TGAC Installs largest SGI UV 300 Supercomputer for Life Sciences

By John Russell

May 11, 2016

Two weeks ago, The Genome Analysis Centre (TGAC) based in the U.K. turned on the first of two new SGI UV300 computers. Next week, or thereabouts, TGAC will bring a second identical system online. Combined with its existing SGI UV2000, TGAC will have the largest SGI system dedicated to life sciences in the world. The upgrade will allow TGAC to significantly shorten the time required to assemble wheat genomes, a core activity in TGAC efforts to enhance worldwide food security.

The upgrade is part of TGAC’s central mission to use advanced HPC and bioinformatics to seek solutions to the world food productivity challenge. TGAC’s specialty is wheat, which is a major base component of the world’s food supply.

It turns out the wheat genome is notoriously difficult to work with. For starters, it contains roughly 17 gigabases (nucleotide pairs), which is five times the size of the human genome. The wheat genome contains 80 percent ‘repeats’ – sections of DNA sequence that are especially difficult to assemble and confound most sequencing algorithms. Lastly, the wheat genome is hexaploid, meaning it has six sets of chromosomes versus two for the human genome – the thinking here is that modern wheat is a kind combination of three ancestral strains.

All boiled down, wheat is tough to deal with from a sequence assembly perspective, and when TGAC help produced the first draft of the complete wheat genome a year or so ago, it was heralded as a major achievement.

TGAC SGI wheat genome graphic 385xUnfortunately the world’s wheat yields have been declining for a variety of reasons. “Our work – through genome assembly, alignment, and variant calling – is to help work out what the [gene] functions are and to get that data back to the research community and breeders who hopefully can breed new types of wheat that are less susceptible to heat and pathogens, etc.,” said Tim Stitt, Head of Scientific Computing at TGAC.

Not surprisingly high performance computing is critical to TGAC’s effort. “Because of the work that we do and its size and scale, we need to cutting edge technologies to be able to handle the work quickly and effectively.” TGAC was, for example, one of the first major genomics centers to deploy the specialized FPGA-based DRAGEN processor to accelerate alignment and variant calling. “Alignment used to take 3-4 day, now it takes 3-4 hours using the FPGA,” said Stitt.

By comparison, genome assembly is more difficult than alignment, especially so called de novo sequencing which doesn’t use a reference genome as a guide. On TGAC’s earlier systems, it was taking four weeks to assemble a wheat genome. The new UV300s, which replace a pair of aging UV100s, have been especially configured for assembly work (memory, processor speed) and are expected to shorten the time required to assemble wheat genomes to less than three weeks.

Here’s a brief overview of the new machines:

  • This new TGAC platform comprises two SGI UV 300 systems totaling 24 terabytes (TB) of shared-memory, 512 Intel Xeon Processor E7 v3 cores and 64TB of Intel P3700 SSDs with NVMe storage technology. Each SGI UV 300 flash memory solution features 12TB of shared memory with 7th generation SGI NUMAlink ASIC technology, scaling up to 64 TB of global addressable memory as a single system.
  • Paired with flash storage, the combined 24TB SGI UV 300 supercomputers can increase processing speeds of heavy workloads in scientific research by 80 percent. This combination of leading-edge technology allows TGAC researchers to benefit from the faster processing capabilities of the SGI UV 300, providing an extraordinarily powerful platform for genomics analysis.

“Having a shared memory server is an important element,” said Stitt. “A single assembly typically requires 4-6TB of RAM. What’s somewhat unique about this platform compared to the previous ones are the 32 TB of solid state drives (per machine) with NVME. That should give us a significant boost on the IO side. Our wheat files can be close to 1TB in size and must be read into memory.”

SGI UV300
SGI UV300

Besides memory enhancement, the jump to E7 v3 processors was a major step up from the Sandy Bridge processors in the UV100. “We’ve essentially skipped a generation – Ivy Bridge – and gone straight to Haswell. That alone would give us a boost in performance. Really it’s the whole package – memory, processors, storage, etc. The UV100s were purchased five or six years ago and that’s a lifetime in HPC.”

TGAC runs multiple jobs on SGI computers and is in the process of switching schedulers. Altair’s PBS is used on the old system, but Stitt is transitioning to Slurm, which is being used on the new UV300 that’s running. They both work well, said Stitt. “We’ve evaluated Slurm over past 6 – 8 months. It worked very well for what we want to do and it’s free. Really it was a cost decision and may free up revenue we’d normally spend on licenses and allow us to put it towards more hardware.”

Stitt notes the new UV300 solutions are considerably more dense that the older machines, “The UV300 comes in 5U rack space; the UV100 with effectively less memory, fewer cores, probably took over a rack of space.” He’s expecting greater energy efficiency as a result.

Researchers are still in the early stages of using the first UV300, said Stitt, who like HPC managers throughout life sciences must serve a diverse researcher constituency, many of whom aren’t comfortable with command line tools. “You need to know a little but about Linux to log into our HPC systems. A lot of our users, particularly our external users, don’t have backgrounds in programming and Linux and command lines and things,” Stitt said.

To make things easer, TGAC also allows users to use tools like Galaxy as a front end to the systems. “These researchers can access our systems through the Galaxy interface where they can set up workflows and Galaxy will launch them on the back end. Actually, we have a whole research team that works on data integration and the equivalent of scientific portals to help here.”

TACC_logo-240x62.pngAlong the line of reaching the maximum number of researchers, TGAC is in the midst of a project to forge closer ties with iPlant, a U.S.-based effort also tackling worldwide food production and agriculture. A few key iPlant organization and mission points are bulleted here:

  • Established by the U.S. National Science Foundation (NSF) in 2008 to develop cyberinfrastructure for life sciences research and democratize access to U.S. supercomputing capabilities.
  • A virtual organization lead by The University of Arizona, Texas Advanced Computing Center, Cold Spring Harbor Laboratory, and University of North Carolina at Wilmington.
  • Developing the national cyberinfrastructure for data-intensive biology driven by high-throughput sequencing, phenotypic and environmental datasets.
  • Providing powerful extensible platforms for data storage, bioinformatics, image analyses, cloud services, APIs, and more.
  • Making broadly applicable cyberinfrastructure resources available across the life science disciplines (e.g., plants, animals, and microbes).

“We won an award recently to build an iPlant U.K. here at TGAC. We’re working with iPlant folks to put together an iPlant infrastructure and at some point hopefully federate the two sites together. It’s a big project that we are halfway through,” said Stitt. The goal is to facilitate and speed dissemination of TGAC result by having an open system for sharing data.

Stitt is also working to make better use of the DRAGEN FPGA system, “It’s working brilliantly and we certainly haven’t exceeded our limits on it. We are expecting to generate more data coming from new lines of wheat and our interest lies is streamlining the two technologies – the DRAGEN chip with the SGI system.” That’s part of TGAC’s IO challenge generally. “We have raw data coming off the sequencing machines that we need to get onto the SGI platform, particularly the SSD drives. That data is used to generate an assembly, which we’ll store on our file system, and we need to pipe that into our DRAGEN FPGA [which sits on another system.]”

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!

Is Time Running Out for Compromise on America COMPETES/USICA Act?

June 22, 2022

You may recall that efforts proposed in 2020 to remake the National Science Foundation (Endless Frontier Act) have since expanded and morphed into two gigantic bills, the America COMPETES Act in the U.S. House of Representatives and the U.S. Innovation and Competition Act in the U.S. Senate. So far, efforts to reconcile the two pieces of legislation have snagged and recent reports... Read more…

Cerebras Systems Thinks Forward on AI Chips as it Claims Performance Win

June 22, 2022

Cerebras Systems makes the largest chip in the world, but is already thinking about its upcoming AI chips as learning models continue to grow at breakneck speed. The company’s latest Wafer Scale Engine chip is indeed the size of a wafer, and is made using TSMC’s 7nm process. The next chip will pack in more cores to handle the fast-growing compute needs of AI, said Andrew Feldman, CEO of Cerebras Systems. Read more…

AMD’s MI300 APUs to Power Exascale El Capitan Supercomputer

June 21, 2022

Additional details of the architecture of the exascale El Capitan supercomputer were disclosed today by Lawrence Livermore National Laboratory’s (LLNL) Terri Quinn in a presentation delivered to the 79th HPC User Forum Read more…

IDC Perspective on Integration of Quantum Computing and HPC

June 20, 2022

The insatiable need to compress time to insights from massive and complex datasets is fueling the demand for quantum computing integration into high performance computing (HPC) environments. Such an integration would allow enterprises to accelerate and optimize current HPC applications and processes by simulating and emulating them on today’s noisy... Read more…

Q&A with Intel’s Jeff McVeigh, an HPCwire Person to Watch in 2022

June 17, 2022

HPCwire presents our interview with Jeff McVeigh, vice president and general manager, Super Compute Group, Intel Corporation, and an HPCwire 2022 Person to Watch. McVeigh shares Intel's plans for the year ahead, his pers Read more…

AWS Solution Channel

Shutterstock 152995403

Bayesian ML Models at Scale with AWS Batch

This post was contributed by Ampersand’s Jeffrey Enos, Senior Machine Learning Engineer, Daniel Gerlanc, Senior Director for Data Science, and Brandon Willard, Data Science Lead. Read more…

Microsoft/NVIDIA Solution Channel

Shutterstock 261863138

Using Cloud-Based, GPU-Accelerated AI for Financial Risk Management

There are strict rules governing financial institutions with a number of global regulatory groups publishing financial compliance requirements. Financial institutions face many challenges and legal responsibilities for risk management, compliance violations, and failure to catch financial fraud. Read more…

Nvidia, Intel to Power Atos-Built MareNostrum 5 Supercomputer

June 16, 2022

The long-troubled, hotly anticipated MareNostrum 5 supercomputer finally has a vendor: Atos, which will be supplying a system that includes both Nvidia and Intel CPUs and GPUs across multiple partitions. The newly reimag Read more…

Is Time Running Out for Compromise on America COMPETES/USICA Act?

June 22, 2022

You may recall that efforts proposed in 2020 to remake the National Science Foundation (Endless Frontier Act) have since expanded and morphed into two gigantic bills, the America COMPETES Act in the U.S. House of Representatives and the U.S. Innovation and Competition Act in the U.S. Senate. So far, efforts to reconcile the two pieces of legislation have snagged and recent reports... Read more…

Cerebras Systems Thinks Forward on AI Chips as it Claims Performance Win

June 22, 2022

Cerebras Systems makes the largest chip in the world, but is already thinking about its upcoming AI chips as learning models continue to grow at breakneck speed. The company’s latest Wafer Scale Engine chip is indeed the size of a wafer, and is made using TSMC’s 7nm process. The next chip will pack in more cores to handle the fast-growing compute needs of AI, said Andrew Feldman, CEO of Cerebras Systems. Read more…

AMD’s MI300 APUs to Power Exascale El Capitan Supercomputer

June 21, 2022

Additional details of the architecture of the exascale El Capitan supercomputer were disclosed today by Lawrence Livermore National Laboratory’s (LLNL) Terri Read more…

IDC Perspective on Integration of Quantum Computing and HPC

June 20, 2022

The insatiable need to compress time to insights from massive and complex datasets is fueling the demand for quantum computing integration into high performance computing (HPC) environments. Such an integration would allow enterprises to accelerate and optimize current HPC applications and processes by simulating and emulating them on today’s noisy... Read more…

Q&A with Intel’s Jeff McVeigh, an HPCwire Person to Watch in 2022

June 17, 2022

HPCwire presents our interview with Jeff McVeigh, vice president and general manager, Super Compute Group, Intel Corporation, and an HPCwire 2022 Person to Watc Read more…

Nvidia, Intel to Power Atos-Built MareNostrum 5 Supercomputer

June 16, 2022

The long-troubled, hotly anticipated MareNostrum 5 supercomputer finally has a vendor: Atos, which will be supplying a system that includes both Nvidia and Inte Read more…

D-Wave Debuts Advantage2 Prototype; Seeks User Exploration and Feedback

June 16, 2022

Starting today, D-Wave Systems is providing access to a 500-plus-qubit prototype of its forthcoming 7000-qubit Advantage2 quantum annealing computer, which is d Read more…

AMD Opens Up Chip Design to the Outside for Custom Future

June 15, 2022

AMD is getting personal with chips as it sets sail to make products more to the liking of its customers. The chipmaker detailed a modular chip future in which customers can mix and match non-AMD processors in a custom chip package. "We are focused on making it easier to implement chips with more flexibility," said Mark Papermaster, chief technology officer at AMD during the analyst day meeting late last week. Read more…

Nvidia R&D Chief on How AI is Improving Chip Design

April 18, 2022

Getting a glimpse into Nvidia’s R&D has become a regular feature of the spring GTC conference with Bill Dally, chief scientist and senior vice president of research, providing an overview of Nvidia’s R&D organization and a few details on current priorities. This year, Dally focused mostly on AI tools that Nvidia is both developing and using in-house to improve... Read more…

Royalty-free stock illustration ID: 1919750255

Intel Says UCIe to Outpace PCIe in Speed Race

May 11, 2022

Intel has shared more details on a new interconnect that is the foundation of the company’s long-term plan for x86, Arm and RISC-V architectures to co-exist in a single chip package. The semiconductor company is taking a modular approach to chip design with the option for customers to cram computing blocks such as CPUs, GPUs and AI accelerators inside a single chip package. Read more…

The Final Frontier: US Has Its First Exascale Supercomputer

May 30, 2022

In April 2018, the U.S. Department of Energy announced plans to procure a trio of exascale supercomputers at a total cost of up to $1.8 billion dollars. Over the ensuing four years, many announcements were made, many deadlines were missed, and a pandemic threw the world into disarray. Now, at long last, HPE and Oak Ridge National Laboratory (ORNL) have announced that the first of those... Read more…

AMD/Xilinx Takes Aim at Nvidia with Improved VCK5000 Inferencing Card

March 8, 2022

AMD/Xilinx has released an improved version of its VCK5000 AI inferencing card along with a series of competitive benchmarks aimed directly at Nvidia’s GPU line. AMD says the new VCK5000 has 3x better performance than earlier versions and delivers 2x TCO over Nvidia T4. AMD also showed favorable benchmarks against several Nvidia GPUs, claiming its VCK5000 achieved... Read more…

Top500: Exascale Is Officially Here with Debut of Frontier

May 30, 2022

The 59th installment of the Top500 list, issued today from ISC 2022 in Hamburg, Germany, officially marks a new era in supercomputing with the debut of the first-ever exascale system on the list. Frontier, deployed at the Department of Energy’s Oak Ridge National Laboratory, achieved 1.102 exaflops in its fastest High Performance Linpack run, which was completed... Read more…

Newly-Observed Higgs Mode Holds Promise in Quantum Computing

June 8, 2022

The first-ever appearance of a previously undetectable quantum excitation known as the axial Higgs mode – exciting in its own right – also holds promise for developing and manipulating higher temperature quantum materials... Read more…

Nvidia Launches Hopper H100 GPU, New DGXs and Grace Superchips

March 22, 2022

The battle for datacenter dominance keeps getting hotter. Today, Nvidia kicked off its spring GTC event with new silicon, new software and a new supercomputer. Speaking from a virtual environment in the Nvidia Omniverse 3D collaboration and simulation platform, CEO Jensen Huang introduced the new Hopper GPU architecture and the H100 GPU... Read more…

PsiQuantum’s Path to 1 Million Qubits

April 21, 2022

PsiQuantum, founded in 2016 by four researchers with roots at Bristol University, Stanford University, and York University, is one of a few quantum computing startups that’s kept a moderately low PR profile. (That’s if you disregard the roughly $700 million in funding it has attracted.) The main reason is PsiQuantum has eschewed the clamorous public chase for... Read more…

Leading Solution Providers

Contributors

ISC 2022 Booth Video Tours

AMD
AWS
DDN
Dell
Intel
Lenovo
Microsoft
PENGUIN SOLUTIONS

Intel Reiterates Plans to Merge CPU, GPU High-performance Chip Roadmaps

May 31, 2022

Intel reiterated it is well on its way to merging its roadmap of high-performance CPUs and GPUs as it shifts over to newer manufacturing processes and packaging technologies in the coming years. The company is merging the CPU and GPU lineups into a chip (codenamed Falcon Shores) which Intel has dubbed an XPU. Falcon Shores... Read more…

AMD Opens Up Chip Design to the Outside for Custom Future

June 15, 2022

AMD is getting personal with chips as it sets sail to make products more to the liking of its customers. The chipmaker detailed a modular chip future in which customers can mix and match non-AMD processors in a custom chip package. "We are focused on making it easier to implement chips with more flexibility," said Mark Papermaster, chief technology officer at AMD during the analyst day meeting late last week. Read more…

India Launches Petascale ‘PARAM Ganga’ Supercomputer

March 8, 2022

Just a couple of weeks ago, the Indian government promised that it had five HPC systems in the final stages of installation and would launch nine new supercomputers this year. Now, it appears to be making good on that promise: the country’s National Supercomputing Mission (NSM) has announced the deployment of “PARAM Ganga” petascale supercomputer at Indian Institute of Technology (IIT)... Read more…

Nvidia Dominates MLPerf Inference, Qualcomm also Shines, Where’s Everybody Else?

April 6, 2022

MLCommons today released its latest MLPerf inferencing results, with another strong showing by Nvidia accelerators inside a diverse array of systems. Roughly fo Read more…

AMD’s MI300 APUs to Power Exascale El Capitan Supercomputer

June 21, 2022

Additional details of the architecture of the exascale El Capitan supercomputer were disclosed today by Lawrence Livermore National Laboratory’s (LLNL) Terri Read more…

Nvidia, Intel to Power Atos-Built MareNostrum 5 Supercomputer

June 16, 2022

The long-troubled, hotly anticipated MareNostrum 5 supercomputer finally has a vendor: Atos, which will be supplying a system that includes both Nvidia and Inte Read more…

Industry Consortium Forms to Drive UCIe Chiplet Interconnect Standard

March 2, 2022

A new industry consortium aims to establish a die-to-die interconnect standard – Universal Chiplet Interconnect Express (UCIe) – in support of an open chipl Read more…

Covid Policies at HPC Conferences Should Reflect HPC Research

June 6, 2022

Supercomputing has been indispensable throughout the Covid-19 pandemic, from modeling the virus and its spread to designing vaccines and therapeutics. But, desp Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire