Containers with Singularity

The Jackson Laboratory

Online

Mar 17, 2022

9:00 am - 12:00 pm EST (1:00 pm - 4:00 pm UTC)

Instructors: Jason Macklin, Kurt Showmaker, Aaron McDivitt, Richard Yanicky, Lucie Hutchins, David McKenzie

Helpers:

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General Information

Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters in the world, local university or company clusters, a single server, in the cloud, or on a workstation down the hall. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system. Singularity is key to research reproducibility.

Who: The course is aimed at graduate students and other researchers. For IT security reasons this course is only open to JAX employees.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Mar 17, 2022. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.). They should have a few specific software packages installed (listed below).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email susan.mcclatchy@jax.org for more information.

Surveys

Post-workshop Survey

Schedule

Thursday Mar 17

09:00 Introductions
09:10 What is a container?
09:25 Singularity Basics
09:55 Scientific Containers
10:10 Break
10:20 Building and Modifying Containers
10:55 Using Containers & Questions
11:40 Post-workshop surveyEND
12:00 END

Setup

To participate in a workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

  1. Download and install MobaXterm.
  2. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.