PRACTICAL: HMMER (1 of 2)

Overview

Teaching: 10 min
Exercises: 25 min

Questions

• How does genomic sequence alignment software run in parallel using HPC?

Objectives

• Gain experience compiling software on an HPC machine, and running jobs in parallel

• Understand how a concrete software application divides up work, and what implications this has for parallel performance

• Measure how efficiently a software application uses many cores

Introductory slides

Instruction sheet

Key Points

• To run an application in parallel we should understand how it uses threads and/or MPI and how the scheduler and parallel application launcher interact

• Looking at parallel performance can tell us the most efficient way to run software to get a fast answer