University of Adelaide Provides Seamless Bioinformatics Training Using AWS

By Amazon Web Services

August 12, 2020

The University of Adelaide, established in South Australia in 1874, maintains a rich history of scientific innovation. For more than 140 years, the institution and its researchers have had an impact all over the world—making vital contributions to the invention of X-ray crystallography, insulin, penicillin, and the Olympic torch.

Bioinformaticians from the university’s School of Biological Sciences are carrying on this tradition of innovation. The researchers foster collaborations across the university with the aim of shaping the future of bioscience research at the institution. To support their goals, they develop and deliver bioinformatics training on campus. Recently, in collaboration with Dr. Radosław Suchecki, research scientist at the Commonwealth Scientific and Industrial Research Organization, they offered hands-on virtual training in the Snakemake workflow engine and Nextflow workflow manager to bioinformaticians across Australia, with the support of Australian BioCommons.

To deliver this training, they needed to quickly spin up automated virtual training environments, which presented unique challenges. “In this field, the compute requirements can be very large and usually beyond what one can expect in a computing suite at any one institution,” says Dr. Nathan Watson-Haigh, research fellow in bioinformatics at the university’s School of Biological Sciences. “In addition, we needed to set up a training environment where everyone could access the same resources, regardless of where they were or what their local infrastructure was. These were capabilities we didn’t have ourselves.”

The bioinformaticians engaged RONIN, a Select Consulting Partner in the Amazon Web Services (AWS) Partner Network (APN), to help design and deploy an AWS-based compute cluster that runs on hundreds of Amazon Elastic Compute Cloud (Amazon EC2) instances. The cluster uses AWS Auto Scaling for automatic on-demand scalability, and it takes advantage of the Slurm open-source cluster management system.

“We wanted to develop training for tools that would work in a cluster environment that bioinformatics researchers would typically work on,” says Watson-Haigh. “We knew the AWS Cloud was the right technology, and RONIN was a trusted technology partner we had worked with previously.”

The university collaborated with RONIN to conduct a trial of the cluster before the training event. “The barrier to entry seemed significant at the time, so when we conducted the trial, we clearly saw how good the technology was, as well as the support from RONIN. Just the fact that we could spin something up with no more than a few clicks and have infrastructure at our fingertips was very powerful.”

Using the RONIN solution, the university’s bioinformaticians created a workshop that ran simultaneously across eight locations spanning four time zones in Australia.

With the RONIN compute cluster, the trainers were able to quickly create virtual training for event participants. “Using RONIN and AWS, we spun up training environments in minutes outside of the institutional firewall, so more than 150 bioinformaticians got access to the same virtual resources, regardless of their location,” says Watson-Haigh.

 

Read the full story here and learn more about Amazon HPC solution.

Get started with running your CAE/CFD workloads now – fill the form and get a $100 AWS credit!

Return to Solution Channel Homepage
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!

Quantinuum Debuts Quantum-based Cryptographic Key Service – Is this Quantum Advantage?

December 7, 2021

Quantinuum – the newly-named company resulting from the merger of Honeywell’s quantum computing division and UK-based Cambridge Quantum – today launched Quantum Origin, a service to deliver “completely unpredicta Read more…

SC21 Was Unlike Any Other — Was That a Good Thing?

December 3, 2021

For a long time, the promised in-person SC21 seemed like an impossible fever dream, the assurances of a prominent physical component persisting across years of canceled conferences, including two virtual ISCs and the virtual SC20. With the advent of the Delta variant, Covid surges in St. Louis and contention over vaccine requirements... Read more…

The Green500’s Crystal Anniversary Sees MN-3 Crystallize Its Winning Streak

December 2, 2021

“This is the 30th Green500,” said Wu Feng, custodian of the Green500 list, at the list’s SC21 birds-of-a-feather session. “You could say 15 years of Green500, which makes it, I guess, the crystal anniversary.” Indeed, HPCwire marked the 15th anniversary of the Green500 – which ranks supercomputers by flops-per-watt, rather than just by flops – earlier this year with... Read more…

AWS Arm-based Graviton3 Instances Now in Preview

December 1, 2021

Three years after unveiling the first generation of its AWS Graviton chip-powered instances in 2018, Amazon Web Services announced that the third generation of the processors – the AWS Graviton3 – will power all-new Amazon Elastic Compute 2 (EC2) C7g instances that are now available in preview. Debuting at the AWS re:Invent 2021... Read more…

Nvidia Dominates Latest MLPerf Results but Competitors Start Speaking Up

December 1, 2021

MLCommons today released its fifth round of MLPerf training benchmark results with Nvidia GPUs again dominating. That said, a few other AI accelerator companies participated and, one of them, Graphcore, even held a separ Read more…

AWS Solution Channel

Running a 3.2M vCPU HPC Workload on AWS with YellowDog

Historically, advances in fields such as meteorology, healthcare, and engineering, were achieved through large investments in on-premises computing infrastructure. Upfront capital investment and operational complexity have been the accepted norm of large-scale HPC research. Read more…

HPC Career Notes: December 2021 Edition

December 1, 2021

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it’s a promotion, new company hire, or even an accolade, we’ Read more…

Quantinuum Debuts Quantum-based Cryptographic Key Service – Is this Quantum Advantage?

December 7, 2021

Quantinuum – the newly-named company resulting from the merger of Honeywell’s quantum computing division and UK-based Cambridge Quantum – today launched Q Read more…

SC21 Was Unlike Any Other — Was That a Good Thing?

December 3, 2021

For a long time, the promised in-person SC21 seemed like an impossible fever dream, the assurances of a prominent physical component persisting across years of canceled conferences, including two virtual ISCs and the virtual SC20. With the advent of the Delta variant, Covid surges in St. Louis and contention over vaccine requirements... Read more…

The Green500’s Crystal Anniversary Sees MN-3 Crystallize Its Winning Streak

December 2, 2021

“This is the 30th Green500,” said Wu Feng, custodian of the Green500 list, at the list’s SC21 birds-of-a-feather session. “You could say 15 years of Green500, which makes it, I guess, the crystal anniversary.” Indeed, HPCwire marked the 15th anniversary of the Green500 – which ranks supercomputers by flops-per-watt, rather than just by flops – earlier this year with... Read more…

Nvidia Dominates Latest MLPerf Results but Competitors Start Speaking Up

December 1, 2021

MLCommons today released its fifth round of MLPerf training benchmark results with Nvidia GPUs again dominating. That said, a few other AI accelerator companies Read more…

At SC21, Experts Ask: Can Fast HPC Be Green?

November 30, 2021

HPC is entering a new era: exascale is (somewhat) officially here, but Moore’s law is ending. Power consumption and other sustainability concerns loom over the enormous systems and chips of this new epoch, for both cost and compliance reasons. Reconciling the need to continue the supercomputer scale-up while reducing HPC’s environmental impacts... Read more…

Raja Koduri and Satoshi Matsuoka Discuss the Future of HPC at SC21

November 29, 2021

HPCwire's Managing Editor sits down with Intel's Raja Koduri and Riken's Satoshi Matsuoka in St. Louis for an off-the-cuff conversation about their SC21 experience, what comes after exascale and why they are collaborating. Koduri, senior vice president and general manager of Intel's accelerated computing systems and graphics (AXG) group, leads the team... Read more…

Jack Dongarra on SC21, the Top500 and His Retirement Plans

November 29, 2021

HPCwire's Managing Editor sits down with Jack Dongarra, Top500 co-founder and Distinguished Professor at the University of Tennessee, during SC21 in St. Louis to discuss the 2021 Top500 list, the outlook for global exascale computing, and what exactly is going on in that Viking helmet photo. Read more…

SC21: Larry Smarr on The Rise of Supernetwork Data Intensive Computing

November 26, 2021

Larry Smarr, founding director of Calit2 (now Distinguished Professor Emeritus at the University of California San Diego) and the first director of NCSA, is one of the seminal figures in the U.S. supercomputing community. What began as a personal drive, shared by others, to spur the creation of supercomputers in the U.S. for scientific use, later expanded into a... Read more…

IonQ Is First Quantum Startup to Go Public; Will It be First to Deliver Profits?

November 3, 2021

On October 1 of this year, IonQ became the first pure-play quantum computing start-up to go public. At this writing, the stock (NYSE: IONQ) was around $15 and its market capitalization was roughly $2.89 billion. Co-founder and chief scientist Chris Monroe says it was fun to have a few of the company’s roughly 100 employees travel to New York to ring the opening bell of the New York Stock... Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

US Closes in on Exascale: Frontier Installation Is Underway

September 29, 2021

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, held by Zoom this week (Sept. 29-30), it was revealed that the Frontier supercomputer is currently being installed at Oak Ridge National Laboratory in Oak Ridge, Tenn. The staff at the Oak Ridge Leadership... Read more…

AMD Launches Milan-X CPU with 3D V-Cache and Multichip Instinct MI200 GPU

November 8, 2021

At a virtual event this morning, AMD CEO Lisa Su unveiled the company’s latest and much-anticipated server products: the new Milan-X CPU, which leverages AMD’s new 3D V-Cache technology; and its new Instinct MI200 GPU, which provides up to 220 compute units across two Infinity Fabric-connected dies, delivering an astounding 47.9 peak double-precision teraflops. “We're in a high-performance computing megacycle, driven by the growing need to deploy additional compute performance... Read more…

Intel Reorgs HPC Group, Creates Two ‘Super Compute’ Groups

October 15, 2021

Following on changes made in June that moved Intel’s HPC unit out of the Data Platform Group and into the newly created Accelerated Computing Systems and Graphics (AXG) business unit, led by Raja Koduri, Intel is making further updates to the HPC group and announcing... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Killer Instinct: AMD’s Multi-Chip MI200 GPU Readies for a Major Global Debut

October 21, 2021

AMD’s next-generation supercomputer GPU is on its way – and by all appearances, it’s about to make a name for itself. The AMD Radeon Instinct MI200 GPU (a successor to the MI100) will, over the next year, begin to power three massive systems on three continents: the United States’ exascale Frontier system; the European Union’s pre-exascale LUMI system; and Australia’s petascale Setonix system. Read more…

Leading Solution Providers

Contributors

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was Read more…

D-Wave Embraces Gate-Based Quantum Computing; Charts Path Forward

October 21, 2021

Earlier this month D-Wave Systems, the quantum computing pioneer that has long championed quantum annealing-based quantum computing (and sometimes taken heat fo Read more…

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... Read more…

The Latest MLPerf Inference Results: Nvidia GPUs Hold Sway but Here Come CPUs and Intel

September 22, 2021

The latest round of MLPerf inference benchmark (v 1.1) results was released today and Nvidia again dominated, sweeping the top spots in the closed (apples-to-ap Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer... Read more…

Three Chinese Exascale Systems Detailed at SC21: Two Operational and One Delayed

November 24, 2021

Details about two previously rumored Chinese exascale systems came to light during last week’s SC21 proceedings. Asked about these systems during the Top500 media briefing on Monday, Nov. 15, list author and co-founder Jack Dongarra indicated he was aware of some very impressive results, but withheld comment when asked directly if he had... Read more…

2021 Gordon Bell Prize Goes to Exascale-Powered Quantum Supremacy Challenge

November 18, 2021

Today at the hybrid virtual/in-person SC21 conference, the organizers announced the winners of the 2021 ACM Gordon Bell Prize: a team of Chinese researchers leveraging the new exascale Sunway system to simulate quantum circuits. The Gordon Bell Prize, which comes with an award of $10,000 courtesy of HPC pioneer Gordon Bell, is awarded annually... Read more…

Quantum Computer Market Headed to $830M in 2024

September 13, 2021

What is one to make of the quantum computing market? Energized (lots of funding) but still chaotic and advancing in unpredictable ways (e.g. competing qubit tec Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire