undefined symbol: H5FD_subfiling_init #1199
Description
We are trying to track down an error that we get.
Julia version 1.10.5 at location /gpfs1/sw/rh9/pkgs/julia/1.10.5/bin will be used.
Loading setup script for JuliaCall...
Finish loading setup script for JuliaCall.
Attempt 1 to run jl.prep()...
jl.prep() failed with error: Error happens in Julia.
InitError: could not load library "/users/c/d/cdrasher/.julia/artifacts/2117b531439d782e1cb0ebffcc4dcf11d274cc39/lib/libhdf5_fortran.so"
/users/c/d/cdrasher/.julia/artifacts/2117b531439d782e1cb0ebffcc4dcf11d274cc39/lib/../lib/libhdf5_f90cstub.so.310: undefined symbol: H5FD_subfiling_init
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/GfYNv/src/products/library_generators.jl:63 [inlined]
[4] __init__()
@ HDF5_jll ~/.julia/packages/HDF5_jll/NQMjC/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx11-mpi+mpich.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] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1481
[9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
@ Base ./loading.jl:1574
[10] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1938
[11] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1812
[12] #invoke_in_world#3
@ ./essentials.jl:926 [inlined]
[13] invoke_in_world
@ ./essentials.jl:923 [inlined]
[14] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1803
[15] macro expansion
@ ./loading.jl:1790 [inlined]
[16] macro expansion
@ ./lock.jl:267 [inlined]
[17] __require(into::Module, mod::Symbol)
@ Base ./loading.jl:1753
[18] #invoke_in_world#3
@ ./essentials.jl:926 [inlined]
[19] invoke_in_world
@ ./essentials.jl:923 [inlined]
[20] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1746
[21] eval
@ ./boot.jl:385 [inlined]
[22] eval_string(x::String)
@ Main.JuliaCall /gpfs1/home/c/d/cdrasher/R/x86_64-pc-linux-gnu-library/4.4/JuliaCall/julia/setup.jl:203
[23] docall(call1::Ptr{Nothing})
@ Main.JuliaCall /gpfs1/home/c/d/cdrasher/R/x86_64-pc-linux-gnu-library/4.4/JuliaCall/julia/setup.jl:176
during initialization of module HDF5_jll
Looking at the libraries for the installed HDF5.jl, I find
$ pwd
/users/c/d/cdrasher/.julia/artifacts/2117b531439d782e1cb0ebffcc4dcf11d274cc39/lib
$ nm libhdf5_f90cstub.so.310.3.2 | grep H5FD_subfiling_init
libhdf5_f90cstub.so.310.3.2
U H5FD_subfiling_init
# nm libhdf5.so.310.5.1 | grep H5FD_subfiling_init
000000000017e000 T H5FD_subfiling_init
I use
# ldd libhdf5_f90cstub.so.310.3.2 | grep libhdf5.so
libhdf5.so.310 => /gpfs1/home/c/d/cdrasher/.julia/artifacts/2117b531439d782e1cb0ebffcc4dcf11d274cc39/lib/./../lib/libhdf5.so.310 (0x00007f2f7c42c000)
followed by
$ nm libhdf5.so.310 | grep H5FD_subfiling_init
000000000017e000 T H5FD_subfiling_init
It seems that the symbol should be resolvable. Any thoughts on this?
Thanks, -- bennet