Using Containers in Science (Docker and Singularity)

A container is a set of processes that are isolated from the rest of the system.

A container provides all files necessary to support the processes

The one big difference between containers and VMs is that containers share the host system’s kernel with other containers.

Containers simplify the way how to ship, build and run applications.

Use docker pull to fetch images from a Docker registry and to save them locally.

docker run creates a container from a Docker image and runs a command inside.

Use the option -v with the docker run command to mount a local folder into the docker container.

To cleanup leftover containers use the command docker rm.

A Dockerfile is a text file containing instructions for building a Docker image.

Use the command docker build to build an image from a Dockerfile.

Specify your bild instruction in a file called Dockerfile.

Pushing Docker images.

Tagging Docker images.

Deleting Docker images or tags.

Using Docker Compose makes developing and using dockerized applications easier most of the time

Use a docker-compose.yml to configure your container(s)

Use docker-compose up -d to start your container(s)

Use docker-compose down to stop your container(s)

Tools which help to understand complex systems

Use the singularity run command to run a Singularity image.

Define the construction manual of a Singularity image in a definitions file.

Singularity is more often available in HPC systems.