SageMath Docker Image

This is an attempt to standardize and streamline computational work that combines SnapPy, SageMath, and friends via a custom Docker image that is based around Ubuntu 20.04 LTS and the latest and greatest SageMath. It is indirectly derived from the official sagemath/sagemath Docker image, but includes SnapPy, and the Python interfaces to Regina, and PHCPack.

A container instance of this image starts a shell as the user sage with all the environment variables set as if you had executed sage -sh.

This image takes a long time to build, even on a fast computer, since it compiles SageMath from source, and weighs in at 5.2 GB (1.6 GB compressed). We recommend you use the posted image on DockerHub via:

docker pull computop/sage
docker run -it computop/sage

Here, the first command downloads the image from DockerHub and the second starts a container that is running said image. Moving files between the container and the rest of the world can be done using scp or having the container mount a local directory as in this example:

docker run -it --mount type=bind,source="$HOME/Dropbox/linux_share",target=/home/sage/linux_share computop/sage

where the directory linux_share inside the user's Dropbox folder is shared.

If you want to use Sage's Jupyter notebook interface, start the container via:

docker run -it -p 127.0.0.1:8888:8888 computop/sage

and in said container type:

sage --notebook

and then point your computer's web browser to http://localhost:8888. If you want to use the beta JupyterLab, which will eventually superseded Jupyter, you can instead do:

sage --notebook jupyterlab

In JupyterLab, you have access not just to notebooks but also Python consoles and shell terminal windows.

Python 2 versus Python 3

The images for SageMath 8.9 and older use Python 2 (and Ubuntu 16.04) and those for SageMath 9.0 and newer use Python 3 (and Ubuntu 18.04 or 20.04). You can always request Docker run a particular version of the image, for example if you want SageMath 8.9 do:

docker run -it computop/sage:8.9

Components

A partial list of included software:

• SageMath
• SnapPy
• Regina
• Two Python interfaces to PHCPack
• pandas
• pe
• gridlink
• flipper and curver
• heegaard
• pygraphviz
• snap

We no longer include HIKMOT as it is not compatible with Python 3.

Building

To build from scratch, which takes 1.3 hours using all 8 cores on a Mac Pro:

docker build --tag=computop/sage sage

If compiling Sage fails, make sure the Docker application is configured so that it can use at least 4GB of memory.

Put out on DockerHub:

docker push computop/sage