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danifr/gist:34f2cde14a92e88a639b28ad1ce32bc6

Created March 6, 2025 14:44
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  1. danifr created this gist Mar 6, 2025.
    103 changes: 103 additions & 0 deletions gistfile1.txt
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    #!/bin/bash

    sudo apt update
    sudo apt install nfs-common -y
    sudo mount -t nfs4 -o nfsvers=4.1,rsize=1048576,wsize=1048576,hard,timeo=600,retrans=2,noresvport ${HOMEDIRS_EFS}:/ ${HOMEDIRS_PATH}

    curl -L https://tljh.jupyter.org/bootstrap.py \
    | sudo python3 - \
    --admin ${ADMIN_USER}:${ADMIN_PASS} \
    --version 0.2.0 \
    --show-progress-page \

    sudo tljh-config set base_url ${BASE_PATH}

    # limit session to 30 mins
    sudo tljh-config set services.cull.max_age 1800

    # Setup Keycloak as a GenericOAuthenticator
    cat <<EOF > /opt/tljh/config/jupyterhub_config.d/keycloak.py
    c.JupyterHub.authenticator_class = "generic-oauth"
    c.GenericOAuthenticator.client_id = "${KC_CLIENT_ID}"
    c.GenericOAuthenticator.client_secret = "${KC_CLIENT_SECRET}"
    c.GenericOAuthenticator.oauth_callback_url = "https://${PRIMARY_DOMAIN}${BASE_PATH}/hub/oauth_callback"
    c.GenericOAuthenticator.authorize_url = "https://${PRIMARY_DOMAIN}/auth/realms/${KC_REALM}/protocol/openid-connect/auth"
    c.GenericOAuthenticator.token_url = "https://${PRIMARY_DOMAIN}/auth/realms/${KC_REALM}/protocol/openid-connect/token"
    c.GenericOAuthenticator.userdata_url = "https://${PRIMARY_DOMAIN}/auth/realms/${KC_REALM}/protocol/openid-connect/userinfo"
    c.GenericOAuthenticator.login_service = "Keycloak login"
    c.GenericOAuthenticator.username_key = "preferred_username"
    c.GenericOAuthenticator.scope = ["openid"]
    c.GenericOAuthenticator.allow_all = True
    c.GenericOAuthenticator.auto_login = True
    c.GenericOAuthenticator.auto_login_oauth2_authorize = True
    c.GenericOAuthenticator.validate_server_cert = False
    EOF

    # Julia installation
    JULIA_VERSION="1.6.6"
    JULIA_VER=$(cut -d '.' -f -2 <<< "$JULIA_VERSION")
    BASE_URL="https://julialang-s3.julialang.org/bin/linux/x64"
    URL="$BASE_URL/$JULIA_VER/julia-$JULIA_VERSION-linux-x86_64.tar.gz"

    wget -nv $URL -O /tmp/julia.tar.gz
    tar -x -f /tmp/julia.tar.gz -C /usr/local --strip-components 1
    rm /tmp/julia.tar.gz
    ln -s /usr/local/bin/julia /opt/tljh/user/bin/julia

    export JULIA_DEPOT_PATH=/opt/tljh/user/share/julia/
    export JUPYTER_DATA_DIR=/opt/tljh/user/share/jupyter/

    declare -A JULIA_PACKAGES=(
    ["IJulia"]="1.26.0"
    ["BenchmarkTools"]="1.5.0"
    ["DifferentialEquations"]="7.2.0"
    ["JSON"]="0.21.4"
    ["ModelingToolkit"]="8.11.0"
    ["Plots"]="1.31.1"
    ["Symbolics"]="4.3.0"
    ["WebIO"]="0.8.21"
    ["Interact"]="0.10.5"
    ["PyCall"]="1.96.4"
    )

    # Install packages
    for PKG in "$${!JULIA_PACKAGES[@]}"
    do
    PKG_VERSION="$${JULIA_PACKAGES[$PKG]}"
    echo "Installing Julia package $PKG $PKG_VERSION..."
    julia -e "using Pkg; Pkg.add(name=\"$${PKG}\", version=\"$${PKG_VERSION}\"); precompile;"
    done

    julia -e 'using Pkg; Pkg.build("Interact")'

    # Install kernel
    JULIA_NUM_THREADS=8
    echo "Installing IJulia kernel..."
    julia -e 'using IJulia; IJulia.installkernel("julia", env=Dict(
    "JULIA_NUM_THREADS"=>"'"$JULIA_NUM_THREADS"'",
    "JULIA_DEPOT_PATH"=>"'"$JULIA_DEPOT_PATH"'",
    "JUPYTER_DATA_DIR"=>"'"$JUPYTER_DATA_DIR"'"
    ))'

    # downgrade bcrypt to avoid AttributeError: module 'bcrypt' has no attribute '__about__' error
    source /opt/tljh/hub/bin/activate
    pip install --upgrade bcrypt==4.0.1
    deactivate

    source /opt/tljh/user/bin/activate
    pip install webio_jupyter_extension webio_jupyterlab_provider
    pip install --upgrade jupyterlab-pygments==0.2.0
    conda deactivate

    # Give jupyterhub-users groups access to $JULIA_DEPOT_PATH
    chgrp -R jupyterhub-users $${JULIA_DEPOT_PATH}
    chmod 664 $${JULIA_DEPOT_PATH}/logs/repl_history.jl
    chmod 664 $${JULIA_DEPOT_PATH}/logs/manifest_usage.toml

    # Restart JupyterHub service to apply changes
    sudo tljh-config reload proxy
    sudo tljh-config reload