Trouble with shared libraries on slurm server

[mkschleg]

I'm getting some weird issues with git on a slurm server.

/home/mkschleg/.julia/artifacts/43eef4d016f011145955de2ba33450dda0536252/bin/git: relocation error: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.6.2/bin/../lib/julia/libpthread.so.0: symbol __tsearch, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference
ERROR: failed process: Process(setenv(`/home/mkschleg/.julia/artifacts/43eef4d016f011145955de2ba33450dda0536252/bin/git rev-parse HEAD`,["HDF5_USE_FILE_LOCKING=FALSE", "EBVERSIONOPENMPI=4.0.3", "SQUEUE_SORT=-t,e,S", "LMOD_FAMILY_HDF5=hdf5", "MODULEPATH=/opt/software/modulefiles:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/MPI/intel2020/openmpi4:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Compiler/intel2020:/home/mkschleg/.local/easybuild/modules/2020/avx2/Core:/home/mkschleg/.local/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/custom/modules", "EBVERSIONPYTHON=3.8.2", "_ModuleTable_Sz_=11", "_ModuleTable005_=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", "EBDEVELPYTHON=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/python/3.8.2/easybuild/avx2-Core-python-3.8.2-easybuild-devel", "SSL_CERT_FILE=/etc/pki/tls/certs/ca-bundle.crt"  …  "_ModuleTable004_=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", "LMOD_FAMILY_MPI_VERSION=4.0.3", "LMOD_FAMILY_HDF5_VERSION=1.10.6", "LMOD_SETTARG_FULL_SUPPORT=no", "JULIA_LOAD_PATH=::", "CC_RESTRICTED=true", "__SCRATCH_PURGE_REPORTED=1", "EBVERSIONIMKL=2020.1.217", "EPREFIX=/cvmfs/soft.computecanada.ca/gentoo/2020", "LS_COLORS=rs"]), ProcessExited(127)) [127]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:525 [inlined]
 [2] read(cmd::Cmd)
   @ Base ./process.jl:412
 [3] read(cmd::Cmd, #unused#::Type{String})
   @ Base ./process.jl:421
 [4] git_head()
   @ Reproduce /project/6010404/mkschleg/Reproduce.jl/src/Reproduce.jl:7
 [5] top-level scope
   @ REPL[2]:1

When trying to run the git executable installed by Git_jll.jl outside of julia I get:

.julia/artifacts/43eef4d016f011145955de2ba33450dda0536252/bin/git: error while loading shared libraries: libpcre2-8.so.0: cannot open shared object file: No such file or directory

This is on a completely fresh install. Any advice?

[giordano]

What version of glibc do you use? We support glibc 2.12.2 on x86_64, which is very old, do you have something even older?

[mkschleg]

Great question. I'm pretty sure the server is using 2.30.

%> /cvmfs/soft.computecanada.ca/gentoo/2020/lib64/libc.so.6
GNU C Library (Gentoo 2.30-r8 p10) stable release version 2.30.