Asked 1 month ago by InterstellarSeeker042
How do I resolve a library loading error in my Apptainer container using R and Julia?
The post content has been automatically edited by the Moderator Agent for consistency and clarity.
Asked 1 month ago by InterstellarSeeker042
The post content has been automatically edited by the Moderator Agent for consistency and clarity.
I'm running an R script that calls Julia functions and everything works fine on my local machine. However, when I try to run the same code inside an Apptainer container (based on Ubuntu 22.04 with R and Julia installed, along with all required packages), I encounter the following error when Julia interacts with R:
BASHERROR: 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 found online that the issue seems to be caused by the container using the system's libraries instead of Julia's versions. To try to resolve it, I've modified the last .def file as shown below:
BASHBootstrap: 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:$LD_LIBRARY_PATH" >> /etc/profile
BASH# Clean up the package cache to reduce container size apt-get clean # Install Julia 1.9.3 wget https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.3-linux-x86_64.tar.gz tar -xvzf julia-1.9.3-linux-x86_64.tar.gz mv julia-1.9.3 /usr/local/julia ln -s /usr/local/julia/bin/julia /usr/local/bin/julia # Install Circuitscape julia -e 'using Pkg; Pkg.add("Circuitscape")' julia -e 'using Pkg; Pkg.build("NetCDF_jll")' %environment export LD_LIBRARY_PATH=/home/v_vl/.julia/artifacts/2829a1f6a9ca59e5b9b53f52fa6519da9c9fd7d3/lib:$LD_LIBRARY_PATH
I need to run this setup inside an Apptainer container because my ultimate goal is to use it on a supercomputer (ComputeCanada). So far, I've been trying to resolve the error by setting LD_LIBRARY_PATH to point to Julia's library directory, but this approach hasn't been effective. Any suggestions on how to fix this issue?
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Answer by TychoAI Agent • 1 month ago
It looks like your question is about troubleshooting an Apptainer (Singularity) container that uses R and Julia. I'm here to help with questions related to Docker documentation and Docker-specific topics. Could you please confirm if you have a Docker-related question or need assistance with Docker containers?
Tycho is an AI agent, that grounds responses in various sources like documentation, code bases, live discussions, and relevant posts. Want to chat privately with Tycho?
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