Can we run jupyter lab in a docker container using --user / -u

Question

I am trying to add jupyter-lab to one of my existing docker image (with R, python, and work-specific libraries) for interactive tests.

A working example is this Dockefile:

FROM my_existing_image

# Install jupyter lab (assuming python3 and pip3 already installed)
RUN pip3 install jupyterlab

# Declare port used by jupyter-lab
EXPOSE 8888

# Set default command
CMD ["jupyter", "lab", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]

However, we have a shared NFS drive which we mount on all users machine in /mnt/NAS . To access shared folders from docker containers with correct permissions, we typically start them with the following flags:

docker run -u $(id -u ${USER}):$(id -g ${USER}) -v /mnt:/mnt my_image

However, the -u ( --user ) option prevents juyter-lab to start properly and I get this error message:

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/dist-packages/traitlets/traitlets.py", line 528, in get
    value = obj._trait_values[self.name]
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/jupyter-lab", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/dist-packages/jupyter_core/application.py", line 270, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/usr/local/lib/python3.7/dist-packages/traitlets/config/application.py", line 663, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-7>", line 2, in initialize
  File "/usr/local/lib/python3.7/dist-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/usr/local/lib/python3.7/dist-packages/notebook/notebookapp.py", line 1766, in initialize
    self.init_configurables()
  File "/usr/local/lib/python3.7/dist-packages/notebook/notebookapp.py", line 1380, in init_configurables
    connection_dir=self.runtime_dir,
  File "/usr/local/lib/python3.7/dist-packages/traitlets/traitlets.py", line 556, in __get__
    return self.get(obj, cls)
  File "/usr/local/lib/python3.7/dist-packages/traitlets/traitlets.py", line 535, in get
    value = self._validate(obj, dynamic_default())
  File "/usr/local/lib/python3.7/dist-packages/jupyter_core/application.py", line 100, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/usr/local/lib/python3.7/dist-packages/jupyter_core/utils/__init__.py", line 13, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/usr/lib/python3.7/os.py", line 211, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/lib/python3.7/os.py", line 211, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/lib/python3.7/os.py", line 211, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/lib/python3.7/os.py", line 221, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/.local'

I could not figure a proper way to configure my Dockerfile to get access to the drive and jupyter-lab working. We often use Rocker/Rstudio containers in the same way without any problem.

Would you have suggestions? Thank you for your help.

Answer 1

I got the same error message, because the container's $HOME variable was the root / , which is not writable without sudo .

So, for me, the solution was to set $HOME pointing to a writable directory. For example,

mkdir ./.home  # make a virtual home directory
docker run \
    -u $(id -u):$(id -g) -v $(pwd):$(pwd) -w $(pwd) -e HOME=$(pwd)/.home \
    -it --rm --init -p 8888:8888 your_image \
    jupyter lab --ip=0.0.0.0 --port=8888 --no-browser