Introduction to High-Performance Computing: Glossary

Key Points

Why use High Performance Computing?
  • High Performance Computing (HPC) is a tool to calculate faster or larger than is possible on your own system.

  • HPC relies on using parallelism to provide performance improvements.

  • HPC typically involves connecting to very large computing systems elsewhere in the world.

What is an HPC system?
  • A high-performance computer system provides a larger compute capability than is possible to package in a personal computer.

  • HPC systems are typically an aggregation of a bunch computers, each one of which can look pretty similar to your personal computer.

  • HPC systems are usually accessed remotely, over the network.

  • HPC systems are usually shared among many users. Each user typically gets a dedicated portion of the computer’s resources for a period of time.

  • Special measures have to be taken to provide a file system that can keep up with an HPC system.

  • HPC systems often provide a lot of different software packages, and provide ways of selecting and configuring them to get the environment you need.

Connecting to the HPC system
  • To connect to a remote HPC system using SSH: ssh

Transferring files
  • wget downloads a file from the internet.

  • sftp/scp transfer files to and from your computer.

  • You can use an SFTP client like FileZilla to transfer files through a GUI.

Scheduling jobs
  • The scheduler handles how compute resources are shared between users.

  • Everything you do should be run through the scheduler.

  • A job is just a shell script.

  • If in doubt, request more resources than you will need.

Accessing software
  • Load software with module load softwareName

  • The module system handles software versioning and package conflicts for you automatically.

  • Loading modules must also be done in scheduler job scripts.

Using resources effectively
  • The better your resource request estimates, the better throughput you will see.

Using shared resources responsibly
  • Be careful how you use the login node.

  • Again, don’t run stuff on the login node.

  • Don’t be a bad person and run stuff on the login node.

How does parallel computing work
  • There are different parallel strategies available to get performance on HPC systems.

  • The approach you use depends on the software you are using and your research problem.

  • Most HPC systems allow you to use different parallel strategies in combination.

Understanding what resources to use
  • Basic benchmarking allows you to use HPC resources more effecively.

  • Performance is generally more useful metric than runtime or speedup.

  • A small number of measurements can make a large difference.

Future of HPC
  • Future HPC architectures will have more powerful compute nodes through more cores and/or the use of accelerators.

  • Novel memory and I/O technologies will provide new ways to use HPC systems.

Bootstrapping your use of HPC
  • Understand the next steps for you in using HPC.

  • Understand how you can access help and support to use HPC.