Making Python not awful with containers

Overview

Teaching: 10 min
Exercises: 10 min

Questions

Objectives

• Run Python applications using a container

• Use Jupyter Notebook in a container

Why can Python be awful?

Python is a great language for doing all kinds of work, but sometimes it can present issues…

Run a basic Python script from a container

Let’s start by running a very simple hello world example with a basic Python container. To start, cd into the demo directory:

$ cd $ERNZ20/demos/09_python

There is an executable script called helloworld.py.

Use a Python container

Can you use Singularity to run helloworld.py using the container python:3-slim?

Solution

$ singularity exec docker://python:3-slim ./helloworld.py

Hello World!

Build and run a Python container for machine learning

We want to be able to leverage other Python modules to do some actual work, so we need to build Python containers that use tools like pip and conda.

For this example we’ll try installing some ML packages to run a logistic regression model.

Design the def file

Think of how you would write a def file that

• uses jupyter/datascience-notebook:latest from Docker Hub as base image
• installs the Plotly package via /opt/conda/bin/conda install plotly=3.10
• we’ll use this image as an interactive session, so do not care about %startscript

When you are done check this solution

Bootstrap: docker
From: jupyter/datascience-notebook:latest

%post
  /opt/conda/bin/conda install plotly=3.10

Note that we need the full path to the conda executable when using the base image from jupyter/. Because of the way the Docker image was built, without the full path the binary would not be found.

Now, change directory to logistic-regression:

$ cd $ERNZ20/demos/09_python/logistic-regression

Build the container image

The def file above is present as plotly.def. Use it to build an image called plotly.sif. Hint: remember to use sudo!

Solution

$ sudo singularity build plotly.sif plotly.def

In the same directory we have both a Jupyter notebook (LogisticRegression.ipynb) and source code (logreg.py) that we’re going to use.

After you’ve built your image we’ll start up the container and log into our Jupyter notebook server (note the idiomatic expression for Jupyter Notebooks with Singularity):

$ singularity exec -C -B $(pwd):$HOME plotly.sif jupyter notebook --no-browser --port=8888 --ip 0.0.0.0 --notebook-dir=$HOME

Here the -C flag is to completely insulate the container from the host, including the use of a volatile /run directory instead of the host one.

Communication ports

In order to be able to use the web server, you need to ensure that the machine you are running Singularity from has opened the communication port you’re using, in this case 8888.
In cloud virtual machines this will typically involve some setup in the system dashboard.
The machines we provided for this workshop are ready to go in this regard.

The output on the terminal will look like:

[I 14:29:20.678 NotebookApp] JupyterLab extension loaded from /opt/conda/lib/python3.7/site-packages/jupyterlab
[I 14:29:20.679 NotebookApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 14:29:20.682 NotebookApp] Serving notebooks from local directory: /home/ubuntu
[I 14:29:20.682 NotebookApp] The Jupyter Notebook is running at:
[I 14:29:20.682 NotebookApp] http://nimbus1:8888/?token=b2a37a0b893cdbb5949aaad1d27e8fcff80841b0a9ae5b1c
[I 14:29:20.682 NotebookApp]  or http://127.0.0.1:8888/?token=b2a37a0b893cdbb5949aaad1d27e8fcff80841b0a9ae5b1c
[I 14:29:20.682 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:29:20.688 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/ubuntu/.local/share/jupyter/runtime/nbserver-17-open.html
    Or copy and paste one of these URLs:
        http://nimbus1:8888/?token=b2a37a0b893cdbb5949aaad1d27e8fcff80841b0a9ae5b1c
     or http://127.0.0.1:8888/?token=b2a37a0b893cdbb5949aaad1d27e8fcff80841b0a9ae5b1c

Now, locate the last line in the output, and copy in the clipboard the alphanumeric string that follows after token=.
Open your web browser, and type as URL <Singularity machine IP Address>:8888. Paste the clipboard content in the Token field and click on Login.

We’re in the Jupyter Notebook!
From the list of files & directories, click on LogisticRegression.ipynb, and we’ll go through the notebook.

When we’re done, press twice Ctrl-C to kill the Notebook.

Running Python code without Jupyter

Because our Jupyter container has a functioning version of Python installed, we can also use it to run our Python code directly from the command line:

$ singularity exec plotly.sif python ./logreg.py

As a result you should now have a plot saved as a .png file.

Bonus: another machine learning example

If time allows, let’s try another ML example. We’ll build another container image that uses Jupyter. For this this example, change directory to:

$ cd $ERNZ20/demos/09_python/image-classification

In here we have some image data (dataset/), the Jupyter notebook FlowerClassification.ipynb, and a def file.

Write the def file for your Jupyter container

Similar to before, keep the following in mind:

• use jupyter/datascience-notebook:latest from Docker Hub as base image
• install the package mahotas with conda
• install the package opencv-python using pip
• use the complete paths of conda and pip, i.e. /opt/conda/bin/
• do not care about %startscript

Solution

Bootstrap: docker
From: jupyter/datascience-notebook:latest

%post
  /opt/conda/bin/conda install mahotas
  /opt/conda/bin/pip install opencv-python

Build your own container

The current directory has a copy of the def file, class.def; use it to build the image file class.sif.

Solution

$ sudo singularity build class.sif class.def

Launch the Jupyter interactive session

Use the same syntax described above.

Solution

$ singularity exec -C -B $(pwd):$HOME class.sif jupyter notebook --no-browser --port=8888 --ip 0.0.0.0 --notebook-dir=$HOME

Now, locate the last line in the output, and copy in the clipboard the alphanumeric string that follows after token=.
Open your web browser, and type as URL <Singularity machine IP Address>:8888. Paste the clipboard content in the Token field and click on Login.

From the list of files & directories, click on FlowerClassification.ipynb, and we’ll go through the notebook.

When we’re done, press twice Ctrl-C to kill the Notebook.

Key Points

• You can use idiomatic syntaxes of singularity exec to launch interactive sessions of Jupyter Notebooks, similar to RStudio

• Run the same workflow through command line or via Notebook using the same container