jupyter-simple

Jupyter Notebook

This is an example that uses singularity-compose to bring up a jupyter notebook instance. We use continuumio/miniconda3 as a base image. We bind jupyter/notebooks to /opt/notebooks for our notebook directory. You can change this path in the singularity-compose.yml file if needed.

Singularity Compose

First, make sure you have it installed.

$ pip install singularity-compose --user

Clone the repository with this example

$ git clone https://www.github.com/singularityhub/singularity-compose-examples
$ cd singularity-compose-examples/jupyter-simple

Build

Build the containers. You will need sudo to build from a recipe.

$ singularity-compose build

Once you've built, you should see the container jupyter.sif in it's respective folder:

$ ls jupyter/
jupyter.sif  notebooks  Singularity

Up

You can bring up the container as an instances. Since we expose port 8888, this requires sudo (unless you have fakeroot that is working correctly).

$ singularity-compose up
Creating jupyter

Check to see them running:

$ singularity-compose ps

You are going to need to use singularity-compose logs to get your output and error streams:

...
[I 16:32:20.139 NotebookApp] Writing notebook server cookie secret to /root/.local/share/jupyter/runtime/notebook_cookie_secret
[W 16:32:20.403 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[I 16:32:20.436 NotebookApp] JupyterLab extension loaded from /opt/conda/lib/python3.7/site-packages/jupyterlab
[I 16:32:20.436 NotebookApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 16:32:20.438 NotebookApp] Serving notebooks from local directory: /opt/notebooks
[I 16:32:20.438 NotebookApp] The Jupyter Notebook is running at:
[I 16:32:20.438 NotebookApp] http://vanessa-ThinkPad-T490s:8888/?token=2df03ba6a710d262ff5236459f891d7be2d8674aa587626f
[I 16:32:20.438 NotebookApp]  or http://127.0.0.1:8888/?token=2df03ba6a710d262ff5236459f891d7be2d8674aa587626f
[I 16:32:20.438 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 16:32:20.441 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///root/.local/share/jupyter/runtime/nbserver-16-open.html
    Or copy and paste one of these URLs:
        http://vanessa-ThinkPad-T490s:8888/?token=2df03ba6a710d262ff5236459f891d7be2d8674aa587626f
     or http://127.0.0.1:8888/?token=2df03ba6a710d262ff5236459f891d7be2d8674aa587626f

And then of course open your browser to the url (the last in the list) given in the logs to see your notebook.

We don't see files because the notebook directory is empty! Remember that your files are being saved on your local machine under jupyter/notebooks and you can customize this path to save elsewhere.

Shell

If you need to look inside the container or debug, you can use shell:

$ singularity-compose shell jupyter
> cat /etc/hosts
10.22.0.2	jupyter
127.0.0.1	localhost

# The following lines are desirable for IPv6 capable hosts
::1     ip6-localhost ip6-loopback
fe00::0 ip6-localnet
ff00::0 ip6-mcastprefix
ff02::1 ip6-allnodes
ff02::2 ip6-allrouters

Down

And of course when you finish, don't forget to bring the instances down.

$ singularity-compose down
Stopping (instance:jupyter)