Docker setup for SMCE use

Author: andrewdelman

Docker/smce/Dockerfile

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+# Dockerfile to build SMCE OSS environment for running ECCO tutorials.
+FROM public.ecr.aws/smce/smce-images:smce-oss-earth-r-julia-48aae375
+
+ENV NB_USER=jovyan
+ENV HOME=/home/${NB_USER}
+
+# USER ${NB_USER}
+WORKDIR ${HOME}
+
+
+# retrieve ECCO Python tutorials
+RUN git clone https://github.com/ECCO-GROUP/ECCO-v4-Python-Tutorial.git
+
+# install any additional Python packages needed
+RUN mamba install -y -n notebook matplotlib ecco_v4_py
+
+# install packages needed to run Julia notebooks
+RUN julia -e 'import Pkg; Pkg.add("Pluto"); using Pluto'
+RUN julia -e 'import Pkg; Pkg.add("OceanStateEstimation")'
+
+# create symlink from home directory to jupyter_lab_start_docker.sh
+RUN ln -s ${HOME}/ECCO-v4-Python-Tutorial/Docker/smce/jupyter_lab_start_smce.sh \
+            ${HOME}/jupyter_lab_start_smce.sh
+
+EXPOSE 8888
+
+# start jupyter lab inside the container
+ENTRYPOINT ["./jupyter_lab_start_smce.sh"]

Docker/smce/jupyter_lab_start_smce.sh

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+#!/bin/bash
+
+# Shell script to start a Jupyter lab session
+# in a tmux window (so it persists even if ssh tunnel is disconnected)
+
+red_start='\033[0;31m'
+blue_start='\033[0;34m'
+nocolor_start='\033[0m'
+
+
+# Add Earthdata credentials to ~/.netrc if they are not already present
+sh ~/ECCO-v4-Python-Tutorial/Docker/earthdata_auth_docker.sh
+
+echo "Starting Jupyter lab session!"
+echo ""
+
+read -p 'Which container port do you want to use [default 8888]: ' user_port
+user_port=${user_port:-8888}
+echo "using port ${user_port}"
+echo ""
+
+# Start configuration for Jupyter lab
+echo "Enter password to access Jupyter lab from browser,"
+echo "or leave blank to not require a password."
+
+PW="$(python3 -c 'from jupyter_server.auth import passwd; import getpass; print(passwd(getpass.getpass(), algorithm="sha256"))')"
+
+
+# Start Jupyter lab
+source /srv/conda/bin/activate
+conda activate notebook
+jupyter lab --no-browser --autoreload --port=${user_port} --ip='0.0.0.0' --NotebookApp.token='' --NotebookApp.password=\"$PW\" --notebook-dir=\"./ECCO-v4-Python-Tutorial\"
+
+# Print info about session
+echo -e "${red_start}Started Jupyter lab in Docker container"
+echo -e "${red_start}Access from your local machine in a browser window"
+echo -e "${red_start}by tunneling to host machine at the port"
+echo -e "${red_start}you are using to connect to the Docker container, e.g., "
+echo -e "${blue_start}ssh -i ~/.ssh/ec2_auth.pem -L 8888:localhost:8888 ec2-user@100.104.70.127"
+echo -e "${red_start}and opening the URL in your browser"
+echo -e "${blue_start}http://127.0.0.1:8888/ ${red_start}or ${blue_start}http://localhost:8888/"
+echo -e "${red_start}If you are already running Jupyter on your local machine"
+echo -e "${red_start}on port 8888, you need to use a different local port, e.g.,"
+echo -e "${blue_start}ssh -i ~/.ssh/ec2_auth.pem -L 9889:localhost:8888 ec2-user@100.104.70.127${nocolor_start}"