Newcastle University’s first institution-wide service for high-performance computing is up and running based on a new HPC cluster called Rocket, designed and configured by OCF with a £2 million investment from the university. Rocket comprises Huawei, Mellanox and DDN Storage technologies and supports a wide swath of applications, including flood simulations, brain geometry and the replacement of ‘in vitro’ research with ‘in silicon’ research.
Rocket is a centralized 5,000-core, 122-node HPC system that will replace existing departmental clusters as they reach end of life. The system incorporates E9000 Huawei servers with a mix of extra-large, large and medium memory nodes (see details), connected with Mellanox EDR InfiniBand. A DDN EXAScaler ES7KX platform provides 500 terabytes of high speed Lustre storage, and the university’s Research Data Warehouse provides two petabytes of storage for data at rest.
Rocket’s installation is part of a concerted effort to create an ‘HPC culture’ at Newcastle University, with an emphasis on cross-departmental research and collaboration among the university’s 15 departments. The resource is available to all university researchers with computations that are too large or too numerous to be accommodated on a desktop machine. It is free at the point of use but projects with HPC funding will be granted enhanced access.
“Workloads are driving an ever-growing set of data intensive challenges that can only be met with accelerated infrastructure,” said Werner Hofer, Dean of Research & Innovation at Newcastle University. ”Rocket provides the significant memory and fast processing we need for bulky, complex numerical computation. My post-doctoral researcher was able to process half a million CPU hours’ worth of calculations which was not at all possible with our previous processing power.”
“We have a data explosion in every single aspect of science and society and we need the appropriate computational resources to be able to process this data,” said Dr Jaume Bacardit, Reader in Machine Learning at Newcastle University.
“People have to spend a lot of time writing proposals to get access to the big national or regional supercomputers so it’s a lot of work for us as academics. It’s much easier for us if we can just have a local machine that we can use,” said Dr Tamara Rogers, Reader in Computational Astrophysics at Newcastle University.
Since entering production on October 31, 2017, Rocket is advancing the pace and scope of science at the university. Some of the benefits cited by high-end computing integrator OCF include:
Assessing the extent of changes in flood simulation can now be simulated in 11 hours rather than 18 days on a desktop computer by using a change quantification algorithm.
Brain geometry which used to take the equivalent of 270 people years can now be performed in just a few hours.
Drug testing can be done with preliminary ‘in silicon’ research rather than ‘in vitro’, significantly reducing the need for animal research as computational chemistry is used to model and predict compounds which will be effective drugs.
Using Deep Learning for the early detection of respiratory disease in pigs takes only two days to carry out 17,250,000 particle evaluations. This method used outperforms any other method and drastically improves time for Particle Swarm Optimisation (PSO).
Identifying genetic mutation in genomes arising in cancerous cells. With Rocket, the run time for 30 genomes is now 12 hours compared to 28 days if it was run on a single core. The pipeline identified 100% of cancer-causing mutations creating the potential for more accurate, faster, targeted diagnosis of leukaemia types, resulting in improved, targeted treatment and better outcomes for patients.
Identifying rare genetic diseases, Rocket can compare whole-exome sequences, looking for alignment and variant (across millions of sequences per genome), making it possible to search almost the entire protein coding region of a patient’s genome for nuclear genetic defects in one experiment in approximately one day.
Here’s a video made by Newcastle University introducing Rocket:
Feature image source: Huawei YouTube product video