DRC Energizes Smith-Waterman, Opens Door to On-Demand Service

By Nicole Hemsoth

February 9, 2011

News emerged recently that might reshape how genomics researchers think about the speed and accuracy of gene sequencing analysis projects that rely on the Smith-Waterman algorithm.

Sunnyvale, California-based coprocessor company, DRC Computer Corporation, announced a world record-setting genetic sequencing analysis appliance that was benchmarked in the multi-trillion cell updates per second range—a figure that could have gone higher, according to DRC’s Roy Graham. Although similar claims to supremacy have been made in the past, the company states that this marks a 5x improvement over previously published results.

While it might be tempting to think this is just another acceleration story about toppling old benchmarks, this one does have something of a unique slant.

While one of their FPGAs has the equivalent performance of 1000 cores, and this is interesting in itself, the company has advocated that there is a defined cloud computing angle since ideally, their FPGA-based Accelium board can be plugged into a standard x86 server via standard PCIe slots.

DRC claims that the “time and cost to complete [gene sequence analysis] can be reduced by a factor of 20 using standard Intel-based servers installed with their own DRC Accelium processors running on Windows HPC Server 2008 R2. They suggest that analysis time is sliced in addition to “over 90% the computing cost, power, real estate and infrastructure required to obtain the results.”

The beauty here, as they see it, is that standard commodity hardware can be significantly enhanced in a plug and play fashion that becomes thus cloud-enabled and more accessible to a broader array of potential users than before.

DRC is pitching this solution as cloud-ready when built in a private cloud, which was the environment they chose for their benchmarking effort. All debates about the validity (or newness) of private clouds aside, there could be changes coming for life sciences companies who want to make use of Smith-Waterman but have been barred due to the high costs of running this hungry algorithm in-house.

Roy Graham from DRC stated that the cloud value of the company’s announcement lies in the fact that eventually, many common sequencing services will be cloud-based and right now, what they’re looking at is a very high volume, scalable and cost-effective platform. He claims that the company is currently in discussions with a number of cloud services companies and at this point, what they’re looking for is a proof point.

DRC claims that due to the inherent parallelism of their reconfigurable coprocessors, such solutions are extremely scalable and adaptable to modern cloud computing environments where computing resources can be shared across multiple users and applications.

According to Steve Casselman, CEO of DRC Computer Corporation, there is definitely a future in the clouds for Smith-Waterman. During a conversation with HPC in the Cloud last week, he speculated on the concept of a “corporate biocloud” where users will be able to run Smith-Waterman on as much the hardware as needed while at the same time running other processes in an on-demand format. This is what he calls an example of “acceleration on-demand,” noting that there are several different algorithms ripe for this kind of capability.

Casselman insists that the main takeaway is that “it doesn’t require a very controlled environment to build this type of network or structure so it lends itself very well to a general cloud environment.”

There are some solid reasons to support efforts to refine the infrastructure concerns for an algorithm like Smith-Waterman. It has been around for over two decades and produces refined results, but the user base behind it is small given the high costs of achieving the precise output. This means that companies that want to make use of Smith-Waterman face far higher costs if they require the specificity that other genomic applications cannot match. This could make good cost sense for companies that need the specificity of results but cannot invest up-front for the hardware required.

While Smith-Waterman is considered by some to be the gold standard for this type of work, the associated costs have led to companies using heuristic applications like BLAST to achieve results, in part because it is a cost-efficient fit for modern CPU architectures, according to Steve Casselman, CEO of DRC.

Will Smith-Waterman be delivered as a service (with an application wrapped around it) so more refined results from genetic sequencing projects can be realized by a broader class of researchers and life sciences companies? Would it require a friendly interface and inherent ease of use–and if so, who would champion the middleware cause if it was made attractive enough by efforts from companies like DRC?

Microsoft (which already offers some applications via its Azure cloud to lure in life sciences) might be the source of such a project and did take initialinterest in DRC’s benchmarking effort. The coprocessor company approached them before undertaking the benchmark as they felt that some of their big life sciences customers who were using Windows HPC Server needed benchmarks not based on Linux (although by the way the results between Linux and HPC Server were comparable).

Jason Stowe, CEO of Cycle Computing noted that there is demand for Smith-Waterman as a service and that it can be successful. In a short interview Stowe noted that, “When it comes to Smith-Waterman, we have nVidia GPU-enabled versions (CUDA SW++) deployed on our CycleCloud Clusters-as-a-Service, that accelerate this algorithm to run 10-50x as fast as BLAST on comparable queries. CycleCloud’s ability to start up 64 GPU clusters on Amazon EC2 in 15 minutes enables users to take advantage of both GPU-acceleration, and cloud cost-cutting, to analyze whole genomes using Smith-Waterman, at a fraction of the cost.”

If the algorithm, which produces superior results but has been prohibitively expensive finds the needed acceleration to make it more affordable, demand could rise for the decades-old code, especially if it is being run remotely on a pay-as-you-go basis.

While there is certainly some speculation here, what is clear is that there could be a new slant on old tools to cure diseases. As DRC’s Roy Graham stated, “The FPGA is a means to an end, so although this is a nice FPGA story, the real story is now we have the ability to provide highly accurate assessments of an individual’s affinity to a specific disease condition. In predictive diagnosis, accuracy is key and so far it’s been compromised because of a lack of cost effective computing resources. We now have the platform that can bridge the cost/accuracy divide.”
 

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

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

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

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