Introduction to High Performance Computing (Part 2): Cheatsheets for Queuing System Quick Reference

Key Points

Case Study: Constructing Complex Mesoscopic Surfaces

  • HPC systems are a tool that can be used in many research areas
Working on a remote HPC system

  • An HPC system is a set of networked machines.

  • HPC systems typically provide a login node and a set of worker nodes.

  • Files saved on one node are available everywhere.
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

  • Unload software with module purge

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

  • The smaller your job, the faster it will schedule.
Using shared resources responsibly

  • Be careful how you use the login node.

  • Your data on the system is your responsibility.

  • Plan and test large data transfers.

  • It is often best to convert many files to a single archive file before trasferring.
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.

Cheatsheets for Queuing System Quick Reference

Glossary

The following list captures terms that need to be added to this glossary. This is a great way to contribute.

Accelerator
to be defined
Beowulf cluster
to be defined
Central processing unit
to be defined
Cloud computing
to be defined
Cluster
a collection of computers configured to enable collaboration on a common task by means of purposefully configured hardware (e.g., networking) and software (e.g. workload management).
Distributed memory
to be defined
Grid computing
to be defined
High availability computing
to be defined
High performance computing
to be defined
Interconnect
to be defined
Node
to be defined
Parallel
to be defined
Serial
to be defined
Server
to be defined
Shared memory
to be defined
Slurm
to be defined
Supercomputer
… “a major scientific instrument” …
Workstation
to be defined
Grid Engine
to be defined
Parallel File System
to be defined