Mounting volume to a directory in $NB_USER breaks init.sh

[njacobson-nci]

It appears that mounting a volume to $NB_USER/work will cause a failure in before-notebook.d init.sh.

The only change between these two commands is the volume mounting location inside the container. I removed everything except the bare minimum from the commands I'm running to see what causes the failure. Even explicitly setting the workdir to /home/njacobson or /home/jovyan fails.

It's not an unworkable issue, but it is strange and it's not specific to the work/ folder name. Figure it's worth documenting at least so others don't have to debug it.

Love the repo though, really great work.

docker run --gpus all -it -p 8888:8888 --user root -e NB_USER="njacobson" -v /home/nvadmin/data:/home/njacobson/work/ jupyterlab/cuda/python/scipy:latest
Entered start.sh with args: jupyter lab
/usr/local/bin/start.sh: running hooks in /usr/local/bin/start-notebook.d as uid / gid: 0 / 0
/usr/local/bin/start.sh: running script /usr/local/bin/start-notebook.d/populate.sh
/usr/local/bin/start.sh: done running hooks in /usr/local/bin/start-notebook.d
Updated the jovyan user:
- username: jovyan       -> njacobson
- home dir: /home/jovyan -> /home/njacobson
Ensuring /home/njacobson is owned by 1000:100 
/usr/local/bin/start.sh: running hooks in /usr/local/bin/before-notebook.d as uid / gid: 0 / 0
/usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/init.sh
mv: cannot stat '.local/share/code-server/User/settings.json': No such file or directory

docker run --gpus all -it -p 8888:8888 --user root -e NB_USER="njacobson" -v /home/nvadmin/data:/home/njacobson/ jupyterlab/cuda/python/scipy:latest
Entered start.sh with args: jupyter lab
/usr/local/bin/start.sh: running hooks in /usr/local/bin/start-notebook.d as uid / gid: 0 / 0
/usr/local/bin/start.sh: running script /usr/local/bin/start-notebook.d/populate.sh
/usr/local/bin/start.sh: done running hooks in /usr/local/bin/start-notebook.d
Updated the jovyan user:
- username: jovyan       -> njacobson
- home dir: /home/jovyan -> /home/njacobson
Populating home dir /home/njacobson...
Success!
Ensuring /home/njacobson is owned by 1000:100 
/usr/local/bin/start.sh: running hooks in /usr/local/bin/before-notebook.d as uid / gid: 0 / 0
/usr/local/bin/start.sh: running script /usr/local/bin/before-notebook.d/init.sh
/usr/local/bin/start.sh: done running hooks in /usr/local/bin/before-notebook.d
Running as njacobson: jupyter lab
....

[benz0li]

It appears that mounting a volume to $NB_USER/work will cause a failure in before-notebook.d init.sh.

If "${NB_USER}" != "jovyan", any folder mounted in "/home/${NB_USER}" will prevent the startup from succeeding.

👉 This is because of

jupyterlab-python-docker-stack/base/scripts/usr/local/bin/start.sh

Line 128 in 35b38bc

# The home directory could be bind mounted. Populate it if it is empty

The bind mounted home directory is only populated if it is empty.

[benz0li]

That's one of many reasons why I'm building my own Jupyter docker stack incorporating the changes listed above and mounting the entire home directory.

– jupyter/docker-stacks#1478

[benz0li]

Figure it's worth documenting at least so others don't have to debug it.

Will do.

[njacobson-nci]

That also precludes having any data in the host mounting location as well. Is the solution to mount a working directory to another location?

[benz0li]

That also precludes having any data in the host mounting location as well.

Correct. Bind mounting is only supported for empty folders.

Is the solution to mount a working directory to another location?

I suggest mounting any other [host] folder as a subfolder of /mnt in the container.
ℹ️ Filesystem Hierarchy Standard > ... > 3.12. /mnt : Mount point for a temporarily mounted filesystem

[benz0li]

I had the following in mind:

• Mounting the entire home directory preserves
  1. user specific configuration files for applications ("dot files/directories") and
  2. user generated content that only the user is supposed to have access to.
• ~/projects is the so called working directory.
  1. Every project (e.g. git repository) should be placed in its own subfolder.
  2. My credo and advice: Projects should contain only code and no data¹.
• Data should be provided in separate locations.
  1. As subfolders of /mnt, in data bases, via Hadoop, via Spark, etc.
  2. Access rights to the data can thus also be managed separately.

Footnotes

1. An exception may be made for small sample data sets. ↩

[benz0li]

@njacobson-nci Is https://github.com/b-data/jupyterlab-python-docker-stack/blob/main/CUDA.md#run-container OK?

If yes, please close this issue.

[njacobson-nci]

Yeah thanks for documenting that!

[benz0li]

❗ Bind mounting a subfolder of the home directory is only possible for images with Python version ≥ 3.12.2.