Running Docker containers via enroot

Running Docker containers via enroot

You can't run Docker containers directly via `docker` on the SCF because of security considerations. However you can import a Docker container and run it using software called `enroot`. One can also use `udocker`, however we haven't documented that.

Here's an example using the Docker container for R/RStudio available from the Rocker project.

First we download the image from DockerHub and create the enroot image.

# Download Docker image:
$ enroot import docker://rocker/r-ver:latest
# Create container from image:
$ enroot create --name=myRimage rocker-r.sqsh

The image, in this case `rocker-r.sqsh`, is saved as a single file (in SquashFS format) in your working directory.

We can run the default application in the container (R in this case) like this. By default the user inside the container is the same as the user outside the container.

$ enroot start myRimage 

We can install additional software in the container as follows. Here we need to be the root user once we are inside the container and we need the container to be writeable (`-w`):

$ enroot start --root -w myRimage bash
# run some admin-level commands in the container as the root user in the container, then exit
root@arwen:/# apt update && apt install <some packages>; exit 

Mounting your directories inside the container

You can access your SCF directories (both for reading and writing) inside the container by mounting a directory using `--mount`, specifying where in the container filesystem to make it available.

If you're mounting your home directory, one option is to mount it at the same location inside the container as its location outside the container. This allows applications inside the container to work with your home directory seamlessly. This also allows the applications to modify files in your home directory. For example you could end up installing R or Python packages from inside the container that are then available in the future either from inside the container or not. Of course that might or might not be what you want.

$ enroot start -w --mount ${HOME}:${HOME} myRimage bash
username@arwen:/> cd  # change to home directory
username@arwen:~> pwd

Alternatively you might not want to mount your home directory to the same path, to avoid modifying your home directory outside the container. But you might still want to mount the home directory somewhere else inside the container to provide access to files. Here we mount the home directory at `/home`.

$ enroot start -w --mount ${HOME}:/home myRimage bash
username@arwen:/$ cd   # go to home directory
username@arwen:~$ pwd
username@arwen:~$ ls
username@arwen:~$ touch test
username@arwen:~$ ls
username@arwen:~$ cd /home
username@arwen:/home$ ls     # files in SCF home directory, mounted at /home output.txt