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!

AI-Focused ‘Genius’ Supercomputer Installed at KU Leuven

April 24, 2018

Hewlett Packard Enterprise has deployed a new approximately half-petaflops supercomputer, named Genius, at Flemish research university KU Leuven. The system is built to run artificial intelligence (AI) workloads and, as Read more…

By Tiffany Trader

New Exascale System for Earth Simulation Introduced

April 23, 2018

After four years of development, the Energy Exascale Earth System Model (E3SM) will be unveiled today and released to the broader scientific community this month. The E3SM project is supported by the Department of Energy Read more…

By Staff

RSC Reports 500Tflops, Hot Water Cooled System Deployed at JINR

April 18, 2018

RSC, developer of supercomputers and advanced HPC systems based in Russia, today reported deployment of “the world's first 100% ‘hot water’ liquid cooled supercomputer” at Joint Institute for Nuclear Research (JI Read more…

By Staff

HPE Extreme Performance Solutions

Hybrid HPC is Speeding Time to Insight and Revolutionizing Medicine

High performance computing (HPC) is a key driver of success in many verticals today, and health and life science industries are extensively leveraging these capabilities. Read more…

New Device Spots Quantum Particle ‘Fingerprint’

April 18, 2018

Majorana particles have been observed by university researchers employing a device consisting of layers of magnetic insulators on a superconducting material. The advance opens the door to controlling the elusive particle Read more…

By George Leopold

AI-Focused ‘Genius’ Supercomputer Installed at KU Leuven

April 24, 2018

Hewlett Packard Enterprise has deployed a new approximately half-petaflops supercomputer, named Genius, at Flemish research university KU Leuven. The system is Read more…

By Tiffany Trader

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’ Read more…

By John Russell

IBM: Software Ecosystem for OpenPOWER is Ready for Prime Time

April 16, 2018

With key pieces of the IBM/OpenPOWER versus Intel/x86 gambit settling into place – e.g., the arrival of Power9 chips and Power9-based systems, hyperscaler sup Read more…

By John Russell

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Cloud-Readiness and Looking Beyond Application Scaling

April 11, 2018

There are two aspects to consider when determining if an application is suitable for running in the cloud. The first, which we will discuss here under the title Read more…

By Chris Downing

Transitioning from Big Data to Discovery: Data Management as a Keystone Analytics Strategy

April 9, 2018

The past 10-15 years has seen a stark rise in the density, size, and diversity of scientific data being generated in every scientific discipline in the world. Key among the sciences has been the explosion of laboratory technologies that generate large amounts of data in life-sciences and healthcare research. Large amounts of data are now being stored in very large storage name spaces, with little to no organization and a general unease about how to approach analyzing it. Read more…

By Ari Berman, BioTeam, Inc.

IBM Expands Quantum Computing Network

April 5, 2018

IBM is positioning itself as a first mover in establishing the era of commercial quantum computing. The company believes in order for quantum to work, taming qu Read more…

By Tiffany Trader

FY18 Budget & CORAL-2 – Exascale USA Continues to Move Ahead

April 2, 2018

It was not pretty. However, despite some twists and turns, the federal government’s Fiscal Year 2018 (FY18) budget is complete and ended with some very positi Read more…

By Alex R. Larzelere

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

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

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

Leading Solution Providers

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

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