Introduction to HPC

The aims of this lesson are that you should:

  • Be able to login to the University HPC service, Balena
  • Understand the different resources and partitions available on Balena
  • Understand what storage is available on Balena
  • Be able to find the software you want to use
  • Understand why we use a scheduler and be familiar with its capabilities.
  • Know how to create you own jobscript
  • Be able to submit and manage workloads on Balena
  • Be able to use interactive nodes for Test and Development
  • Be able to use use visualisation tools
  • Know where to find more information and how to ask for help

Prerequisites:

To complete this lesson you should:

  • Be familar with working in the Linux teminal (see Introduction to Linux)
  • Want or need to use compute resource beyond your personal computer

Registration

If you ateend a delivery of this course, or just work through it in your own time please complete the registration form for our records:

Registration/Attendence form

Useful Links and emails

  • Balena Wiki

There is a wiki with information about Balena at: https://wiki.bath.ac.uk/display/BalenaHPC/Getting+Started

  • ARC website

https://www.bath.ac.uk/professional-services/advancing-research-computing/

  • Research Software Skills Moodle Page

https://moodle.bath.ac.uk/course/view.php?id=58752

  • HPC Support: hpc-support@bath.ac.uk
  • RSE-Support: rse-support@bath.ac.uk

Schedule:

Time Episode Description
0:00 Introduction Introduction
0:15 Accessing Balena Access and Login to Balena
0:30 Data and storage on Balena Filesystems on Balena and how to use them
0:45 Balena Architecture Overview of Balena's architecture
1:00 How to access pre-built software Use module to access software, libraries and tools
1:15 Slurm on Balena How to interact with the scheduler
1:30 Running Jobs Run batch and interactive jobs
1:50 Running Visualisation Jobs Running jobs on Visualisation Nodes

Housekeeping

  • Look up from the screen!
  • Attendence/registration form link above or tab at top of Team
  • Refreshment/comfort breaks
  • Questions anytime – lets us know if you need any assistance - it's why we're here.
  • Polls to check progress
  • Feedback at the end of the training

Housekeeping: Face-to-face

  • Attendance sheet
  • Fire alarm
  • Refreshment/comfort breaks
  • Questions anytime – lets us know if you need any assistance - it's why we're here.
  • Post-it notes
  • Feedback at the end of the training

bash magic

Throughout the lesson you will be asked to run commands, which will be in code cells which are sections with In and a number next to the, something like:

In [5]:

This teaching material is generated using Jupyter notebooks with nbfancy which help us to generate and maintain the material. In order to execute commands in the terminal we make use of bash magic which allows us to make calls to the terminal from within the notebook. Whenever you see a code block containing commands you are asked to run you it will be preceded by %%bash2. You do not need to enter this and it will return an error. Wherever this is used we have tried to include a reminder for you not to enter it:

%%bash2 # Ignore this line, it is to help us prepare teaching materials
# You should just run the commands that follow