New OCF Supercomputer at the University of Aberdeen Supports Ground Breaking Genomics Research

July 7, 2020

July 7, 2020 — Researchers at the University of Aberdeen are benefitting from an investment in High Performance Computing (HPC). The new HPC cluster, called Maxwell, is supporting ground breaking research at the University’s Centre for Genome-Enabled Biology and Medicine (CGEBM) and provides a centralized HPC system for the whole University with applications in medicine, biological sciences, engineering, chemistry, maths and computing science. The new HPC system is designed, integrated and managed by high performance compute, storage, cloud and AI integrator, OCF. The supercomputer is part of the University’s expansion to improve facilities for staff and students.

Image courtesy of the University of Aberdeen

With Maxwell, the University’s CGEBM is able to rapidly analyze complex genomics datasets from known and novel organisms and help researchers to revolutionize the study of the Earth’s biodiversity and complex ecosystems important to health and disease, agriculture or the environment. It is estimated that only around 1 percent of the Earth’s biodiversity is easily culturable in a laboratory, and there is little knowledge on most living organisms on the planet.

With the use of HPC, University researchers can analyze microbiomes associated with a diverse array of ecosystems, such as the human gut, fish important to Scottish aquaculture, glaciers, deep-sea sediments, soil and bioreactors for the production of sustainable and environmentally friendly biofuels. These state-of-the-art studies provide new understanding of important and diverse biological processes such as antimicrobial drug resistance; pathogen detection, evolution and virulence; mechanisms of drug efficacy and toxicity; development; inflammation; tumorigenesis; nutrition and satiety; and degradation of hydrocarbons.

Scotia Biologics, a SME research company, is working with the University’s CGEBM, using Maxwell’s capacity to speed up its existing pipeline and generating a more comprehensive dataset using genomics compared to traditional methods typically used in its field.

The new HPC system is also being used to teach graduates and post-graduate students in specialist subjects such as AI and bioinformatics, fields important to modern research and STEM careers, providing them with a unique opportunity to access HPC capacity. With 300 users, the cluster is providing a centralized HPC system to support all researchers and post-graduate students across the University.

With twenty times more storage than the University’s previous HPC system, Maxwell comprises four Lenovo ThinkSystem SD530 servers, 40 compute nodes, ThinkParkQ supported BeeGFS Parallel FileSystem hosted on Lenovo Servers and Storage and NVIDIA GPUs. OCF is also providing an OpenSource Software Stack and its OCF Remote HPC Admin Managed Service to support the in-house HPC team.

Image courtesy of the University of Aberdeen

Dean Phillips, Assistant Director, Digital and Information Services of the University of Aberdeen says: “Aberdeen is a research-intensive university and we’ve already seen an increase of 50 percent in registered users of our Maxwell HPC cluster. Having our own HPC system helps the University to attract new researchers, research funding and expand on existing programs of research and teaching. It is highly beneficial for our researchers to have on-site access to HPC infrastructure, particularly when securing start-up funds.”

Phillips continues: “OCF’s Remote Admin Service is an extension of our team and really helps to ensure the smooth day to day running of our HPC cluster and dealing with support issues, user requests and keeping on top of software and security updates.”

Dr Elaina Collie-Duguid, Manager, Centre for Genome Enabled Biology & Medicine at the University of Aberdeen says: “Genomics is a dynamic discipline that rapidly evolves into new applications and approaches to interrogate complex systems. The new HPC cluster, with its expanded capacity and advanced GPU capabilities, enables us to use new analysis methods and work at a much quicker rate than before. It really is an exciting time for genomics, which is revolutionizing the study of organisms and complex ecosystems to address issues of global importance, and HPC is a critical tool for analysis of these data.”

Russell Slack, Managing Director of OCF comments: “The new HPC cluster helps the University remain ahead of a fiercely competitive market. It attracts researchers, students and grants to its facility. Aberdeen’s investment in its HPC is a credit to its foresight in the importance of HPC in research that impacts people and everyday lives.”

Keith Charlton, CEO of Scotia Biologics, says, “As part of our drive to introduce new services to offer to the life sciences sector, Scotia is developing phage display library capabilities based around a growing number of animal species. With access to Maxwell, we’ve been able to quickly generate a large volume of data relatively inexpensively whilst significantly advancing our R&D program.”


Source: University of Aberdeen

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

University of Chicago Researchers Generate First Computational Model of Entire SARS-CoV-2 Virus

January 15, 2021

Over the course of the last year, many detailed computational models of SARS-CoV-2 have been produced with the help of supercomputers, but those models have largely focused on critical elements of the virus, such as its Read more…

By Oliver Peckham

Pat Gelsinger Returns to Intel as CEO

January 14, 2021

The Intel board of directors has appointed a new CEO. Intel alum Pat Gelsinger is leaving his post as CEO of VMware to rejoin the company that he parted ways with 11 years ago. Gelsinger will succeed Bob Swan, who will remain CEO until Feb. 15. Gelsinger previously spent 30 years... Read more…

By Tiffany Trader

Roar Supercomputer to Support Naval Aircraft Research

January 14, 2021

One might not think “aircraft” when picturing the U.S. Navy, but the military branch actually has thousands of aircraft currently in service – and now, supercomputing will help future naval aircraft operate faster, Read more…

By Staff report

DOE and NOAA Extend Computing Partnership, Plan for New Supercomputer

January 14, 2021

The National Climate-Computing Research Center (NCRC), hosted by Oak Ridge National Laboratory (ORNL), has been supporting the climate research of the National Oceanic and Atmospheric Administration (NOAA) for the last 1 Read more…

By Oliver Peckham

Using Micro-Combs, Researchers Demonstrate World’s Fastest Optical Neuromorphic Processor for AI

January 13, 2021

Neuromorphic computing, which uses chips that mimic the behavior of the human brain using virtual “neurons,” is growing in popularity thanks to high-profile efforts from Intel and others. Now, a team of researchers l Read more…

By Oliver Peckham

AWS Solution Channel

Now Available – Amazon EC2 C6gn Instances with 100 Gbps Networking

Amazon EC2 C6gn instances powered by AWS Graviton2 processors are now available!

Compared to C6g instances, this new instance type provides 4x higher network bandwidth, 4x higher packet processing performance, and 2x higher EBS bandwidth. Read more…

Intel® HPC + AI Pavilion

Intel Keynote Address

Intel is the foundation of HPC – from the workstation to the cloud to the backbone of the Top500. At SC20, Intel’s Trish Damkroger, VP and GM of high performance computing, addresses the audience to show how Intel and its partners are building the future of HPC today, through hardware and software technologies that accelerate the broad deployment of advanced HPC systems. Read more…

Honing In on AI, US Launches National Artificial Intelligence Initiative Office

January 13, 2021

To drive American leadership in the field of AI into the future, the National Artificial Intelligence Initiative Office has been launched by the White House Office of Science and Technology Policy (OSTP). The new agen Read more…

By Todd R. Weiss

Pat Gelsinger Returns to Intel as CEO

January 14, 2021

The Intel board of directors has appointed a new CEO. Intel alum Pat Gelsinger is leaving his post as CEO of VMware to rejoin the company that he parted ways with 11 years ago. Gelsinger will succeed Bob Swan, who will remain CEO until Feb. 15. Gelsinger previously spent 30 years... Read more…

By Tiffany Trader

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

By John Russell

Intel ‘Ice Lake’ Server Chips in Production, Set for Volume Ramp This Quarter

January 12, 2021

Intel Corp. used this week’s virtual CES 2021 event to reassert its dominance of the datacenter with the formal roll out of its next-generation server chip, the 10nm Xeon Scalable processor that targets AI and HPC workloads. The third-generation “Ice Lake” family... Read more…

By George Leopold

Researchers Say It Won’t Be Possible to Control Superintelligent AI

January 11, 2021

Worries about out-of-control AI aren’t new. Many prominent figures have suggested caution when unleashing AI. One quote that keeps cropping up is (roughly) th Read more…

By John Russell

AMD Files Patent on New GPU Chiplet Approach

January 5, 2021

Advanced Micro Devices is accelerating the GPU chiplet race with the release of a U.S. patent application for a device that incorporates high-bandwidth intercon Read more…

By George Leopold

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

By Tracey Bryant

Intel Touts Optane Performance, Teases Next-gen “Crow Pass”

January 5, 2021

Competition to leverage new memory and storage hardware with new or improved software to create better storage/memory schemes has steadily gathered steam during Read more…

By John Russell

Farewell 2020: Bleak, Yes. But a Lot of Good Happened Too

December 30, 2020

Here on the cusp of the new year, the catchphrase ‘2020 hindsight’ has a distinctly different feel. Good riddance, yes. But also proof of science’s power Read more…

By John Russell

Esperanto Unveils ML Chip with Nearly 1,100 RISC-V Cores

December 8, 2020

At the RISC-V Summit today, Art Swift, CEO of Esperanto Technologies, announced a new, RISC-V based chip aimed at machine learning and containing nearly 1,100 low-power cores based on the open-source RISC-V architecture. Esperanto Technologies, headquartered in... Read more…

By Oliver Peckham

Azure Scaled to Record 86,400 Cores for Molecular Dynamics

November 20, 2020

A new record for HPC scaling on the public cloud has been achieved on Microsoft Azure. Led by Dr. Jer-Ming Chia, the cloud provider partnered with the Beckman I Read more…

By Oliver Peckham

NICS Unleashes ‘Kraken’ Supercomputer

April 4, 2008

A Cray XT4 supercomputer, dubbed Kraken, is scheduled to come online in mid-summer at the National Institute for Computational Sciences (NICS). The soon-to-be petascale system, and the resulting NICS organization, are the result of an NSF Track II award of $65 million to the University of Tennessee and its partners to provide next-generation supercomputing for the nation's science community. Read more…

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

By John Russell

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Programming the Soon-to-Be World’s Fastest Supercomputer, Frontier

January 5, 2021

What’s it like designing an app for the world’s fastest supercomputer, set to come online in the United States in 2021? The University of Delaware’s Sunita Chandrasekaran is leading an elite international team in just that task. Chandrasekaran, assistant professor of computer and information sciences, recently was named... Read more…

By Tracey Bryant

Leading Solution Providers

Contributors

Top500: Fugaku Keeps Crown, Nvidia’s Selene Climbs to #5

November 16, 2020

With the publication of the 56th Top500 list today from SC20's virtual proceedings, Japan's Fugaku supercomputer – now fully deployed – notches another win, Read more…

By Tiffany Trader

Texas A&M Announces Flagship ‘Grace’ Supercomputer

November 9, 2020

Texas A&M University has announced its next flagship system: Grace. The new supercomputer, named for legendary programming pioneer Grace Hopper, is replacing the Ada system (itself named for mathematician Ada Lovelace) as the primary workhorse for Texas A&M’s High Performance Research Computing (HPRC). Read more…

By Oliver Peckham

At Oak Ridge, ‘End of Life’ Sometimes Isn’t

October 31, 2020

Sometimes, the old dog actually does go live on a farm. HPC systems are often cursed with short lifespans, as they are continually supplanted by the latest and Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

Gordon Bell Special Prize Goes to Massive SARS-CoV-2 Simulations

November 19, 2020

2020 has proven a harrowing year – but it has produced remarkable heroes. To that end, this year, the Association for Computing Machinery (ACM) introduced the Read more…

By Oliver Peckham

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chipmaker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the European Union begin scrutinizing the impact of the blockbuster deal on semiconductor industry competition and innovation, the deal has at the very least... Read more…

By George Leopold

Intel Xe-HP GPU Deployed for Aurora Exascale Development

November 17, 2020

At SC20, Intel announced that it is making its Xe-HP high performance discrete GPUs available to early access developers. Notably, the new chips have been deplo Read more…

By Tiffany Trader

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This