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!

GDPR’s Impact on Scientific Research Uncertain

May 24, 2018

Amid the angst over preparations—or lack thereof—for new European Union data protections entering into force at week’s end is the equally worrisome issue of the rules’ impact on scientific research. Among the Read more…

By George Leopold

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Francisco, one would be tempted to dismiss its claims of inventing Read more…

By John Russell

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Mastering the Big Data Challenge in Cognitive Healthcare

Patrick Chain, genomics researcher at Los Alamos National Laboratory, posed a question in a recent blog: What if a nurse could swipe a patient’s saliva and run a quick genetic test to determine if the patient’s sore throat was caused by a cold virus or a bacterial infection? Read more…

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been emerging from stealth over the last year and a half, is unveili Read more…

By Tiffany Trader

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Franci Read more…

By John Russell

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been eme Read more…

By Tiffany Trader

Japan Meteorological Agency Takes Delivery of Pair of Crays

May 21, 2018

Cray has supplied two identical Cray XC50 supercomputers to the Japan Meteorological Agency (JMA) in northwestern Tokyo. Boasting more than 18 petaflops combine Read more…

By Tiffany Trader

ASC18: Final Results Revealed & Wrapped Up

May 17, 2018

It was an exciting week at ASC18 in Nanyang, China. The student teams braved extreme heat, extremely difficult applications, and extreme competition in order to cross the cluster competition finish line. The gala awards ceremony took place on Wednesday. The auditorium was packed with student teams, various dignitaries, the media, and other interested parties. So what happened? Read more…

By Dan Olds

Spring Meetings Underscore Quantum Computing’s Rise

May 17, 2018

The month of April 2018 saw four very important and interesting meetings to discuss the state of quantum computing technologies, their potential impacts, and th Read more…

By Alex R. Larzelere

Quantum Network Hub Opens in Japan

May 17, 2018

Following on the launch of its Q Commercial quantum network last December with 12 industrial and academic partners, the official Japanese hub at Keio University is now open to facilitate the exploration of quantum applications important to science and business. The news comes a week after IBM announced that North Carolina State University was the first U.S. university to join its Q Network. Read more…

By Tiffany Trader

Democratizing HPC: OSC Releases Version 1.3 of OnDemand

May 16, 2018

Making HPC resources readily available and easier to use for scientists who may have less HPC expertise is an ongoing challenge. Open OnDemand is a project by t Read more…

By John Russell

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

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

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

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

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

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

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

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

CFO Steps down in Executive Shuffle at Supermicro

January 31, 2018

Supermicro yesterday announced senior management shuffling including prominent departures, the completion of an audit linked to its delayed Nasdaq filings, and Read more…

By John Russell

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

Deep Learning Portends ‘Sea Change’ for Oil and Gas Sector

February 1, 2018

The billowing compute and data demands that spurred the oil and gas industry to be the largest commercial users of high-performance computing are now propelling Read more…

By Tiffany Trader

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

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

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

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