GLMakie precompilation fails ( julia 1.10.2; WSL2)

lgmendes · September 3, 2024, 9:48am

Hi,

The precompilation of GLMakie is failing:

show(err)
1-element ExceptionStack:
The following 1 direct dependency failed to precompile:
 
GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a]
 
Failed to precompile GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a] to "/home/lgmendes/.julia/compiled/v1.10/GLMakie/jl_ebAnmb".
[3085727] signal (11.1): Segmentation fault
in expression starting at /home/lgmendes/.julia/packages/Makie/8h0bl/precompile/shared-precompile.jl:4
unknown function (ip: 0x7feff6617a96)
unknown function (ip: (nil))
Allocations: 38929905 (Pool: 38904946; Big: 24959); GC: 5
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
  [2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, _from_loading::Bool, kwargs::@Kwargs{io::Base.TTY})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1659
  [3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{_from_loading::Bool})
    @ Pkg.API ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
  [4] precompile
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
  [5] #precompile#114
    @ ~/.julia/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
  [6] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [7] invokelatest
    @ ./essentials.jl:889 [inlined]
  [8] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1963
  [9] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
[10] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
[11] invoke_in_world
    @ ./essentials.jl:923 [inlined]
[12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
[13] macro expansion
    @ ./loading.jl:1790 [inlined]
[14] macro expansion
    @ ./lock.jl:267 [inlined]
[15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
[16] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
[17] invoke_in_world
    @ ./essentials.jl:923 [inlined]
[18] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746
[19] eval
    @ ./boot.jl:385 [inlined]
[20] eval
    @ ./Base.jl:88 [inlined]
[21] repleval(m::Module, code::Expr, ::String)
    @ VSCodeServer ~/.vscode-server/extensions/julialang.language-julia-1.120.2/scripts/packages/VSCodeServer/src/repl.jl:229
[22] (::VSCodeServer.var"#112#114"{Module, Expr, REPL.LineEditREPL, REPL.LineEdit.Prompt})()
    @ VSCodeServer ~/.vscode-server/extensions/julialang.language-julia-1.120.2/scripts/packages/VSCodeServer/src/repl.jl:192
[23] with_logstate(f::Function, logstate::Any)
    @ Base.CoreLogging ./logging.jl:515
[24] with_logger
    @ ./logging.jl:627 [inlined]
[25] (::VSCodeServer.var"#111#113"{Module, Expr, REPL.LineEditREPL, REPL.LineEdit.Prompt})()
    @ VSCodeServer ~/.vscode-server/extensions/julialang.language-julia-1.120.2/scripts/packages/VSCodeServer/src/repl.jl:193
[26] #invokelatest#2
    @ ./essentials.jl:892 [inlined]
[27] invokelatest(::Any)
    @ Base ./essentials.jl:889
[28] (::VSCodeServer.var"#64#65")()
    @ VSCodeServer ~/.vscode-server/extensions/julialang.language-julia-1.120.2/scripts/packages/VSCodeServer/src/eval.jl:34
has context menu

nilshg · September 3, 2024, 9:59am

Any reason you are using 1.10.2 (current release is 1.10.5)?

I just checked and for me precompilation of GLMakie on Win11 WSL2 (Ubuntu) fails as expected with the warning that GLFW couldn't create an OpenGL window (as I don’t have any graphics support set up for WSL2)

lgmendes · September 3, 2024, 10:41am

Just update to 1.10.5.
Now the error is

using GLMakie
┌ Warning: Circular dependency detected. Precompilation will be skipped for:
│   CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
│   AlgebraOfGraphics [cbdf2221-f076-402e-a563-3d30da359d67]
│   MLJFlow [7b7b8358-b45c-48ea-a8ef-7ca328ad328f]
│   CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0]
│   FilePathsBaseMmapExt [968c5e7e-8fc3-5f0f-93d2-8a5e0e125e4f]
│   MLJ [add582a8-e3ab-11e8-2d5e-e98b27df1bc7]
│   FilePathsBaseTestExt [36f6b4e4-024d-52bd-a01f-148eb20c09de]
│   GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a]
│   Makie [ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a]
│   MLFlowClient [64a0f543-368b-4a9a-827a-e71edb2a0b83]
│   FilePaths [8fc22ac5-c921-52a6-82fd-178b2807b824]
└ @ Pkg.API ~/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/share/julia/stdlib/v1.10/Pkg/src/API.jl:1279
[ Info: Precompiling GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a]
 
[3104509] signal (11.1): Segmentation fault
in expression starting at /home/lgmendes/.julia/packages/Makie/8h0bl/precompile/shared-precompile.jl:4
unknown function (ip: 0x7f9ccce17a96)
unknown function (ip: (nil))
Allocations: 39767849 (Pool: 39743039; Big: 24810); GC: 61
ERROR: Failed to precompile GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a] to "/home/lgmendes/.julia/compiled/v1.10/GLMakie/jl_aSnkH9".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2468
  [3] compilecache
    @ ./loading.jl:2340 [inlined]
  [4] (::Base.var"#968#969"{Base.PkgId})()
    @ Base ./loading.jl:1974
  [5] mkpidlock(f::Base.var"#968#969"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
  [6] #mkpidlock#6
    @ ~/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
  [7] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.10.5+0.x64.linux.gnu/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
  [8] #invokelatest#2
    @ ./essentials.jl:894 [inlined]
  [9] invokelatest
    @ ./essentials.jl:889 [inlined]
[10] maybe_cachefile_lock(f::Base.var"#968#969"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:2983
[11] maybe_cachefile_lock
    @ ./loading.jl:2980 [inlined]
[12] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1970
[13] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1812
[14] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
[15] invoke_in_world
    @ ./essentials.jl:923 [inlined]
[16] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1803
[17] macro expansion
    @ ./loading.jl:1790 [inlined]
[18] macro expansion
    @ ./lock.jl:267 [inlined]
[19] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1753
[20] #invoke_in_world#3
    @ ./essentials.jl:926 [inlined]
[21] invoke_in_world
    @ ./essentials.jl:923 [inlined]
[22] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1746

When I create a new env and add GLMakie the error is

err
PkgPrecompileError: The following 1 direct dependency failed to precompile:
 
GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a]
 
Failed to precompile GLMakie [e9467ef8-e4e7-5192-8a1a-b1aee30e663a] to "/home/lgmendes/.julia/compiled/v1.10/GLMakie/jl_67cvph".
[3110179] signal (11.1): Segmentation fault
in expression starting at /home/lgmendes/.julia/packages/Makie/8h0bl/precompile/shared-precompile.jl:4
unknown function (ip: 0x7f5182e17a96)
unknown function (ip: (nil))
Allocations: 39523406 (Pool: 39498662; Big: 24744); GC: 6

nilshg · September 3, 2024, 11:39am

How did you install Julia?

lgmendes · September 3, 2024, 11:53am

With juliaup

sdanisch · September 3, 2024, 11:55am

There’s a known problem on WSL2: Precompilation segfault on WSL2 with GLMakie 0.10.6 · Issue #4148 · MakieOrg/Makie.jl · GitHub
I just noticed we never tagged the fix…

lgmendes · September 3, 2024, 1:24pm

I hope it will be fixed soon.