Application Protability through Singularity

This was presented by Jaeyoung Chun on Feb 3, 2017. The presentation covers the following topics, and the presentation file can be found here.

• Goals
• Virtualization
• Docker vs. Singularity at 10,000 ft.
• Creating Image
• Running Container
• Physical Size of Image File
• Memory Usage at Runtime
• Data Access Issues

Examples

Here are some of the examples you can try out.

Virtual Machines

Most of the examples here requires Singularity to be installed on your machine. The following virtual machines comes pre-built with Singularity. But, you need to have Vagrant on your machine to programatically manage virtual machines and environments.

• Singularity on CentOS
• Singularity on Ubuntu

Running Containers

• Running samtools by creating a container image from a Singularity image definition file
• Running samtools by creating a container image from a Docker image definition file

File Sharing

Two primary methods are provided to share files on the host with the container.

By Replacing User's Home Directory:

$ singularity shell --home /home/chunj/tmp-home samtool.img

By Using Bind Points

$ singularity shell --bind /ifs/data:/ifs/data samtools.img

This only works when the following two conditions are met:

1. The system administrator has enabled user control of binds (via user bind control = yes) in singularity.conf.

2. Either

   • the system administrator has enabled the use of file system overlay (via enable overlay = yes) in singularity.conf)

   or

   • the bind point (/ifs/data in this case) already exists within the container.