image.def

Bootstrap: docker
From: nvidia/cuda:12.6.2-base-ubuntu22.04

%environment
    # Set environment variables accessible within the container
    export USERNAME=${USER:-$(id -un)}
    export INTERNAL_DIR=/home/
    export SINIMAGE_DIR=/mnt/local/$USERNAME/sinimage/home
    export CONDA_PKGS_DIRS=$SINIMAGE_DIR/conda/pkgs
    export CONDA_ENVS_DIRS=$SINIMAGE_DIR/conda/envs
    export CONDA_CACHE_DIR=$SINIMAGE_DIR/.local/cache/conda
    export CONDA_PREFIX=/opt/conda
    export PYTHONUSERBASE=$SINIMAGE_DIR/.local
    export JUPYTER_RUNTIME_DIR=$SINIMAGE_DIR/.local/share/jupyter/runtime
    export IPYTHONDIR=$SINIMAGE_DIR/.local/share/ipython
    export JUPYTER_CONFIG_DIR=$SINIMAGE_DIR/.local/etc/jupyter
    export JUPYTER_DATA_DIR=$SINIMAGE_DIR/.local/share/jupyter
    export MPLCONFIGDIR=$SINIMAGE_DIR/.local/share/matplotlib
    export XDG_CONFIG_HOME=$SINIMAGE_DIR/.local/etc
    export XDG_DATA_HOME=$SINIMAGE_DIR/.local/share
    export XDG_CACHE_HOME=$SINIMAGE_DIR/.local/cache
    export CODE_SERVER_CONFIG=$SINIMAGE_DIR/.local/etc/code-server/config.yaml
    export JUPYTER_IP=0.0.0.0
    export PATH=/opt/conda/bin:$SINIMAGE_DIR/.local/bin:$PATH
    export CONDA_NO_PLUGIN=True
    export NVM_DIR=/opt/.nvm
    export CODE_SERVER_CONFIG="/opt/code-server/config/config.yaml"
    export SHELL=/opt/conda/bin/zsh
    export XDG_STATE_HOME=$SINIMAGE_DIR/.local/state
    export CUDA_CACHE_PATH=$SINIMAGE_DIR/.cache/nv
    export TMPDIR=$SINIMAGE_DIR/.local/tmp
    export mumax_port=35999
    export code_port=8090
    export SCREENDIR=$SINIMAGE_DIR/tmp
    export ZELLIJ_TMP_DIR=$HOME/.zellij
    export RUST_BACKTRACE=1

%files
    # Copy configuration files to container
    ./starship.toml /opt/temp_files/starship.toml
    ./.zshrc /opt/temp_files/.zshrc
    ./code-server/config.yaml /opt/code-server/config/config.yaml
    ./code-server/extensions-list.txt /opt/temp_files/extensions-list.txt

%post
    # ===========================
    # 1. Install System Packages
    # ===========================
    apt-get update && apt-get install -y \
        curl \
        ca-certificates \
        git \
        bzip2 \
        libx11-6 \
        gcc \
        llvm \
        cmake \
        libfftw3-dev \
        exa \
        nano \
        rclone \
        make \
        g++ \
        libsndfile1 \
        screen \
        tmux \
        autossh \
        wget 

    # ===========================
    # 2. Install Miniconda
    # ===========================
    wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh

    # Add conda to PATH
    export PATH="/opt/conda/bin:$PATH"

    # Configure conda channels
    conda config --file /.condarc --add channels defaults
    conda config --file /.condarc --add channels conda-forge

    # Update conda and install essential Python packages
    conda update -y conda
    conda install -y python=3.12 pip

    # Clean up unused packages to reduce image size
    conda clean --all -y

    # ===========================
    # 3. Install Amumax and Mumax
    # ===========================
    sh -c "$(curl -fsSL https://raw.githubusercontent.com/MathieuMoalic/amumax/main/install.sh)" -- /opt/conda/bin/
    
    # Download and install Mumax3
    MUMAX_VERSION="mumax3.10_linux_cuda11.0"
    MUMAX_URL="https://mumax.ugent.be/mumax3-binaries/${MUMAX_VERSION}.tar.gz"
    MUMAX_INSTALL_DIR="/opt/conda/bin/mumax3"

    # Create installation directory in /opt/conda/bin
    mkdir -p $MUMAX_INSTALL_DIR

    # Download and extract Mumax3 directly into /opt/conda/bin
    curl -L $MUMAX_URL | tar -xz -C /opt/conda/bin --strip-components=1

    # Ensure mumax3 binary is accessible
    chmod +x /opt/conda/bin/mumax3

    # ===========================
    # 4. Install Additional Conda Packages
    # ===========================
    conda install -y conda-forge::zsh       # ZSH shell
    ln -s /opt/conda/bin/zsh /bin/zsh
    conda install -y -c conda-forge zoxide  # Directory navigation
    conda install -y conda-forge::bat       # Enhanced 'cat' command
    conda install -y conda-forge::starship  # Starship prompt
    conda install -y conda-forge::atuin
    conda install -y dnachun::btop
    conda install conda-forge::zellij

    # ===========================
    # 5. Install NVM and Node.js
    # ===========================
    # Set up NVM environment
    export NVM_DIR="/opt/.nvm"
    git clone https://github.com/nvm-sh/nvm.git "$NVM_DIR"
    cd "$NVM_DIR"
    git checkout `git describe --abbrev=0 --tags --match "v[0-9]*" $(git rev-list --tags --max-count=1)`
    . "$NVM_DIR/nvm.sh"

    # Load NVM scripts for persistent availability
    [ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh"  # Loads nvm
    [ -s "$NVM_DIR/bash_completion" ] && . "$NVM_DIR/bash_completion"  # Loads nvm bash_completion

    # Install and set up Node.js version 20
    nvm install 20
    nvm use 20
    nvm alias default 20

    # ===========================
    # 6. Install Code Server
    # ===========================
    mkdir -p /opt/code/
    export VSCODE_EXTENSIONS=/opt/code/

    curl -fOL https://github.com/coder/code-server/releases/download/v4.95.1/code-server_4.95.1_amd64.deb
    dpkg -i code-server_4.95.1_amd64.deb

    # Install each extension listed in `extensions-list.txt`
    EXTENSIONS_LIST=/opt/temp_files/extensions-list.txt
    while IFS= read -r extension; do
        echo "Installing extension: $extension"
        code-server --install-extension "$extension" --force
    done < "$EXTENSIONS_LIST"

    cp -r /root/.config/code-server /opt/code-server-settings
    cp -r /root/.local/share/code-server /opt/code-server-settings
    chmod -R 755 /opt/code-server-settings

    # ===========================
    # 7. Install Python Packages with pip
    # ===========================
    pip install pyzfn \
                uv \
                rust \
                pydantic \
                mypy \
                scipy \
                cmcrameri \
                seaborn \
                pandas

    # ===========================
    # 8. Install JupyterLab and Build
    # ===========================
    conda install -y -c conda-forge jupyterlab
    jupyter-lab build
    
%runscript
    # Move configuration files to a new home directory if they don't exist there
    if [ ! -f "$SINIMAGE_DIR/home/.zshrc" ]; then
        cp /opt/temp_files/.zshrc "$SINIMAGE_DIR/.zshrc"
        mkdir $SCREENDIR
        chmod 700 $SCREENDIR
        mkdir -p $HOME/.zellij
        chmod 700 $HOME/.zellij    
    fi

    if [ ! -f "$SINIMAGE_DIR/home/.config/starship.toml" ]; then
        cp /opt/temp_files/starship.toml "$SINIMAGE_DIR/.config/starship.toml"
        chmod 644 $SINIMAGE_DIR/.config/starship.toml
    fi
    
    [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # Load nvm
    [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # Load nvm bash_completion

    . /opt/conda/etc/profile.d/conda.sh
    
    if [ ! -d "$HOME/.local/share/code-server" ]; then
        rclone copy /opt/code-server-settings/code-server "$HOME/.local/share/code-server"
    fi
    
    exec zsh