Summary and Schedule
This lesson is created using The Carpentries Workbench and is based on Introduction to High-Performance Compting. It has been customised to fit users of WEHI Milton.
Some of the examples used in this lesson are based on material developed by Lev Lafayette from Research Platform Services at the University of Melbourne.
This course is for scientists who have no experience with high performance computing (HPC) and want to learn how to start using WEHI HPC, Milton. The course teaches basics of interacting with HPC and what it means to use a batch system (scheduling system) like SLURM. Scientists will learn how to login into Milton, prepare their scripts and submit jobs. It will also cover, estimating resources and job efficiency.
This course will be delivered mostly using live-coding demonstrations and exercises. The entire workshop is delivered in approximately 3 1-hour chunks with breaks in between.
This course is maintained by WEHI Research computing
- Julie Iskander @jIskCoder
- Adam Taranto @eAdamtaranto
- Michael Milton @multimeric
Course Prerequisites
- Attending Introduction to Linux workshop or watching recording that will be available here
- Read this page as a refresher to Linux commands
- Access to Milton is required and can be done by sending email to support@wehi.edu.au
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. What is a HPC? | Why would I be interested in High Performance Computing (HPC)? |
| Duration: 00h 15m | 2. Accessing Milton |
How do I log in to Milton?Where can I store my data? |
| Duration: 00h 36m | 3. Environment Modules | How do we load and unload software packages? |
| Duration: 00h 53m | 4. Introducing Slurm |
What is a scheduler and why does a cluster need one? What is a partition? |
| Duration: 01h 13m | 5. Submitting a Job |
How do I launch a program to run on a compute node in the
cluster? How do I capture the output of a program that is run on a node in the cluster? How do I change resource requested or time-limit |
| Duration: 02h 00m | 6. Lunch Break | |
| Duration: 02h 40m | 7. Evaluating Jobs |
How to evaluate a completed job? How to set event notification for your jobs? |
| Duration: 03h 02m | 8. Slurm Commands | How to use Slurm commands? |
| Duration: 03h 24m | 9. Interactive Slurm Jobs | How to start and exit an interactive Slurm job? |
| Duration: 03h 34m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Excercise Sets
Download the exercise files to your home directory.
# Go to HOME dir
cd ~
# Download the demo.tar.gz file
curl -L -o demo.tar.gz https://github.com/WEHI-Education/Workshop-IntroToHPC-Slurm/raw/main/episodes/src/demo.tar.gz
# Decompress the tar.gz file
tar -xzvf demo.tar.gz
# Clean up the downloaded tar.gz file
rm demo.tar.gzSoftware Setup
Details
To follow this course you will need access to Milton and a terminal application. You can request access, if you do not already have via sending an email to support@wehi.edu.au
Use GitBash (also available from the WEHI Managed Software Centre)
Use Terminal.app
Use Terminal