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Containers

This page gives background on what containers are and why we use them.

What are Containers?

Containers:

• Includes all dependencies (frameworks, libraries, etc.) required to run an application in an efficient and bug-free.
  • They lack external dependencies.
• Lightweight (occupies less free memory space) makes them easy/quick to move “between” computers.
• Application runs in isolation.

Benefits:

• Portable: This allows applications to work efficiently in different computer environments (portable).
• Reproducible: Ensures scientific results are consistent
• Shareable: Standard mechanism for deploying complex applications

Types of Containers

The most common types of container are Docker and Singlularity, but more are coming out including Shifter, CharlieCloud and Podman.

What are Docker Containers?

Docker is an open-source platform that helps a user to package an application and its dependencies into a Docker Container for the development and deployment of software.

What is Singularity?

Singularity, was built in 2015 at Lawrence Berkeley National Labs. It is free and open source. Singularity does not rely on the docker ecosystem to build its containers, while Shifter and CharlieCloud do.

Singularity will work with StaPH-B’s docker images!!

The paper for Singularity is here.

Singularity vs Docker

Features	Docker	Singularity
Capable of running Docker containers	X	X
Zero configuration in SCBS environment		X
Needs elevated privileges to run	X

Docker needs root access to run - this leads to security issues.

In summary Singlularity is:

• More Secure
• No layers – Singularity images are stored as read-only .sif files. This makes them easy to share
• Makes different assumptions
  • user inside container == user outside the container
    • Docker assumes (unless you tell it otherwise) you want to be the root user and if you generate files like this inside the container they will be “owned” by the root and you won’t have permissions to modify them.
  • Auto-mounts home dir inside container (when you use shell) – allows you to use the same paths both inside and outside the container.
    • You can add the flag(s) --no-home and -B $PWD:/dataif you don’t want to mount the home dir and want to do something else.
    • With docker we typically mount what we want in /data
• More likely to be supported on a HPC systems – AKA you can’t have docker on Aspen, but you can have Singularity

Learn More About Containers

Scicomp gives a ~45min Container Seminar, which some of this material and images are pulled from.