Missing /.julia/artifacts/69e85a392db842d919cf5759941f8f3e8a0e569e/lib/libhdf5_fortran.so"
libmpi_usempif08.so.40: cannot open shared object file: No such file or directory
? Any idea what that is about?
The missing library was found for a different artifact:
So there is such a library in circulation, but for some reason MPIExt fails to install/ find it?
What operating system and platform is this? The output of versioninfo() should suffice.
This happens both on a Mac and on Linux. Julia 1.10.0 (Mac) and 1.10.3 (Linux).
julia> versioninfo()
Julia Version 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 24 × Apple M2 Ultra
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 1 on 16 virtual cores
Now upgraded to 1.10.4, erased the depot. Still the same error.
julia> err
PkgPrecompileError: The following 7 direct dependencies failed to precompile:
FinEtoolsHeatDiff [972d1c22-8bdd-11e9-11cf-cdcb7577b041]
Failed to precompile FinEtoolsHeatDiff [972d1c22-8bdd-11e9-11cf-cdcb7577b041] to "/Users/pkrysl/.julia/compiled/v1.10/FinEtoolsHeatDiff/jl_GN5XKf".
ERROR: LoadError: InitError: could not load library "/Users/pkrysl/.julia/artifacts/1ca9a5d2ef01daeca735b28c3ce62406fc87e2ab/lib/libhdf5_fortran.310.dylib"
dlopen(/Users/pkrysl/.julia/artifacts/1ca9a5d2ef01daeca735b28c3ce62406fc87e2ab/lib/libhdf5_fortran.310.dylib, 0x0001): Library not loaded: @rpath/libmpi_usempif08.40.dylib
Referenced from: <2DED3716-8217-3BFA-898A-DB658BC608DA> /Users/pkrysl/.julia/artifacts/1ca9a5d2ef01daeca735b28c3ce62406fc87e2ab/lib/libhdf5_fortran.310.dylib
Reason: tried: '/Users/pkrysl/.julia/artifacts/1ca9a5d2ef01daeca735b28c3ce62406fc87e2ab/lib/./libmpi_usempif08.40.dylib' (no such file), '/Users/pkrysl/.julia/artifacts/1ca9a5d2ef01daeca735b28c3ce62406fc87e2ab/lib/./libmpi_usempif08.40.dylib' (no such file), '/Users/pkrysl/julia-1.10.4/lib/julia/libmpi_usempif08.40.dylib' (no such file), '/Users/pkrysl/julia-1.10.4/lib/julia/../libmpi_usempif08.40.dylib' (no such file), '/Users/pkrysl/julia-1.10.4/lib/libmpi_usempif08.40.dylib' (no such file), '/usr/local/lib/libmpi_usempif08.40.dylib' (no such file), '/usr/lib/libmpi_usempif08.40.dylib' (no such file, not in dyld cache)
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:116
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/pG9bm/src/products/library_generators.jl:63 [inlined]
[4] __init__()
@ HDF5_jll ~/.julia/packages/HDF5_jll/pjOXH/src/wrappers/aarch64-apple-darwin-libgfortran5-mpi+openmpi.jl:48
[5] run_module_init(mod::Module, i::Int64)
@ Base ./loading.jl:1134
[6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1122
[7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1067
[8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
@ Base ./loading.jl:1581
[9] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1938
[10] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1812
[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] top-level scope
@ ~/.julia/packages/HDF5/Z859u/src/api/api.jl:11
[21] include(mod::Module, _path::String)
@ Base ./Base.jl:495
[22] include(x::String)
@ HDF5 ~/.julia/packages/HDF5/Z859u/src/HDF5.jl:1
[23] top-level scope
@ ~/.julia/packages/HDF5/Z859u/src/HDF5.jl:68
[24] include
@ ./Base.jl:495 [inlined]
[25] 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
[26] top-level scope
@ stdin:3
during initialization of module HDF5_jll
in expression starting at /Users/pkrysl/.julia/packages/HDF5/Z859u/src/api/api.jl:1
in expression starting at /Users/pkrysl/.julia/packages/HDF5/Z859u/src/HDF5.jl:1
in expression starting at stdin:3
ERROR: LoadError: Failed to precompile HDF5 [f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f] to "/Users/pkrysl/.julia/compiled/v1.10/HDF5/jl_hVlw7e".
I can’t find any mention of this lib in MPIExt, so perhaps MPI.jl is at fault?
It was MPIPreferences. I had it in the environment, I removed it and the errors went away.
I see. Perhaps you got caught in a transition to package extensions with regard to MPI and HDF5?
I am currently facing the exact same issue trying to build HDF5 on an MPI-enabled system. When you said you removed it from the environment, do you mean you completely removed MPIPreferneces from your project? or is there a specific setting in MPIPreferences that you removed in order for it to build correctly?
I updated the environment, and now I have no troubles from that quarter. Sorry I cannot be more help.