NicoMosty/jupyterlab-julia-docker-stack

See the CUDA-enabled JupyterLab Julia docker stack for GPU accelerated docker images.

JupyterLab Julia docker stack

Multi-arch (linux/amd64, linux/arm64/v8) docker images:

glcr.b-data.ch/jupyterlab/julia/base
- glcr.b-data.ch/jupyterlab/julia/ver (1.5.4 ≤ version < 1.7.3)
glcr.b-data.ch/jupyterlab/julia/pubtools

Images considered stable for Julia versions ≥ 1.7.3.
👉 The current state may eventually be backported to versions ≥ 1.5.4.

🔬 Check out jupyterlab/julia/pubtools at https://demo.jupyter.b-data.ch.

Build chain

base → pubtools

Features

JupyterLab: A web-based interactive development environment for Jupyter notebooks, code, and data. The images include
- code-server: VS Code in the browser without MS branding/telemetry/licensing.
- Git: A distributed version-control system for tracking changes in source code.
- Git LFS: A Git extension for versioning large files.
- Julia: A high-level, high-performance dynamic language for technical computing.
- Pandoc: A universal markup converter.
- Python: An interpreted, object-oriented, high-level programming language with dynamic semantics.
- Quarto: A scientific and technical publishing system built on Pandoc.
  ℹ️ pubtools image
- TinyTeX: A lightweight, cross-platform, portable, and easy-to-maintain LaTeX distribution based on TeX Live.
  ℹ️ pubtools image
- Zsh: A shell designed for interactive use, although it is also a powerful scripting language.

👉 See the Version Matrix for detailed information.

The following extensions are pre-installed for code-server:

Subtags

{JULIA_VERSION,latest}-root: Container runs as root
{JULIA_VERSION,latest}-devtools: Includes the requirements according to
- coder/code-server > Docs > Contributing
- julia-vscode/julia-vscode > Contributing
{JULIA_VERSION,latest}-devtools-root: The combination of both
{JULIA_VERSION,latest}-docker: Includes
- docker-ce-cli
- docker-buildx-plugin
- docker-compose-plugin
- docker-scan-plugin
{JULIA_VERSION,latest}-docker-root: The combination of both
{JULIA_VERSION,latest}-devtools-docker: The combination of both
{JULIA_VERSION,latest}-devtools-docker-root: The combination of all three

Prerequisites

This projects requires an installation of docker.

Install

To install docker, follow the instructions for your platform:

Usage

Build image (base)

latest:

cd base && docker build \
  --build-arg JULIA_VERSION=1.8.5 \
  -t jupyterlab/julia/base \
  -f latest.Dockerfile .

version:

cd base && docker build \
  -t jupyterlab/julia/base:MAJOR.MINOR.PATCH \
  -f MAJOR.MINOR.PATCH.Dockerfile .

For MAJOR.MINOR.PATCH ≥ 1.7.3.

Create home directory

Create an empty directory using docker:

docker run --rm \
  -v "${PWD}/jupyterlab-jovyan":/dummy \
  alpine chown 1000:100 /dummy

It will be bind mounted as the JupyterLab user's home directory and automatically populated on first run.

Run container

❗ Always mount the user's entire home directory. Mounting a subfolder prevents the container from starting.¹

self built:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  jupyterlab/julia/base[:MAJOR.MINOR.PATCH]

from the project's GitLab Container Registries:

docker run -it --rm \
  -p 8888:8888 \
  -u root \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  -e NB_UID=$(id -u) \
  -e NB_GID=$(id -g) \
  -e CHOWN_HOME=yes \
  -e CHOWN_HOME_OPTS='-R' \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

IMAGE being one of

The use of the -v flag in the command mounts the empty directory on the host (${PWD}/jupyterlab-jovyan in the command) as /home/jovyan in the container.

-e NB_UID=$(id -u) -e NB_GID=$(id -g) instructs the startup script to switch the user ID and the primary group ID of ${NB_USER} to the user and group ID of the one executing the command.

-e CHOWN_HOME=yes -e CHOWN_HOME_OPTS='-R' instructs the startup script to recursively change the ${NB_USER} home directory owner and group to the current value of ${NB_UID} and ${NB_GID}.
ℹ️ This is only required for the first run.

The server logs appear in the terminal.

Using Docker Desktop

Creating a home directory might not be required. Also

docker run -it --rm \
  -p 8888:8888 \
  -v "${PWD}/jupyterlab-jovyan":/home/jovyan \
  IMAGE[:MAJOR[.MINOR[.PATCH]]]

might be sufficient.

Similar project

jupyter/docker-stacks

What makes this project different:

Multi-arch: linux/amd64, linux/arm64/v8
ℹ️ Since Julia v1.5.4 (2021-03-11)
Base image: Debian instead of Ubuntu
IDE: code-server next to JupyterLab
Just Python – no Conda / Mamba

See Notes for tweaks, settings, etc.

Contributing

PRs accepted.

This project follows the Contributor Covenant Code of Conduct.

License

The only exception is the use case described at Jupyter Docker Stacks > Quick Start > Example 2. ↩