Multi-million pound supercomputer speeds up research at the University of Bristol
26 May 2017
Research and teaching at the University of Bristol will now benefit from one of the fastest and most advanced supercomputing facilities in the UK, capable of up to 600 trillion calculations per second.
The new multi-million pound system, called Blue Crystal 4 (BC4), is three times faster than its predecessor and will allow researchers to process vast amounts of complex data at record speeds.
Over 1,000 researchers and PhD students in areas such as paleobiology, biochemistry, physics, molecular modelling, life sciences, and aerospace engineering will benefit from the new system.
Supercomputers are regarded as the 'third pillar' of modern research due to their important role in speeding up calculations and analysis which would previously have taken many years to complete.
The University of Bristol has invested £16 million in High Performance Computing (HPC) and research data storage in the last 10 years. Uses for Blue Crystal have evolved to include teaching, with students on six courses learning how to use HPC for research projects and real-life applications.
Professor Nishan Canagarajah, Pro Vice-Chancellor for Research at the University of Bristol, said: "This new supercomputer reinforces Bristol's position as one of the leading centres for HPC in the world. Over the past 10 years, its role in world-leading, often life-saving research, has become even more evident and we’re committed to staying ahead of the game.
"In addition to research, we take pride in offering taught courses on HPC for our students which prepare them for their future in this important field."
Designed, integrated and configured by the HPC, storage and data analytics integrator OCF, BC4 has more than 15,000 cores making it the largest UK university system by core count and a theoretical peak performance of 600 Teraflops.
Dr Christopher Woods, EPSRC Research Software Engineer Fellow at the University of Bristol, said: "We have researchers looking at whole-planet modelling with the aim of trying to understand the earth's climate, climate change and how that’s going to evolve, as well as others looking at rotary blade design for helicopters, the mutation of genes, the spread of disease and where diseases come from.
"Early benchmarking is showing that the new system is three times faster than our previous cluster – research that used to take a month now takes a week, and what took a week now only takes a few hours. That's a massive improvement that'll be a great benefit to research at the University."
The Blue Crystal supercomputer facility played a pivotal part in a €1.8 million study into Ebola, looking at the speed of virus evolution, and the corresponding effect on vaccines, diagnostics and treatment.
Dr David Matthews, Senior Lecturer in Virology at the University of Bristol, who led the Bristol component of the study, explained: "The capabilities of Blue Crystal were invaluable to our research. We used it to analyse raw data on the Ebola virus in 179 patient blood samples to determine the precise genetic make-up of the virus in each case. This allowed the team to examine how the virus evolved over the previous year, informing public health policy in key areas such as diagnostic testing, vaccine deployment and experimental treatment options."
This complex data analysis process took around 560 days of supercomputer processing time, generating nine thousand billion letters of genetic data before reaching the virus's 18,000 letters long genetic sequence for all 179 blood samples.
Dr Matthews will use BC4 to help with his latest research into Dengue fever and Zika virus.
Caroline Gardiner, Academic Research Facilitator at the University of Bristol, said: "We're now in our tenth year of using HPC in our facility. We’ve endeavoured to make each phase of BlueCrystal bigger and better than the last, embracing new technology for the benefit of our users and researchers."
The new system is ranked 301 in the world, according to the Top500 list which analyses the world's 500 fastest supercomputers. Was launched at a special symposium in Bristol on the 24 May.
Simon Burbidge, the University's new Director of Advanced Computing, said: "It is with great excitement that I take on the role of Director of Advanced Computing. My predecessor, Ian Stewart, has made a tremendous contribution in developing the Blue Crystal facility. I look forward to building on this foundation and enabling the University's ambitious research programmes through the provision of the latest computational techniques and simulations."
Technical information about Blue Crystal 4 (BC4)
BC4 uses Lenovo NeXtScale compute nodes, each comprising of two 14 core 2.4 GHz Intel Broadwell CPUs with 128 GiB of RAM. It also includes 32 nodes of two NVIDIA Pascal P100 GPUs plus one GPU login node, designed into the rack by Lenovo’s engineering team to meet the specific requirements of the University.
Connecting the cluster are several high-speed networks, the fastest of which is a two-level Intel Omni-Path Architecture network running at 100Gb/s. BC4's storage is composed of one PetaByte of disk provided by DDN's GS7k and IME systems running the parallel file system Spectrum Scale from IBM.
Effective benchmarking and optimisation, using the benchmarking capabilities of Lenovo's HPC research centre in Stuttgart, the first of its kind, has ensured that BC4 is highly efficient in terms of physical footprint, while fully utilising the 30KW per rack energy limit. Lenovo's commitment to third party integration has allowed the University to avoid vendor lock-in while permitting new hardware to be added easily between refresh cycles.
To help with the interactive use of the cluster, BC4 has a visualisation node equipped with NVIDIA Grid vGPUs to help scientists visualise the work they're doing, so researchers can use the system even if they’ve not used an HPC machine before.
Currently numbering in the hundreds, applications running on the University's previous cluster will be replicated onto the new system, which will allow researchers to create more applications and better scaling software. Applications are able to be moved directly onto BC4 without the need for re-engineering.