Jupyter & Climate Docker Image

Docker/Podman image to load Jupyter and Conda, with a few additional packages useful for climatological data analysis. For an image with some additional packages useful for Earth climate science, see hannahwoodward/docker-jupyter-climate-earth

Useful links

• Jupyter Docker stacks github
• Jupyter Docker stacks docs
• Docker build help
• Docker run help

Installation & Use

• Install Docker desktop
• Ensure Docker desktop is running
• Navigate to your project directory (i.e. with Jupyter notebook files)
• Download published image:

docker pull woodwardsh/jupyter-climate:latest

• Run published image, mounting local working directory to container directory /home/jovyan:

docker run -it --rm -p 8888:8888 -v ${PWD}:/home/jovyan -w /home/jovyan woodwardsh/jupyter-climate:latest

# Options:
# -it           interactive && TTY (starts shell inside container)
# --rm          delete container on exit
# --volume|-v   mount local directory inside container
# -w PATH       sets working directory inside container

Podman

• Podman requires additional arguments to enable volume mounting with correct permissions (see podman run, nb :Z|z is not supported in macOS ):

podman run -it --rm -p 8888:8888 --userns=keep-id -v ${PWD}:/home/jovyan:z -w /home/jovyan woodwardsh/jupyter-climate

Exporting the Conda environment

• Start the container
• Open a new terminal inside JupyterLab
• Run sh ~/generate-config.sh to generate config climate.yml into your working directory
• Download climate.yml from the JupyterLab UI, or copy straight from the directory if mounted

Building & running image from scratch

• Clone repo & navigate inside:

git clone git@github.com:hannahwoodward/docker-jupyter-climate.git && cd docker-jupyter-climate

• Build image from Dockerfile (takes ~15 minutes):

docker build -t jupyter-climate .

# -t = name/tag the image, format `name:tag`

• Navigate to your project directory (i.e. with Jupyter notebook files)
• Run locally built image, mounting local working directory to container directory /home/jovyan:

docker run -it --rm -p 8888:8888 -v ${PWD}:/home/jovyan -w /home/jovyan jupyter-climate

# Options:
# -it           interactive && TTY (starts shell inside container)
# --rm          delete container on exit
# --volume|-v   mount local directory inside container
# -w PATH       sets working directory inside container

Publishing image

docker login && docker tag jupyter-climate woodwardsh/jupyter-climate && docker push woodwardsh/jupyter-climate

Troubleshooting

• Exit code 137 - need to increase Docker memory e.g. to 4GB
• No space left on device - docker system prune