the extensions end up loading each other back and forth. This will happen whenever:

• You have two or more extensions
• The triggers for these extensions are in the set of your transitive dependencies.

https://github.com/JuliaLang/julia/pull/53112 was an attempt to fix this but I have heard some uncertainty from other people if that way is correct.

[omlins]

@KristofferC : thanks a lot for looking into this.

ParallelStencil does now not anymore have AMDGPU and CUDA as fixed dependencies, but as weak dependencies - the corresponding functionality has been moved into extensions (merged into main: https://github.com/omlins/ParallelStencil.jl/pull/144). Nevertheless, the issue remains the same. @KristofferC : Does your explanation from above also apply to this case?

[omlins]

@KristofferC : thanks a lot for looking into this.

ParallelStencil does now not anymore have AMDGPU and CUDA as fixed dependencies, but as weak dependencies - the corresponding functionality has been moved into extensions (merged into main: omlins/ParallelStencil.jl#144). Nevertheless, the issue remains the same. @KristofferC : Does your explanation from above also apply to this case?

@KristofferC : Here is the error message with Julia 1.10.2:

Precompiling project...
  2 dependencies successfully precompiled in 19 seconds. 111 already precompiled.
┌ Warning: Module D3D_AMDGPUExt with build ID ffffffff-ffff-ffff-002f-4a235d13a0fd is missing from the cache.
│ This may mean D3D_AMDGPUExt [9a3b1ebd-8fe2-5d0d-b584-c82f9b26749a] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1948
┌ Error: Error during loading of extension D3D_AMDGPUExt of Diffusion3D_minimal, use `Base.retry_load_extensions()` to retry.
│   exception =
│    1-element ExceptionStack:
│    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│    Stacktrace:
│      [1] _require(pkg::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1952
│      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│        @ Base ./loading.jl:1812
│      [3] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│      [4] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│      [5] _require_prelocked
│        @ ./loading.jl:1803 [inlined]
│      [6] _require_prelocked
│        @ ./loading.jl:1802 [inlined]
│      [7] run_extension_callbacks(extid::Base.ExtensionId)
│        @ Base ./loading.jl:1295
│      [8] run_extension_callbacks(pkgid::Base.PkgId)
│        @ Base ./loading.jl:1330
│      [9] run_package_callbacks(modkey::Base.PkgId)
│        @ Base ./loading.jl:1164
│     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1819
│     [11] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [12] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│        @ Base ./loading.jl:1803
│     [14] macro expansion
│        @ ./loading.jl:1790 [inlined]
│     [15] macro expansion
│        @ ./lock.jl:267 [inlined]
│     [16] __require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1753
│     [17] #invoke_in_world#3
│        @ ./essentials.jl:926 [inlined]
│     [18] invoke_in_world
│        @ ./essentials.jl:923 [inlined]
│     [19] require(into::Module, mod::Symbol)
│        @ Base ./loading.jl:1746
│     [20] include
│        @ ./Base.jl:495 [inlined]
│     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│        @ Base ./loading.jl:2222
│     [22] top-level scope
│        @ stdin:3
│     [23] eval
│        @ ./boot.jl:385 [inlined]
│     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│        @ Base ./loading.jl:2076
│     [25] include_string
│        @ ./loading.jl:2086 [inlined]
│     [26] exec_options(opts::Base.JLOptions)
│        @ Base ./client.jl:316
│     [27] _start()
│        @ Base ./client.jl:552
└ @ Base loading.jl:1301

[lmiq]

I have a similar error (I think), which can be reproduced by (in 1.10.2):

julia> import Pkg; Pkg.add(["Plots", "MolSimToolkit"])

MolSimToolkit.jl has some simple extensions to provide plotting recipes. I get the following error:

(jl_9T3sAS) pkg> add Plots, MolSimToolkit
   Resolving package versions...
   Installed Missings ─── v1.2.0
   Installed ColorTypes ─ v0.11.5
    Updating `/tmp/jl_9T3sAS/Project.toml`
  [054db54f] + MolSimToolkit v1.12.5
  [91a5bcdd] + Plots v1.40.3
    Updating `/tmp/jl_9T3sAS/Manifest.toml`
  [79e6a3ab] + Adapt v4.0.4
  [4fba245c] + ArrayInterface v7.9.0
  [a963bdd2] + AtomsBase v0.3.5
  [d1d4a3ce] + BitFlags v0.1.8
  [49dc2e85] + Calculus v0.5.1
  [69e1c6dd] + CellListMap v0.8.26
  [46823bd8] + Chemfiles v0.10.41
  [944b1d66] + CodecZlib v0.7.4
  [35d6a980] + ColorSchemes v3.24.0
  [3da002f7] + ColorTypes v0.11.5
  [c3611d14] + ColorVectorSpace v0.10.0
  [5ae59095] + Colors v0.12.10
  [bbf7d656] + CommonSubexpressions v0.3.0
  [34da2185] + Compat v4.14.0
  [f0e56b4a] + ConcurrentUtilities v2.4.1
  [187b0558] + ConstructionBase v1.5.5
  [d38c429a] + Contour v0.6.3
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.18.18
  [8bb1440f] + DelimitedFiles v1.9.1
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [31c24e10] + Distributions v0.25.107
  [ffbed154] + DocStringExtensions v0.9.3
  [fa6b7ba4] + DualNumbers v0.6.8
  [fde71243] + EasyFit v0.6.6
  [460bff9d] + ExceptionUnwrapping v0.1.10
  [c87230d0] + FFMPEG v0.4.1
  [1a297f60] + FillArrays v1.10.0
  [6a86dc24] + FiniteDiff v2.23.0
  [53c48c17] + FixedPointNumbers v0.8.4
  [1fa38f19] + Format v1.3.7
  [f6369f11] + ForwardDiff v0.10.36
  [28b8d3ca] + GR v0.73.3
  [42e2da0e] + Grisu v1.0.2
  [cd3eb016] + HTTP v1.10.5
  [34004b35] + HypergeometricFunctions v0.3.23
  [92d709cd] + IrrationalConstants v0.2.2
  [1019f520] + JLFzf v0.1.7
  [692b3bcd] + JLLWrappers v1.5.0
  [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.3.1
  [23fbe1c1] + Latexify v0.16.2
  [2ab3a3ac] + LogExpFunctions v0.3.27
  [e6f89c97] + LoggingExtras v1.0.3
  [2fda8390] + LsqFit v0.15.0
  [1914dd2f] + MacroTools v0.5.13
  [739be429] + MbedTLS v1.1.9
  [442fdcdd] + Measures v0.3.2
  [e1d29d7a] + Missings v1.2.0
  [054db54f] + MolSimToolkit v1.12.5
  [d41bc354] + NLSolversBase v7.8.3
  [77ba4419] + NaNMath v1.0.2
  [6fe1bfb0] + OffsetArrays v1.13.0
  [4d8831e6] + OpenSSL v1.4.2
  [bac558e1] + OrderedCollections v1.6.3
  [e29189f1] + PDBTools v1.5.1
  [90014a1f] + PDMats v0.11.31
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.1
  [7b2266bf] + PeriodicTable v1.2.1
  [b98c9c47] + Pipe v1.3.0
  [ccf2f8ad] + PlotThemes v3.1.0
  [995b91a9] + PlotUtils v1.4.1
  [91a5bcdd] + Plots v1.40.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [92933f4c] + ProgressMeter v1.10.0
  [1fd47b50] + QuadGK v2.9.4
  [3cdcf5f2] + RecipesBase v1.3.4
  [01d81517] + RecipesPipeline v0.6.12
  [189a3867] + Reexport v1.2.2
  [05181044] + RelocatableFolders v1.0.1
  [ae029012] + Requires v1.3.0
  [79098fc4] + Rmath v0.7.1
  [6c6a2e73] + Scratch v1.2.1
  [efcf1570] + Setfield v1.1.1
  [992d4aef] + Showoff v1.0.3
  [777ac1f9] + SimpleBufferStream v1.1.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.3.1
  [90137ffa] + StaticArrays v1.9.3
  [1e83bf80] + StaticArraysCore v1.4.2
  [82ae8749] + StatsAPI v1.7.0
  [2913bbd2] + StatsBase v0.34.3
  [4c63d2b9] + StatsFuns v1.3.1
  [62fd8b95] + TensorCore v0.1.1
  [1c621080] + TestItems v0.1.1
  [3bb67fe8] + TranscodingStreams v0.10.7
  [5c2747f8] + URIs v1.5.1
  [3a884ed6] + UnPack v1.0.2
  [1cfade01] + UnicodeFun v0.4.1
  [1986cc42] + Unitful v1.19.0
  [a7773ee8] + UnitfulAtomic v1.0.0
  [45397f5d] + UnitfulLatexify v1.6.3
  [41fe7b60] + Unzip v0.2.0
  [6e34b625] + Bzip2_jll v1.0.8+1
  [83423d85] + Cairo_jll v1.18.0+1
  [78a364fa] + Chemfiles_jll v0.10.4+0
  [2702e6a9] + EpollShim_jll v0.0.20230411+0
  [2e619515] + Expat_jll v2.5.0+0
⌅ [b22a6f82] + FFMPEG_jll v4.4.4+1
  [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 v0.73.3+0
  [78b55507] + Gettext_jll v0.21.0+0
  [7746bdde] + Glib_jll v2.80.0+0
  [3b182d85] + Graphite2_jll v1.3.14+0
  [2e76f6c2] + HarfBuzz_jll v2.8.1+1
  [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 v2.39.3+0
⌅ [89763e89] + Libtiff_jll v4.5.1+1
  [38a345b3] + Libuuid_jll v2.39.3+1
  [e7412a2a] + Ogg_jll v1.3.5+1
  [458c3c95] + OpenSSL_jll v3.0.13+1
  [efe28fd5] + OpenSpecFun_jll v0.5.5+0
  [91d4177d] + Opus_jll v1.3.2+0
  [30392449] + Pixman_jll v0.42.2+0
  [c0090381] + Qt6Base_jll v6.5.3+1
  [f50d1b31] + Rmath_jll v0.4.0+0
  [a44049a8] + Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] + Wayland_jll v1.21.0+1
  [2381bf8a] + Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] + XML2_jll v2.12.6+0
  [aed1982a] + XSLT_jll v1.1.34+0
  [ffd25f8a] + XZ_jll v5.4.6+0
  [f67eecfb] + Xorg_libICE_jll v1.0.10+1
  [c834827a] + Xorg_libSM_jll v1.2.3+0
  [4f6342f7] + Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] + Xorg_libXau_jll v1.0.11+0
  [935fb764] + Xorg_libXcursor_jll v1.2.0+4
  [a3789734] + Xorg_libXdmcp_jll v1.1.4+0
  [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 v0.1.1+0
  [c7cfdc94] + Xorg_libxcb_jll v1.15.0+0
  [cc61e674] + Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] + Xorg_xcb_util_cursor_jll v0.1.4+0
  [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 v1.4.6+0
  [33bec58e] + Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] + Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] + Zstd_jll v1.5.6+0
  [35ca27e7] + eudev_jll v3.2.9+0
⌅ [214eeab7] + fzf_jll v0.43.0+0
  [1a1c6b14] + gperf_jll v3.1.1+0
  [a4ae2306] + libaom_jll v3.4.0+0
  [0ac62f75] + libass_jll v0.15.1+0
  [2db6ffa8] + libevdev_jll v1.11.0+0
  [f638f0a6] + libfdk_aac_jll v2.0.2+0
  [36db933b] + libinput_jll v1.18.0+0
  [b53b4c65] + libpng_jll v1.6.43+1
  [f27f6e37] + libvorbis_jll v1.3.7+1
  [009596ad] + mtdev_jll v1.1.6+0
  [1270edf5] + x264_jll v2021.5.5+0
  [dfaa095f] + x265_jll v3.5.0+0
  [d8fb68d0] + xkbcommon_jll v1.4.1+1
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [8ba89e20] + Distributed
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [9fa8497b] + Future
  [b77e0a4c] + InteractiveUtils
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.10.0
  [de0858da] + Printf
  [3fa0cd96] + REPL
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.0+0
  [deac9b47] + LibCURL_jll v8.4.0+0
  [e37daf67] + LibGit2_jll v1.6.4+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [05823500] + OpenLibm_jll v0.8.1+2
  [efcefdf7] + PCRE2_jll v10.42.0+1
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
  [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
Precompiling project...
  20 dependencies successfully precompiled in 51 seconds. 185 already precompiled.
  4 dependencies had output during precompilation:
┌ MolSimToolkit → MolSimStylePlotting
│  ┌ Warning: Module REMDPlotting with build ID ffffffff-ffff-ffff-0005-93c30d246efd is missing from the cache.
│  │ This may mean REMDPlotting [e2da7e33-71d8-5845-bdbe-2073996eaa79] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension REMDPlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
│  ┌ Warning: Module MolSimStylePlotting with build ID ffffffff-ffff-ffff-0005-93c2a8c870e5 is missing from the cache.
│  │ This may mean MolSimStylePlotting [47e5d35c-c2d0-5408-acd2-db5e4eb7937b] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension MolSimStylePlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
│  ┌ Warning: Module MolSimStylePlotting with build ID ffffffff-ffff-ffff-0005-93c2a8c870e5 is missing from the cache.
│  │ This may mean MolSimStylePlotting [47e5d35c-c2d0-5408-acd2-db5e4eb7937b] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension MolSimStylePlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
└  
┌ MolSimToolkit → REMDPlotting
│  ┌ Warning: Module REMDPlotting with build ID ffffffff-ffff-ffff-0005-93c03ce6c506 is missing from the cache.
│  │ This may mean REMDPlotting [e2da7e33-71d8-5845-bdbe-2073996eaa79] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension REMDPlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
│  ┌ Warning: Module REMDPlotting with build ID ffffffff-ffff-ffff-0005-93c03ce6c506 is missing from the cache.
│  │ This may mean REMDPlotting [e2da7e33-71d8-5845-bdbe-2073996eaa79] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension REMDPlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
│  ┌ Warning: Module BlockAveragesPlotting with build ID ffffffff-ffff-ffff-0005-93c0956d7fab is missing from the cache.
│  │ This may mean BlockAveragesPlotting [169be7d3-c844-588e-8a3f-7557bbfa2dc9] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension BlockAveragesPlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
└  
┌ MolSimToolkit
│  WARNING: using PDBTools.center_of_mass in module PackmolInputCreator conflicts with an existing identifier.
└  
┌ MolSimToolkit → BlockAveragesPlotting
│  ┌ Warning: Module BlockAveragesPlotting with build ID ffffffff-ffff-ffff-0005-93c1b6a1f29a is missing from the cache.
│  │ This may mean BlockAveragesPlotting [169be7d3-c844-588e-8a3f-7557bbfa2dc9] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension BlockAveragesPlotting of MolSimToolkit, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
└ 

[KristofferC]

On https://github.com/JuliaLang/julia/pull/53972 that prints

(jl_RqaGz1) pkg> precompile
┌ Warning: Circular dependency detected. Precompilation will be skipped for:
│   Base.PkgId(Base.UUID("47e5d35c-c2d0-5408-acd2-db5e4eb7937b"), "MolSimStylePlotting")
│   Base.PkgId(Base.UUID("e2da7e33-71d8-5845-bdbe-2073996eaa79"), "REMDPlotting")
│   Base.PkgId(Base.UUID("169be7d3-c844-588e-8a3f-7557bbfa2dc9"), "BlockAveragesPlotting")
└ @ Base.Precompilation precompilation.jl:555
Precompiling all packages...
  172 dependencies successfully precompiled in 95 seconds. 60 already precompiled. 3 skipped due to circular dependency.
  1 dependency had output during precompilation:
┌ MolSimToolkit
│  WARNING: using PDBTools.center_of_mass in module PackmolInputCreator conflicts with an existing identifier.
└  

I am not sure what exactly happens when those extensions actually load though.

[lmiq]

The extensions work without problems after loading.

I don't see any circular dependency there. In fact, the extensions depend on MolSimToolkit itself (the parent package) and on Plots.

[KristofferC]

All three of the extensions seem to have Plots as their trigger. So the cycle is the following:

1. BlockAveragesPlotting loads MolSimToolkit + Plots
2. This causes MolSimStylePlotting to load.
3. MolSimStylePlotting loads MolSimToolkit + Plots
4. This causes BlockAveragesPlotting to load
5. Go to 1.

I think you should fold all these into one extension.

[lmiq]

That's not clear from my development perspective, as "loading the extension" is not something one does manually in any moment, as what we do is to load the trigger packages. Probably some clarification is needed there.

[KristofferC]

An extension gets loaded when all its triggers (+ parent) get loaded. So if you have two extensions that both load the parent and the triggers they will try to load each other.

https://github.com/JuliaLang/julia/pull/53112 tries to stop this but it is unclear what is the best and right thing to do in situations like this.

[aplavin]

https://github.com/JuliaLang/julia/issues/52132 was closed as duplicate, so reporting on the current state here. The latest release (1.10) still prints a big scary "error" message, confusing users into thinking that something went wrong. Even though everything actually loads and works correctly. Beta (1.11) and nightly print a small warning instead, which seems more reasonable – even if the underlying issue cannot be fixed, at least let's not scare users :) Can that partial fix be backported to 1.10?

❯ JULIA_DEPOT_PATH=$(mktemp -d) julia         
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.4 (2024-06-04)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(v1.10) pkg> activate --temp
  Activating new project at `/var/folders/2j/9vtd991d201dbkh9dnx3wvy00000gq/T/jl_W3ekSA`

(jl_W3ekSA) pkg> add AccessorsExtra@0.1.71
  Installing known registries into `/var/folders/2j/9vtd991d201dbkh9dnx3wvy00000gq/T/tmp.Z5YtpFlNyH`
    Updating registry at `/var/folders/2j/9vtd991d201dbkh9dnx3wvy00000gq/T/tmp.Z5YtpFlNyH/registries/General.toml`
   Resolving package versions...
   Installed ConstructionBase ─ v1.5.5
   Installed Reexport ───────── v1.2.2
   Installed DataPipes ──────── v0.3.16
   Installed CompositionsBase ─ v0.1.2
   Installed MacroTools ─────── v0.5.13
   Installed AccessorsExtra ─── v0.1.71
   Installed InverseFunctions ─ v0.1.14
   Installed Accessors ──────── v0.1.36
    Updating `/private/var/folders/2j/9vtd991d201dbkh9dnx3wvy00000gq/T/jl_W3ekSA/Project.toml`
  [33016aad] + AccessorsExtra v0.1.71
    Updating `/private/var/folders/2j/9vtd991d201dbkh9dnx3wvy00000gq/T/jl_W3ekSA/Manifest.toml`
  [7d9f7c33] + Accessors v0.1.36
  [33016aad] + AccessorsExtra v0.1.71
  [a33af91c] + CompositionsBase v0.1.2
  [187b0558] + ConstructionBase v1.5.5
  [02685ad9] + DataPipes v0.3.16
  [3587e190] + InverseFunctions v0.1.14
  [1914dd2f] + MacroTools v0.5.13
  [189a3867] + Reexport v1.2.2
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [8dfed614] + Test
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [8e850b90] + libblastrampoline_jll v5.8.0+1
Precompiling project...
  14 dependencies successfully precompiled in 8 seconds
  2 dependencies had output during precompilation:
┌ AccessorsExtra → LinearAlgebraExt
│  ┌ Warning: Module LinearAlgebraExt with build ID ffffffff-ffff-ffff-0000-d08d4c3b6ca9 is missing from the cache.
│  │ This may mean LinearAlgebraExt [2e571e4a-e68d-5fe4-9022-ff2e7d6ac6d5] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension LinearAlgebraExt of AccessorsExtra, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
└  
┌ AccessorsExtra → TestExt
│  ┌ Warning: Module TestExt with build ID ffffffff-ffff-ffff-0000-d08d91da0575 is missing from the cache.
│  │ This may mean TestExt [69cf5fdc-2bf6-5cf1-837e-a22f5027a90f] does not support precompilation but is imported by a module that does.
│  └ @ Base loading.jl:1948
│  ┌ Error: Error during loading of extension TestExt of AccessorsExtra, use `Base.retry_load_extensions()` to retry.
│  │   exception =
│  │    1-element ExceptionStack:
│  │    Declaring __precompile__(false) is not allowed in files that are being precompiled.
│  │    Stacktrace:
│  │      [1] _require(pkg::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1952
│  │      [2] __require_prelocked(uuidkey::Base.PkgId, env::Nothing)
│  │        @ Base ./loading.jl:1812
│  │      [3] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │      [4] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │      [5] _require_prelocked
│  │        @ ./loading.jl:1803 [inlined]
│  │      [6] _require_prelocked
│  │        @ ./loading.jl:1802 [inlined]
│  │      [7] run_extension_callbacks(extid::Base.ExtensionId)
│  │        @ Base ./loading.jl:1295
│  │      [8] run_extension_callbacks(pkgid::Base.PkgId)
│  │        @ Base ./loading.jl:1330
│  │      [9] run_package_callbacks(modkey::Base.PkgId)
│  │        @ Base ./loading.jl:1164
│  │     [10] __require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1819
│  │     [11] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [12] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [13] _require_prelocked(uuidkey::Base.PkgId, env::String)
│  │        @ Base ./loading.jl:1803
│  │     [14] macro expansion
│  │        @ ./loading.jl:1790 [inlined]
│  │     [15] macro expansion
│  │        @ ./lock.jl:267 [inlined]
│  │     [16] __require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1753
│  │     [17] #invoke_in_world#3
│  │        @ ./essentials.jl:926 [inlined]
│  │     [18] invoke_in_world
│  │        @ ./essentials.jl:923 [inlined]
│  │     [19] require(into::Module, mod::Symbol)
│  │        @ Base ./loading.jl:1746
│  │     [20] include
│  │        @ ./Base.jl:495 [inlined]
│  │     [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
│  │        @ Base ./loading.jl:2222
│  │     [22] top-level scope
│  │        @ stdin:3
│  │     [23] eval
│  │        @ ./boot.jl:385 [inlined]
│  │     [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│  │        @ Base ./loading.jl:2076
│  │     [25] include_string
│  │        @ ./loading.jl:2086 [inlined]
│  │     [26] exec_options(opts::Base.JLOptions)
│  │        @ Base ./client.jl:316
│  │     [27] _start()
│  │        @ Base ./client.jl:552
│  └ @ Base loading.jl:1301
└  

(jl_W3ekSA) pkg>