Dell Boxes Up HPC for Life Sciences

By Nicole Hemsoth

June 5, 2013

Dell has its sights set on a duo of trends unfolding around high-end computing. On the one side, the pace, price and practically of genomics is converging to create an exploding market. And on that note, the compute infrastructure required to push it all forward is facing some convergence of its own.

There are a range of figures demonstrating the rapid growth of genomics in the last decade, all of which coincide with the deepening dip in the cost to sequence genes. With more companies sequencing more genetic samples to aid in everything from drug discovery, disease cures and the creation of new materials, the time is ripe for an explosion of purpose-built all-in-one infrastructure approaches.

According to IDC, spending on converged systems is predicted to grow “at a compound annual rate of more than 54 percent over the 2011-2016 forecast period, driven by the cost advantages and efficiency related to operations and management of IT, simplification of vendor engagement and faster time to productivity with IT system updates.”

This week at their Dell Enterprise Forum, the company snapped these trends together with the unveiling of their Active Infrastructure for HPC Life Sciences offering. Set for release in August, the company describes their package as a “modular high performance computing and storage building blocks” which include the required bricks stacked into a single rack housing 32 nodes.

The packaged PowerEdge blades are orchestrated with Bright Cluster Manager and come with Intel inside, namely of the 8-core, dual socket Xeon E5-2400 ilk. On their own, these particular blades offer up 16 cores with 2.5 MB cache per core. With this power, Dell says one cabinet can support the data load of two to four sequencers.

In other words, if you have the practical know-how, a cool million bucks should be able to get you up and running with two sequencers (if they’re at the low end like the “commodity” ones set to be offered by Life Technologies) and a nice fridge from Dell to handle all your genomic data. While that may be a bit of a stretch, power costs and general practicality aside, Dell insists that there’s a hungry market of smaller companies eager to remove the IT hassle and stick to the sequencing.

Dell says that users can tap up to 512 cores, 1.5 terabytes of memory, 540 terabytes of Dell NFS and Lustre file system storage, all strung together with either a 10 GbE or Infiniband network.

The company claims that the impetus and research work behind their converged life science offering was based on their work with the Translational Genomics Research Institute (TGen), where they were able to shave genomic analysis time from one week to one day.

Dell is making a number of other big claims for their genomics-flavored tailoring, the most prominent of which is that users can cut their genomic analysis workflows from days to hours via the ability to optimize analytical software and data across the cluster and file system. The end result is the ability to process a reported 38 genomes per day on a single system.

They note that in addition to cutting down the processing time, acquiring, optimizing and maintaining a custom cluster built from commodity parts can add significant overhead to time and cost. Their $650,000 rack, when compared to what simple server math reveals isn’t stunning, but for users who simply want to shed the datacenter hassle and get back to research, the “plug and play” element could be rather attractive.

What will be interesting to watch over the coming couple of years is how the cost line of sequencing is affected by the IT side of the equation. As noted earlier, the sequencers themselves are becoming more widely available due to price point. If the server side of the genomics business follows suit in a more competitive way, the goals of personalized medicine could be closer than we think–and not just because of the work of a relatively few research institutions that had enough funding…Imagine an average clinician’s ability to tailor treatment based on a quick sequence effort at one-twentieth of the cost it would have been in 2009.

According to Jason Corneveaux, a bioinformatician in the neurogenomics division at the Translational Genomics Research Institute, “With diseases like neuroblastoma, hours matter.” He says that their Dell system allows them to score the needed processing in a “clinically relevant amount of time.”

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!

NSF Awards $10M to Extend Chameleon Cloud Testbed Project

September 19, 2017

The National Science Foundation has awarded a second phase, $10 million grant to the Chameleon cloud computing testbed project led by University of Chicago with partners at the Texas Advanced Computing Center (TACC), Ren Read more…

By John Russell

NERSC Simulations Shed Light on Fusion Reaction Turbulence

September 19, 2017

Understanding fusion reactions in detail – particularly plasma turbulence – is critical to the effort to bring fusion power to reality. Recent work including roughly 70 million hours of compute time at the National E Read more…

Kathy Yelick Charts the Promise and Progress of Exascale Science

September 15, 2017

On Friday, Sept. 8, Kathy Yelick of Lawrence Berkeley National Laboratory and the University of California, Berkeley, delivered the keynote address on “Breakthrough Science at the Exascale” at the ACM Europe Conferen Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE Prepares Customers for Success with the HPC Software Portfolio

High performance computing (HPC) software is key to harnessing the full power of HPC environments. Development and management tools enable IT departments to streamline installation and maintenance of their systems as well as create, optimize, and run their HPC applications. Read more…

U of Illinois, NCSA Launch First US Nanomanufacturing Node

September 14, 2017

The University of Illinois at Urbana-Champaign together with the National Center for Supercomputing Applications (NCSA) have launched the United States's first computational node aimed at the development of nanomanufactu Read more…

By Tiffany Trader

Kathy Yelick Charts the Promise and Progress of Exascale Science

September 15, 2017

On Friday, Sept. 8, Kathy Yelick of Lawrence Berkeley National Laboratory and the University of California, Berkeley, delivered the keynote address on “Breakt Read more…

By Tiffany Trader

DARPA Pledges Another $300 Million for Post-Moore’s Readiness

September 14, 2017

The Defense Advanced Research Projects Agency (DARPA) launched a giant funding effort to ensure the United States can sustain the pace of electronic innovation vital to both a flourishing economy and a secure military. Under the banner of the Electronics Resurgence Initiative (ERI), some $500-$800 million will be invested in post-Moore’s Law technologies. Read more…

By Tiffany Trader

IBM Breaks Ground for Complex Quantum Chemistry

September 14, 2017

IBM has reported the use of a novel algorithm to simulate BeH2 (beryllium-hydride) on a quantum computer. This is the largest molecule so far simulated on a quantum computer. The technique, which used six qubits of a seven-qubit system, is an important step forward and may suggest an approach to simulating ever larger molecules. Read more…

By John Russell

Cubes, Culture, and a New Challenge: Trish Damkroger Talks about Life at Intel—and Why HPC Matters More Than Ever

September 13, 2017

Trish Damkroger wasn’t looking to change jobs when she attended SC15 in Austin, Texas. Capping a 15-year career within Department of Energy (DOE) laboratories, she was acting Associate Director for Computation at Lawrence Livermore National Laboratory (LLNL). Her mission was to equip the lab’s scientists and research partners with resources that would advance their cutting-edge work... Read more…

By Jan Rowell

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

MIT-IBM Watson AI Lab Targets Algorithms, AI Physics

September 7, 2017

Investment continues to flow into artificial intelligence research, especially in key areas such as AI algorithms that promise to move the technology from speci Read more…

By George Leopold

Need Data Science CyberInfrastructure? Check with RENCI’s xDCI Concierge

September 6, 2017

For about a year the Renaissance Computing Institute (RENCI) has been assembling best practices and open source components around data-driven scientific researc Read more…

By John Russell

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

Six Exascale PathForward Vendors Selected; DoE Providing $258M

June 15, 2017

The much-anticipated PathForward awards for hardware R&D in support of the Exascale Computing Project were announced today with six vendors selected – AMD Read more…

By John Russell

Top500 Results: Latest List Trends and What’s in Store

June 19, 2017

Greetings from Frankfurt and the 2017 International Supercomputing Conference where the latest Top500 list has just been revealed. Although there were no major Read more…

By Tiffany Trader

Leading Solution Providers

IBM Clears Path to 5nm with Silicon Nanosheets

June 5, 2017

Two years since announcing the industry’s first 7nm node test chip, IBM and its research alliance partners GlobalFoundries and Samsung have developed a proces Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

GlobalFoundries: 7nm Chips Coming in 2018, EUV in 2019

June 13, 2017

GlobalFoundries has formally announced that its 7nm technology is ready for customer engagement with product tape outs expected for the first half of 2018. The Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This