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Interview: starting out in high performance computing

5 March 2020

This month we meet Jonno Bourne, a researcher in the Bartlett who has been using Myriad over the past 6 months. We asked him to tell us a bit about his work and what his experience has been like as a relative newcomer to high performance computing.

Tell us a bit about yourself and your research 

My research is in complex network analysis. I explore the relationships between different parts of a network and how these relationships strengthen or weaken the network when it is under attack. 

How much experience in computational research did you have before starting this project? 

All of my research is computational; however, I had never used an HPC system before. I had tried using some commercial cloud services with limited success and great expense so was keen to trying something else! 

What were you trying to do? 

When I am using Myriad I am simulating hundreds of thousands to millions of attacks on various network configurations, or I am finding the high dimensional embedding of the network which lets me show a network that has hundreds of dimensions in a simple way. When I combine these two datasets I can see how well my embedding predicts the robustness of the network. 

What was the biggest pain in getting it all to work? 

The most challenging thing in using Myriad is getting your head around the concept of using a remote computer and not being able to re-run bits when the code doesn't work. Interpreting the error messages can be hard and writing code that helps you know what stage the computation was at when it crashed is very useful. I print a lot of information so I can see what happened if something goes wrong when the script is running 

What advice would you give to someone who is about to start using a high performance computing platform for the first time? 

If you are doing computation with lots of loops, or you are doing lots of simulations or models, using the HPC is extremely helpful. Calculations that would take days or even weeks are done overnight and it doesn't require your computer to be left with "Do not touch" stickers all over it.  

The introduction to HPC course run by RITS is fantastic if you have never done anything like this before. I was running my code and getting results by the end of the week when I did the course.  

Being able get loads of results quickly can have substantial side benefits as well. It’s not just doing more or bigger jobs; HPC encourages smarter not just faster working. I gained a deeper understanding into my algorithms which allowed me to optimise them, speeding up the rate at which things were completed over 100 times. This has allowed me to do much more with my time and things I previously needed the HPC for I can now run on my laptop anyway.