LoadError for libgomp with Pkg.precompile() on alpine 3.12 (docker)

[kiwiroy]

Trusting that this is a suitable place to report this.

While using the alpine docker image, precompiling a project is failing. The same workflow does not reproduce for the buster image.

docker run -ti --rm julia:1.5.3-alpine3.12 sh
/ # julia
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.5.3 (2020-11-09)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using Pkg; Pkg.add("StatsFuns"); Pkg.precompile();

<snip>

Precompiling project...
[ Info: Precompiling StatsFuns [4c63d2b9-4356-54db-8cca-17b64c39e42c]
ERROR: LoadError: LoadError: InitError: could not load library "/root/.julia/artifacts/82a4d5a335f8504b9e4831f23b99908ec2807982/lib/libgomp.so.1"
Error relocating /root/.julia/artifacts/82a4d5a335f8504b9e4831f23b99908ec2807982/lib/libgomp.so.1: __cxa_finalize: initial-exec TLS resolves to dynamic definition in /root/.julia/artifacts/82a4d5a335f8504b9e4831f23b99908ec2807982/lib/libgomp.so.1
Stacktrace:
 [1] dlopen(::String, ::UInt32; throw_error::Bool) at /buildworker/worker/package_musl64/build/usr/share/julia/stdlib/v1.5/Libdl/src/Libdl.jl:109
 [2] dlopen(::String, ::UInt32) at /buildworker/worker/package_musl64/build/usr/share/julia/stdlib/v1.5/Libdl/src/Libdl.jl:109
 [3] macro expansion at /root/.julia/packages/JLLWrappers/WnWcZ/src/products/library_generators.jl:63 [inlined]
 [4] __init__() at /root/.julia/packages/CompilerSupportLibraries_jll/790hI/src/wrappers/x86_64-linux-musl-libgfortran4.jl:30
 [5] _include_from_serialized(::String, ::Array{Any,1}) at ./loading.jl:697
 [6] _require_from_serialized(::String) at ./loading.jl:749
 [7] _require(::Base.PkgId) at ./loading.jl:1040
 [8] require(::Base.PkgId) at ./loading.jl:928
 [9] require(::Module, ::Symbol) at ./loading.jl:923
 [10] include(::Function, ::Module, ::String) at ./Base.jl:380
 [11] include(::Module, ::String) at ./Base.jl:368
 [12] top-level scope at /root/.julia/packages/JLLWrappers/WnWcZ/src/toplevel_generators.jl:170
 [13] include(::Function, ::Module, ::String) at ./Base.jl:380
 [14] include(::Module, ::String) at ./Base.jl:368
 [15] top-level scope at none:2
 [16] eval at ./boot.jl:331 [inlined]
 [17] eval(::Expr) at ./client.jl:467
 [18] top-level scope at ./none:3
during initialization of module CompilerSupportLibraries_jll
in expression starting at /root/.julia/packages/OpenSpecFun_jll/Xw8XK/src/wrappers/x86_64-linux-musl-libgfortran4.jl:4
in expression starting at /root/.julia/packages/OpenSpecFun_jll/Xw8XK/src/OpenSpecFun_jll.jl:8
ERROR: LoadError: Failed to precompile OpenSpecFun_jll [efe28fd5-8261-553b-a9e1-b2916fc3738e] to /root/.julia/compiled/v1.5/OpenSpecFun_jll/TDl1L_nrrZo.ji.
<snip>

Alpine and other musl based dists use a patch that addresses this error message about relocation.

[giordano]

Unfortunately JLL packages require Julia v1.6 to work reliably on Musl-based systems, like Alpine Linux. For reference: JuliaPackaging/Yggdrasil#1418, fixed by JuliaPackaging/Yggdrasil#1720

[giordano]

You are quite lucky, the first beta version of Julia v1.6 has been just published: https://discourse.julialang.org/t/julia-v1-6-0-beta1-is-now-available/53065. There might be a Docker image of Julia on Alpine soon:tm: