Opening Sequences for HPC on Demand

By Nicole Hemsoth

May 11, 2011

Next generation DNA sequencing has brought a wealth of opportunities in research, pharmaceutical and clinical contexts, but for those who are in the high performance computing space, this particular market is bursting with a different array of opportunities. From specialty clusters dedicated exclusively to crunching the overwhelming amounts of data coming of sequencers (not to mention the storage might to keep it all in check) the biosciences industry is a prime target for vendors of all stripes.

Interestingly, with the rise of cloud computing and on-demand resources, investment in hardware for many companies isn’t always the first option. According to Tom Coull, Senior Vice President at Penguin Computing, a large number of DNA-driven companies are finding on-demand HPC a perfect fit, especially since their demands for high throughput computing are large but generally sporadic.

Providers of on-demand high performance computing that have an eye on this particular industry (Penguin Computing, Cycle Computing, and SGI in particular) have little elbow room in this tight market to garner valuable life sciences business. In addition to competing with public cloud resources like Amazon EC2, not to mention competition from traditional modes of computing (buying your own cluster) such services have to run a tight ship to keep their own hardware investments churning at peak capacity.

This issue of peak capacity is critical for both users of on-demand HPC and for the providers themselves. Naturally a provider like Penguin wants to make sure their investment is being fully utilized and they’re retuning a profit on the core hours spent. On the flip side, however, life sciences companies want to make sure that they’re balancing time-to-market concerns with core competency arguments.

To be more specific about this balance of issues, we spoke to Abe Lietz who heads IT for a major life sciences firm, Life Technologies. This global company provides a range of solutions for customers in the industry, from biological products for research to the instrumentation to back next-generation DNA sequencing efforts. In short, as Abe told us, “our core competency is about keeping pace with a rapidly changing industry; things change quickly and it’s not part of our goal to put the extreme time and resources into running our own IT the right way.”

Life Technologies is using Penguin Computing’s HPC on-demand (POD) offering to back a web interface into one of its most popular software packages for gene sequence analysis, Bioscope. While on the surface this might sound like a simple enough offering, the complexity of Bioscope and the fact that it is residing on collocated servers in Salt Lake City goes deeper than one might imagine.

Users log in through solidbioscope.com and are able to use the pay as you go model to analyze genomic data, using Penguin’s storage and resources exclusively. Penguin’s Coull noted that the pricing is roughly equivalent to what you might get with a similar cloud provider but unlike with a public cloud, users are able to know exactly where their data is at any given moment—an important issue for the HIPPA compliance-aware.

Coull also noted that for genomics researchers considering this from a purely cost-driven basis, if you’ve built and maintained a cluster based on peak requirements and you’re not using it at 35 percent on a full-time basis, you’re better off using an on-demand resource provider.  During our phone interview he was watching POD activity from his screen and noted that of the applications that were running at any given moment, a good estimation is that 50% of users have replaced their in-house systems electing to use POD exclusively while the other half were the sporadic users who make up a nice portion of the life sciences on-demand market due to the spotty need for big computation.

On a side note, Coull says that Penguin expects 4-fold growth over the next year for their POD service with the build-out of two AMD and Intel partnerships for new POD centers. Although he didn’t comment what percent of the business was life sciences driven, he noted this market was “significant” and that they’d seen a surprising uptick from academic institutions that needed extra resources.

Coull noted as well that their software stack has been tweaked by users to be able to bridge over to other cloud computing options, including Amazon’s S3, due to the fact that it seems to be one of the most popular storage options for this type of user.

It’s worth noting, by the way, that this was not Life Technology’s first interaction with Penguin Computing. The company had been providing hardware services to support Life Technologies’ proprietary software since 2007.

According to Penguin, this is a side effect of having a solid reputation with customers who are software-driven—if their in-house systems perform well and they like the service and support, it’s a natural fit for users to consider using their remote resources if they fit the bill.

Coull noted that some users are getting creative about using the POD service. For instance, during his occasional glances at the real-time reports from the POD interface, there were Life Technologies training sessions going on in real time, which gave users the chance to work in a hands-on fashion with the software.

VP of Life Technologies, Jeff Cafferty also weighed on this, noting that beyond sheer training, potential customers interested in evaluating analytics options (since there are many—and many are non-proprietary) could hop on the POD-driven solidbioscope.com resource and compare results, including mappability and other specific factors.

In addition to extolling the benefits of the cloud beyond just analytics, Cafferty told us, “We are in the post-human genome sequencing project phase of life sciences” what’s happened in this last decade is that companies like ours have been developing evermore high throughput technologies for sequencing DNA and furthermore the cost of sequencing has gone down tremendously. What this means is that there’s been a huge explosion in the amount of sequence information available for life sciences researchers.

This is a fact that is driving the next big buzzphrase after cloud computing—“big data”—into every marketing message, particularly on the storage end, for obvious reasons. While the massive data end of the equation is a major factor that is causing genomics researchers to consider looking beyond physical hardware, the computational requirements are nothing to sneeze at either.

Caffrey put this in context, noting that to sequence a human genome researchers are dealing with something that is 3 billion base pairs long. Their instrumentation for next generation sequencing creates what are called “short reads” of DNA and in one genome, this creates billions such reads that then need to be mapped back to a reference genome.

He also elaborated on a topic that is growing nearer and dearer to storage, compute, software and cloud vendors alike: “Life sciences researchers have traditionally functioned on an experimental model that involved a great deal of time generating data (biological samples can be rare or hard to extra information from) and relatively small amounts of time analyzing it, in part because there just wasn’t very much of it. In sequencing in particular this paradigm has been flipped—we’re now generating a tremendous amount of data in a very short period of time and thus the length now is because of the mining, management, comparing and analysis of all that data.”

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!

IBM Unveils Latest Achievements in AI Hardware

December 13, 2019

“The increased capabilities of contemporary AI models provide unprecedented recognition accuracy, but often at the expense of larger computational and energetic effort,” IBM Research wrote in a blog post. “Therefor Read more…

By Oliver Peckham

Focused on ‘Silicon TAM,’ Intel Puts Gary Patton, Former GlobalFoundries CTO, in Charge of Design Enablement

December 12, 2019

Change within Intel’s upper management – and to its company mission – has continued as a published report has disclosed that chip technology heavyweight Gary Patton, GlobalFoundries’ CTO and R&D SVP as well a Read more…

By Doug Black

Quantum Bits: Rigetti Debuts New Gates, D-Wave Cuts NEC Deal, AWS Jumps into the Quantum Pool

December 12, 2019

There’s been flurry of significant news in the quantum computing world. Yesterday, Rigetti introduced a new family of gates that reduces circuit depth required on some problems and D-Wave struck a deal with NEC to coll Read more…

By John Russell

How Formula 1 Used Cloud HPC to Build the Next Generation of Racing

December 12, 2019

Formula 1, Rob Smedley explained, is maybe the biggest racing spectacle in the world, with five hundred million fans tuning in for every race. Smedley, a chief engineer with Formula 1’s performance engineering and anal Read more…

By Oliver Peckham

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has been unveiled in upstate New York that will be used by IBM Read more…

By Doug Black

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

IBM Accelerated Insights

GPU Scheduling and Resource Accounting: The Key to an Efficient AI Data Center

[Connect with LSF users and learn new skills in the IBM Spectrum LSF User Community!]

GPUs are the new CPUs

GPUs have become a staple technology in modern HPC and AI data centers. Read more…

At SC19: Developing a Digital Twin

December 11, 2019

In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location to location. In such a world, there will also be a digital twin for each UAV in the fleet: a virtual model that will follow the UAV through its existence, evolving with time. Read more…

By Aaron Dubrow

Focused on ‘Silicon TAM,’ Intel Puts Gary Patton, Former GlobalFoundries CTO, in Charge of Design Enablement

December 12, 2019

Change within Intel’s upper management – and to its company mission – has continued as a published report has disclosed that chip technology heavyweight G Read more…

By Doug Black

Quantum Bits: Rigetti Debuts New Gates, D-Wave Cuts NEC Deal, AWS Jumps into the Quantum Pool

December 12, 2019

There’s been flurry of significant news in the quantum computing world. Yesterday, Rigetti introduced a new family of gates that reduces circuit depth require Read more…

By John Russell

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has Read more…

By Doug Black

At SC19: Developing a Digital Twin

December 11, 2019

In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location to location. In such a world, there will also be a digital twin for each UAV in the fleet: a virtual model that will follow the UAV through its existence, evolving with time. Read more…

By Aaron Dubrow

Intel’s Jim Clarke on its New Cryo-controller and why Intel isn’t Late to the Quantum Party

December 9, 2019

Intel today introduced the ‘first-of-its-kind’ cryo-controller chip for quantum computing and previewed a cryo-prober tool for characterizing quantum proces Read more…

By John Russell

On the Spack Track @SC19

December 5, 2019

At the annual supercomputing conference, SC19 in Denver, Colorado, there were Spack events each day of the conference. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three U.S. national Department of Energy (DOE) laboratories and Sylabs... Read more…

By Elizabeth Leake

Intel’s New Hyderabad Design Center Targets Exascale Era Technologies

December 3, 2019

Intel's Raja Koduri was in India this week to help launch a new 300,000 square foot design and engineering center in Hyderabad, which will focus on advanced com Read more…

By Tiffany Trader

AWS Debuts 7nm 2nd-Gen Graviton Arm Processor

December 3, 2019

The “x86 Big Bang,” in which market dominance of the venerable Intel CPU has exploded into fragments of processor options suited to varying workloads, has n Read more…

By Doug Black

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

SC19: IBM Changes Its HPC-AI Game Plan

November 25, 2019

It’s probably fair to say IBM is known for big bets. Summit supercomputer – a big win. Red Hat acquisition – looking like a big win. OpenPOWER and Power processors – jury’s out? At SC19, long-time IBMer Dave Turek sketched out a different kind of bet for Big Blue – a small ball strategy, if you’ll forgive the baseball analogy... Read more…

By John Russell

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
CEJN
CJEN
DDN
DDN
MELLANOX
MELLANOX
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann Read more…

By John Russell

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

Cerebras to Supply DOE with Wafer-Scale AI Supercomputing Technology

September 17, 2019

Cerebras Systems, which debuted its wafer-scale AI silicon at Hot Chips last month, has entered into a multi-year partnership with Argonne National Laboratory and Lawrence Livermore National Laboratory as part of a larger collaboration with the U.S. Department of Energy... Read more…

By Tiffany Trader

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

Jensen Huang’s SC19 – Fast Cars, a Strong Arm, and Aiming for the Cloud(s)

November 20, 2019

We’ve come to expect Nvidia CEO Jensen Huang’s annual SC keynote to contain stunning graphics and lively bravado (with plenty of examples) in support of GPU Read more…

By John Russell

IBM Opens Quantum Computing Center; Announces 53-Qubit Machine

September 19, 2019

Gauging progress in quantum computing is a tricky thing. IBM yesterday announced the opening of the IBM Quantum Computing Center in New York, with five 20-qubit 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