Introduction to High Performance Computing

About

This one-day workshop introduces high performance computing using the Jackson Laboratory’s computing cluster. The goal is to teach novice programmers to use powerful tools and computing resources, and to engage in best practices for using these resources. The emphasis of this workshop is to give attendees a strong foundation in the fundamentals of the bash shell and to teach best practices for scientific computing in high performance computing environments. By the end of this workshop, participants will be able to:

• Use the UNIX command line to operate a computer, connect to a cluster, and write simple shell scripts.
• Submit and manage jobs on a cluster using a scheduler, transfer files, and use software through environment modules.
• Find, create and manage containers using Singularity.

This workshop is intended exclusively for Jackson Laboratory employees. The workshop will be offered in conference rooms at The Jackson Laboratory in Farmington, Connecticut and Bar Harbor, Maine, however, remote participation from desks, home, or away will not be supported.

Prerequisites: None; you do not need to have any previous knowledge of the tools that will be presented at the workshop. Participants must bring a laptop with a Mac or Windows operating system (not a tablet, Chromebook, etc.) Windows users: please ask the IT help desk to install MobaXterm or PuTTY.

Syllabus

The Unix Shell

• Files and Directories
• History and Tab Completion
• Pipes and Redirection
• Looping Over Files
• Creating and Running Shell Scripts
• Finding Things

High Performance Computing

• Working on a Remote HPC System
• Scheduling Jobs
• Using Shared Resources Responsibly

Containers with Singularity

• Introduction to Singularity
• Interactive Exploration of Containers
• Build Your Own Containers

For full course information and specifics please click here.