This is almost identical to the problem I have. I am also working on Linux - CentOS 7 (I actually found your username by chance in the home list, so we may be working on the same cluster @affans ) I have no idea how to fix this particular version of the error. I was sincerely hoping @giordano 's accepted solution would solve the issue, but it does not appear to be so. Julia adds certain packages without trouble, but it gets stuck on the package Singular (a package I need to add the real target package, Oscar).
To check the library it is pointed at, I ran the following code a la this answer,
>> using Libdl
>> libstdcpp_path = filter!(contains("libstdc++"), dllist()) |> first |> abspath
"/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/lib/julia/libstdc++.so.6"
so I know it is pointing to the internal library. I am not a computer scientist/HPC expert, so it is entirely possible I am missing some obvious dependency declaration (though I followed all the instructions to the letter on the documentation). I have also attempted to load different versions of Julia, including a version 8 and and a version 10. I even “rm -rf julia” for the proper julia files to make sure I started with a clean slate, so I know it is not a mixed dependency issue.
Below is my stacktrace for the package Singular. Any help would be greatly appreciated.
Precompiling project...
✗ Singular
0 dependencies successfully precompiled in 10 seconds. 26 already precompiled.
ERROR: The following 1 direct dependency failed to precompile:
Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c]
Failed to precompile Singular [bcd08a7b-43d2-5ff7-b6d4-c458787f915c] to "/home/ecar10/.julia/compiled/v1.9/Singular/jl_LM3ajV".
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libpthread.so.0: version `GLIBC_PRIVATE' not found (required by /lib64/librt.so.1)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_ABI_DT_RELR' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libpthread.so.0)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.33' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.25' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.32' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.36' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libstdc++.so.6)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.35' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libgcc_s.so.1)
/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse: /lib64/libc.so.6: version `GLIBC_2.34' not found (required by /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia/libgcc_s.so.1)
ERROR: LoadError: failed process: Process(setenv(`/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin/libparse /home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/share/singular/LIB/GND.lib`,["CC_CLUSTER=cedar", "PATH=/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Core/mii/1.1.2/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Core/flexiblascore/3.3.1/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcc12/openmpi/4.1.5/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/ucc/1.2.0/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/pmix/4.2.4/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/libfabric/1.18.0/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/ucx/1.14.1/bin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/hwloc/2.9.1/sbin:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/hwloc/2.9.1/bin:/cvmfs/soft.(supercomputer_address)/gentoo/2023/x86-64-v3/usr/x86_64-pc-linux-gnu/gcc-bin/12:/cvmfs/soft.(supercomputer_address)/easybuild/bin:/cvmfs/soft.(supercomputer_address)/custom/bin:/cvmfs/soft.(supercomputer_address)/gentoo/2023/x86-64-v3/usr/bin:/cvmfs/soft.(supercomputer_address)/custom/bin/(supercomputer_address):/opt/software/bin:/opt/software/slurm/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/puppetlabs/bin:/opt/dell/srvadmin/bin:/home/ecar10/.local/bin:/home/ecar10/bin", "SSH_USER_AUTH=publickey: RSA SHA256:ZoHPZ0CBXRXQ63SeHOQSsVy3iPq+nn1nDNaMPWIbHxQ, keyboard-interactive", "LMOD_ROOT=/cvmfs/soft.(supercomputer_address)/custom/software/lmod", "EBVERSIONJULIA=1.9.3", "__LMOD_STACK_LESSOPEN=fGxlc3NwaXBlICVz:fHwvdXNyL2Jpbi9sZXNzcGlwZS5zaCAlcw==", "SACCT_FORMAT=Account,User,JobID,Start,End,AllocCPUS,Elapsed,AllocTRES%30,CPUTime,AveRSS,MaxRSS,MaxRSSTask,MaxRSSNode,NodeList,ExitCode,State%20", "ARCH=x86_64", "EBROOTIMKL=/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0", "LD_LIBRARY_PATH=/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia:/home/ecar10/.julia/artifacts/2c602b7b18fbeff1c121a7533547fd7f518d4d7e/lib:/home/ecar10/.julia/artifacts/3f4ae12d938ec5fab4f2d701b8d0baa28d7dea16/lib:/home/ecar10/.julia/artifacts/21e9ee9e284cdb38c560222b1b6e6cc31c4d7e68/lib:/home/ecar10/.julia/artifacts/d742f40bb63b9380341851126ab31d8d64d59941/lib:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib/julia:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/bin/../lib" … "__SCRATCH_PURGE_REPORTED=1", "JULIA_LOAD_PATH=/home/ecar10/.julia/environments/v1.9/Project.toml:/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9", "EBVERSIONIMKL=2023.2.0", "EPREFIX=/cvmfs/soft.(supercomputer_address)/gentoo/2023/x86-64-v3", "EBDEVELOPENMPI=/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcc12/openmpi/4.1.5/easybuild/x86-64-v3-Compiler-gcc12-openmpi-4.1.5-easybuild-devel", "EBROOTGENTOO=/cvmfs/soft.(supercomputer_address)/gentoo/2023/x86-64-v3/usr", "LMOD_ADMIN_FILE=/cvmfs/soft.(supercomputer_address)/config/lmod/admin.list", "MKLROOT=/cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Core/imkl/2023.2.0/mkl/2023.2.0", "LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45::su=00:sg=00:ca=00:ow=00:st=00:tw=00:ex=00:or=00::", "OPENBLAS_MAIN_FREE=1"]), ProcessExited(1)) [1]
Stacktrace:
[1] pipeline_error
@ ./process.jl:565 [inlined]
[2] read(cmd::Cmd)
@ Base ./process.jl:449
[3] read
@ ./process.jl:458 [inlined]
[4] (::Singular.Setup.var"#2#6"{Dict{Symbol, Vector{Tuple{String, String}}}, Vector{String}, String})()
@ Singular.Setup ~/.julia/packages/Singular/C3EMh/src/setup.jl:43
[5] cd(f::Singular.Setup.var"#2#6"{Dict{Symbol, Vector{Tuple{String, String}}}, Vector{String}, String}, dir::String)
@ Base.Filesystem ./file.jl:112
[6] regenerate_libraryfuncdictionary(prefixpath::String)
@ Singular.Setup ~/.julia/packages/Singular/C3EMh/src/setup.jl:39
[7] top-level scope
@ ~/.julia/packages/Singular/C3EMh/src/setup.jl:52
[8] include(mod::Module, _path::String)
@ Base ./Base.jl:457
[9] include(x::String)
@ Singular ~/.julia/packages/Singular/C3EMh/src/Singular.jl:8
[10] top-level scope
@ ~/.julia/packages/Singular/C3EMh/src/Singular.jl:81
[11] include
@ ./Base.jl:457 [inlined]
[12] 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::Nothing)
@ Base ./loading.jl:2049
[13] top-level scope
@ stdin:3
in expression starting at /home/ecar10/.julia/packages/Singular/C3EMh/src/setup.jl:1
in expression starting at /home/ecar10/.julia/packages/Singular/C3EMh/src/Singular.jl:1
in expression starting at stdin:3
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/Types.jl:69
[2] precompile(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; internal_call::Bool, strict::Bool, warn_loaded::Bool, already_instantiated::Bool, timing::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/API.jl:1581
[3] precompile(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/API.jl:156
[4] precompile(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/API.jl:145
[5] precompile(; name::Nothing, uuid::Nothing, version::Nothing, url::Nothing, rev::Nothing, path::Nothing, mode::Pkg.Types.PackageMode, subdir::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/API.jl:171
[6] precompile()
@ Pkg.API /cvmfs/soft.(supercomputer_address)/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.9.3/share/julia/stdlib/v1.9/Pkg/src/API.jl:162
[7] top-level scope
@ REPL[3]:1