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!

Senegal Prepares to Take Delivery of Atos Supercomputer

January 16, 2019

In just a few months time, Senegal will be operating the second largest HPC system in sub-Saharan Africa. The Minister of Higher Education, Research and Innovation Mary Teuw Niane made the announcement on Monday (Jan. 14 Read more…

By Tiffany Trader

Google Cloud Platform Extends GPU Instance Options

January 16, 2019

If it's Nvidia GPUs you're after to power your AI/HPC/visualization workload, Google Cloud has them, now claiming "broadest GPU availability." Each of the three big public cloud vendors has by turn touted the latest and Read more…

By Tiffany Trader

A Big Data Journey While Seeking to Catalog our Universe

January 16, 2019

It turns out, astronomers have lots of photos of the sky but seek knowledge about what the photos mean. Sound familiar? Big data problems are often characterized as transforming data into insights – which is exactly wh Read more…

By James Reinders

HPE Extreme Performance Solutions

HPE Systems With Intel Omni-Path: Architected for Value and Accessible High-Performance Computing

Today’s high-performance computing (HPC) and artificial intelligence (AI) users value high performing clusters. And the higher the performance that their system can deliver, the better. Read more…

IBM Accelerated Insights

Resource Management in the Age of Artificial Intelligence

New challenges demand fresh approaches

Fueled by GPUs, big data, and rapid advances in software, the AI revolution is upon us. Read more…

STAC Floats ML Benchmark for Financial Services Workloads

January 16, 2019

STAC (Securities Technology Analysis Center) recently released an ‘exploratory’ benchmark for machine learning which it hopes will evolve into a firm benchmark or suite of benchmarking tools to compare the performanc Read more…

By John Russell

A Big Data Journey While Seeking to Catalog our Universe

January 16, 2019

It turns out, astronomers have lots of photos of the sky but seek knowledge about what the photos mean. Sound familiar? Big data problems are often characterize Read more…

By James Reinders

STAC Floats ML Benchmark for Financial Services Workloads

January 16, 2019

STAC (Securities Technology Analysis Center) recently released an ‘exploratory’ benchmark for machine learning which it hopes will evolve into a firm benchm Read more…

By John Russell

IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

IBM’s New Global Weather Forecasting System Runs on GPUs

January 9, 2019

Anyone who has checked a forecast to decide whether or not to pack an umbrella knows that weather prediction can be a mercurial endeavor. It is a Herculean task: the constant modeling of incredibly complex systems to a high degree of accuracy at a local level within very short spans of time. Read more…

By Oliver Peckham

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

HPCwire Awards Highlight Supercomputing Achievements in the Sciences

January 3, 2019

In November at SC18 in Dallas, HPCwire Readers’ and Editors’ Choice awards program commemorated its 15th year of honoring achievement in HPC, with categories ranging from Best Use of AI to the Workforce Diversity Leadership Award and recipients across a wide variety of industrial and research sectors. Read more…

By the Editorial Team

White House Top Science Post Filled After Two-Year Vacancy

January 3, 2019

Half-way into Trump's term, the Senate has confirmed a director for the Office of Science and Technology Policy (OSTP), the agency that coordinates science poli Read more…

By Tiffany Trader

Quantum Computing Will Never Work

November 27, 2018

Amid the gush of money and enthusiastic predictions being thrown at quantum computing comes a proposed cold shower in the form of an essay by physicist Mikhail Read more…

By John Russell

Cray Unveils Shasta, Lands NERSC-9 Contract

October 30, 2018

Cray revealed today the details of its next-gen supercomputing architecture, Shasta, selected to be the next flagship system at NERSC. We've known of the code-name "Shasta" since the Argonne slice of the CORAL project was announced in 2015 and although the details of that plan have changed considerably, Cray didn't slow down its timeline for Shasta. Read more…

By Tiffany Trader

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

AMD Sets Up for Epyc Epoch

November 16, 2018

It’s been a good two weeks, AMD’s Gary Silcott and Andy Parma told me on the last day of SC18 in Dallas at the restaurant where we met to discuss their show news and recent successes. Heck, it’s been a good year. Read more…

By Tiffany Trader

US Leads Supercomputing with #1, #2 Systems & Petascale Arm

November 12, 2018

The 31st Supercomputing Conference (SC) - commemorating 30 years since the first Supercomputing in 1988 - kicked off in Dallas yesterday, taking over the Kay Ba Read more…

By Tiffany Trader

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

Contract Signed for New Finnish Supercomputer

December 13, 2018

After the official contract signing yesterday, configuration details were made public for the new BullSequana system that the Finnish IT Center for Science (CSC Read more…

By Tiffany Trader

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

Nvidia’s Jensen Huang Delivers Vision for the New HPC

November 14, 2018

For nearly two hours on Monday at SC18, Jensen Huang, CEO of Nvidia, presented his expansive view of the future of HPC (and computing in general) as only he can do. Animated. Backstopped by a stream of data charts, product photos, and even a beautiful image of supernovae... Read more…

By John Russell

HPE No. 1, IBM Surges, in ‘Bucking Bronco’ High Performance Server Market

September 27, 2018

Riding healthy U.S. and global economies, strong demand for AI-capable hardware and other tailwind trends, the high performance computing server market jumped 28 percent in the second quarter 2018 to $3.7 billion, up from $2.9 billion for the same period last year, according to industry analyst firm Hyperion Research. Read more…

By Doug Black

HPC Reflections and (Mostly Hopeful) Predictions

December 19, 2018

So much ‘spaghetti’ gets tossed on walls by the technology community (vendors and researchers) to see what sticks that it is often difficult to peer through Read more…

By John Russell

Intel Confirms 48-Core Cascade Lake-AP for 2019

November 4, 2018

As part of the run-up to SC18, taking place in Dallas next week (Nov. 11-16), Intel is doling out info on its next-gen Cascade Lake family of Xeon processors, specifically the “Advanced Processor” version (Cascade Lake-AP), architected for high-performance computing, artificial intelligence and infrastructure-as-a-service workloads. Read more…

By Tiffany Trader

Germany Celebrates Launch of Two Fastest Supercomputers

September 26, 2018

The new high-performance computer SuperMUC-NG at the Leibniz Supercomputing Center (LRZ) in Garching is the fastest computer in Germany and one of the fastest i Read more…

By Tiffany Trader

Houston to Field Massive, ‘Geophysically Configured’ Cloud Supercomputer

October 11, 2018

Based on some news stories out today, one might get the impression that the next system to crack number one on the Top500 would be an industrial oil and gas mon Read more…

By Tiffany Trader

Microsoft to Buy Mellanox?

December 20, 2018

Networking equipment powerhouse Mellanox could be an acquisition target by Microsoft, according to a published report in an Israeli financial publication. Microsoft has reportedly gone so far as to engage Goldman Sachs to handle negotiations with Mellanox. Read more…

By Doug Black

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

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