Failed to precompile HDF5 on macOS

[ranocha]

This came up in our CI tests in Trixi.jl:

ERROR: LoadError: InitError: could not load library "/Users/runner/.julia/artifacts/4e3d68673330116b7ef55a34b6d6d405e005fe6d/lib/libhdf5.200.dylib"
dlopen(/Users/runner/.julia/artifacts/4e3d68673330116b7ef55a34b6d6d405e005fe6d/lib/libhdf5.200.dylib, 1): Library not loaded: @rpath/libcurl.4.dylib
  Referenced from: /Users/runner/.julia/artifacts/4e3d68673330116b7ef55a34b6d6d405e005fe6d/lib/libhdf5.200.dylib
  Reason: Incompatible library version: libhdf5.200.dylib requires version 13.0.0 or later, but libcurl.4.dylib provides version 12.0.0
Stacktrace:
  [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
    @ Base.Libc.Libdl ./libdl.jl:117
  [2] dlopen(s::String, flags::UInt32)
    @ Base.Libc.Libdl ./libdl.jl:117
  [3] macro expansion
    @ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
  [4] __init__()
    @ HDF5_jll ~/.julia/packages/HDF5_jll/iXNJT/src/wrappers/x86_64-apple-darwin.jl:12
  [5] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:768
  [6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:854
  [7] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1097
  [8] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
  [9] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
 [11] include(x::String)
    @ HDF5.API ~/.julia/packages/HDF5/7zvRl/src/api/api.jl:1
 [12] top-level scope
    @ ~/.julia/packages/HDF5/7zvRl/src/api/api.jl:8
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
 [14] include(x::String)
    @ HDF5 ~/.julia/packages/HDF5/7zvRl/src/HDF5.jl:1
 [15] top-level scope
    @ ~/.julia/packages/HDF5/7zvRl/src/HDF5.jl:43
 [16] include
    @ ./Base.jl:418 [inlined]
 [17] 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, UInt64}}, source::String)
    @ Base ./loading.jl:1318
 [18] top-level scope
    @ none:1
 [19] eval
    @ ./boot.jl:373 [inlined]
 [20] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [21] top-level scope
    @ none:1
during initialization of module HDF5_jll
in expression starting at /Users/runner/.julia/packages/HDF5/7zvRl/deps/deps.jl:3
in expression starting at /Users/runner/.julia/packages/HDF5/7zvRl/src/api/api.jl:1
in expression starting at /Users/runner/.julia/packages/HDF5/7zvRl/src/HDF5.jl:1
ERROR: LoadError: Failed to precompile HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] to /Users/runner/.julia/compiled/v1.7/HDF5/jl_gB07GO.

[mkitti]

I think this is due to JuliaPackaging/Yggdrasil#4511 (comment) that @visr just brought up.

[mkitti]

HDF5_jll v1.12.2 was yanked in JuliaRegistries/General#65170

The near term solution might be to do

using Pkg
pkg"add [email protected]"

[musm]

Seems like there isn't anything we can do on the HDF5 side to fix this?

[mkitti]

@musm no, not really. The appropriate fix for now is the registry yank.

[musm]

Right, but I thought it was related to fixing the curl library linked in the hdf5 library?

[visr]

I think this can be closed, more recent Trixi builds are working (trixi-framework/Trixi.jl#1189), so the yank is doing it's job.

[ranocha]

I think this can be closed, more recent Trixi builds are working (trixi-framework/Trixi.jl#1189), so the yank is doing it's job.