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I am using an R script with Julia functions to run the code. It works perfectly on my computer, but when I try to set it up in the apptainer, it gives me an error. I've created a container (ubuntu 22.04) with R and Julia installed inside with all the packages required, and upon testing it worked great. However, once I run a specific code, which calls Julia to interact with R, it gives me this error:

    ERROR: LoadError: InitError: could not load library "/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so"
    /usr/lib/x86_64-linux-gnu/libcurl.so: version `CURL_4' not found (required by /home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib/libhdf5.so)

I've looked online, and it says that the main problem is that the script is using the system's lib* files, as opposed to of that from Julia, which creates this error.

So I am trying to modify the last .def file to fix the problem, so far this is what I've added to it:

    Bootstrap: localimage
    From: ubuntu_R_ResistanceGA.sif
    
    %post
    # Install system dependencies for Julia
    apt-get update && \
    apt-get install -y wget tar gnupg lsb-release \
    software-properties-common libhdf5-dev libnetcdf-dev \
    libcurl4-openssl-dev=7.68.0-1ubuntu2.25 \
    libgconf-2-4 \
    libssl-dev
    
    # Run ldconfig to update the linker cache
      ldconfig
    
     # Set environment variable to include the directory where the artifacts are stored
    echo "export LD_LIBRARY_PATH=/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib:\$LD_LIBRARY_PATH" >> /etc/profile

  # Clean up the package cache to reduce container size
  apt-get clean

  # Install Julia 1.9.3
  wget .9/julia-1.9.3-linux-x86_64.tar.gz
  tar -xvzf julia-1.9.3-linux-x86_64.tar.gz
  mv julia-1.9.3 /usr/local/julia
  ln -s /usr/local/julia/bin/julia /usr/local/bin/julia

  # Install Circuitscape
julia -e 'using Pkg; Pkg.add("Circuitscape")'
julia -e 'using Pkg; Pkg.build("NetCDF_jll")'


%environment
  export LD_LIBRARY_PATH=/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib:$LD_LIBRARY_PATH

PS I need to run it in an apptainer because my goal is to use it on a supercomputer (ComputeCanada).

So far, I am trying to use LD_LIBRARY_PATH as a way to fix the problem, but it doesn't seem to work at all

本文标签： dockerLoad library directory error (RJulia and container)Stack Overflow

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