I am using a MPI-enabled HDF5 and suddenly calling up from the Julia package manager fails with
ERROR: Error building `HDF5`:
signal (11): Segmentation fault: 11
in expression starting at /Users/chiel/.julia/packages/HDF5/THb0i/deps/build.jl:8
signal (4): Illegal instruction: 4
in expression starting at /Users/chiel/.julia/packages/HDF5/THb0i/deps/build.jl:8
Line 8 of the mentioned file contains:
1 using Libdl
2
3 const depsfile = joinpath(@__DIR__, "deps.jl")
4
5 libpath = get(ENV, "JULIA_HDF5_PATH",
6 get(ENV, "JULIA_HDF5_LIBRARY_PATH", nothing)) # legacy env variable for compatibility
7
8 new_contents = if libpath === nothing
9 # By default, use HDF5_jll
10 """
11 # This file is automatically generated
12 # Do not edit
13 using HDF5_jll
14 check_deps() = nothing
15 """
16 else
17 @info "using system HDF5"
18
19 libhdf5 = find_library("libhdf5", [libpath, joinpath(libpath, "lib"), joinpath(libpath, "lib64")])
20 libhdf5_hl = find_library("libhdf5_hl", [libpath, joinpath(libpath, "lib"), joinpath(libpath, "lib64")])
21
22 isempty(libhdf5) && error("libhdf5 could not be found")
23 isempty(libhdf5_hl) && error("libhdf5_hl could not be found")
24
25 libhdf5_size = filesize(dlpath(libhdf5))
26
27 """
28 # This file is automatically generated
29 # Do not edit
30
31 function check_deps()
32 if libhdf5_size != filesize(Libdl.dlpath(libhdf5))
33 error("HDF5 library has changed, re-run Pkg.build(\\\"HDF5\\\")")
34 end
35 if h5_get_libversion() < v"1.10.4"
36 error("HDF5.jl requires ≥ v1.10.4 of the HDF5 library.")
37 end
38 end
39 $(:(const libhdf5 = $libhdf5))
40 $(:(const libhdf5_hl = $libhdf5_hl))
41 $(:(const libhdf5_size = $libhdf5_size))
42 """
43 end
I do not know how fix this and I’d like to be able to upgrade my module. I have tried to delete the .julia folder and rebuild everything, but this did not solve the problem. I am using a system provided MPI-enabled HDF5 library.