Blog

By Edward Wallace, School of Biological Sciences, University of Edinburgh.

Why I need sustainable software for my research

I run a lab, or research group, in the School of Biological Sciences at Edinburgh. My group  is funded by the Wellcome Trust, the Royal Society and BBSRC. We're interested in questions about how cells decide which proteins to make and when. Also, how cells change which proteins they make when they learn something from the environment and need to change what they're doing. In the 21st century we collect some very large datasets to measure this. There are datasets based on sequencing the RNA, which encodes protein, and datasets that measure all the proteins in cells at the same time. These datasets are measuring thousands of different things in many samples, often dozens of samples. Each dataset is gigabytes in size, and so it's quite hard work to dig into them and get the simplest and most relevant answers about what cells are doing.

Alexey Bobrick (Lund University(link is external), Sweden) was an HPC-Europa3 visitor hosted by Dr Silvia Toonen (link is external)at the Institute of Gravitational Wave Astronomy(link is external), University of Birmingham, UK. Because of COVID-19 restrictions, Alexey's visit has been split between his time in Birmingham (from 1–23 November), and working remotely from Sweden until 23 December. In this post Alexey tells us about his trip to Birmingham.

I study binary stellar astrophysics at Lund University, Sweden. In Birmingham my host, Dr Silvia Toonen, is one of the leading experts in triple and binary stellar evolution. I arrived at my accommodation in the middle of the autumnal Edgbaston Park area next to Birmingham University, and next morning I met my host. She kindly showed me around the campus and introduced me to her colleagues. The image shows me and my host, on one of the top floors in Birmingham University.  We then launched into many science discussions, which continued in the following weeks, together with meetings, work, calculations and more discussions.

EPCC has embarked on a new collaboration with Prof. Yves Wiaux (Heriot-Watt University) to advance algorithms for high-precision and high-sensitivity computational imaging. 

The EIRA (Extreme-Scale Precision Imaging in Radio Astronomy) collaboration will focus on radio astronomy, which uses radio telescopes to collect data. This allows observation of the sky with antennae arrays at otherwise inaccessible angular resolutions and sensitivities. Algorithms being developed at Heriot-Watt University will address the challenges of building images from these incomplete linear data sets.

Friday 13 November, 11:05–11:35 am ET

This Friday I am presenting work on accelerating Nekbone on FPGAs at the SC20 H2RC workshop. This is driven by our involvement in the EXCELLERAT CoE, which is looking to port specific engineering codes to future exascale machines.

One technology of interest is that of FPGAs, and a question for us was whether porting the most computationally intensive kernel to FPGAs and enabling the continuing streaming of data could provide performance and/or energy benefits against a modern CPU and GPU. We are focusing on the AX kernel, which applies the Poisson operator, and accounts for approximately 75% of the overall code runtime.