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!

AWS Embraces FPGAs, ‘Elastic’ GPUs

December 2, 2016

A new instance type rolled out this week by Amazon Web Services is based on customizable field programmable gate arrays that promise to strike a balance between performance and cost as emerging workloads create requirements often unmet by general-purpose processors. Read more…

By George Leopold

AWS Launches Massive 100 Petabyte ‘Sneakernet’

December 1, 2016

Amazon Web Services now offers a way to move data into its cloud by the truckload. Read more…

By Tiffany Trader

Weekly Twitter Roundup (Dec. 1, 2016)

December 1, 2016

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

HPC Career Notes (Dec. 2016)

December 1, 2016

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high performance computing community. Read more…

By Thomas Ayres

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

IBM and NSF Computing Pioneer Erich Bloch Dies at 91

November 30, 2016

Erich Bloch, a computational pioneer whose competitive zeal and commercial bent helped transform the National Science Foundation while he was its director, died last Friday at age 91. Bloch was a productive force to be reckoned. During his long stint at IBM prior to joining NSF Bloch spearheaded development of the “Stretch” supercomputer and IBM’s phenomenally successful System/360. Read more…

By John Russell

Pioneering Programmers Awarded Presidential Medal of Freedom

November 30, 2016

In an awards ceremony on November 22, President Barack Obama recognized 21 recipients with the Presidential Medal of Freedom, the Nation’s highest civilian honor. Read more…

By Tiffany Trader

Seagate-led SAGE Project Delivers Update on Exascale Goals

November 29, 2016

Roughly a year and a half after its launch, the SAGE exascale storage project led by Seagate has delivered a substantive interim report – Data Storage for Extreme Scale. Read more…

By John Russell

AWS Launches Massive 100 Petabyte ‘Sneakernet’

December 1, 2016

Amazon Web Services now offers a way to move data into its cloud by the truckload. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Seagate-led SAGE Project Delivers Update on Exascale Goals

November 29, 2016

Roughly a year and a half after its launch, the SAGE exascale storage project led by Seagate has delivered a substantive interim report – Data Storage for Extreme Scale. Read more…

By John Russell

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

HPE-SGI to Tackle Exascale and Enterprise Targets

November 22, 2016

At first blush, and maybe second blush too, Hewlett Packard Enterprise’s (HPE) purchase of SGI seems like an unambiguous win-win. SGI’s advanced shared memory technology, its popular UV product line (Hanna), deep vertical market expertise, and services-led go-to-market capability all give HPE a leg up in its drive to remake itself. Bear in mind HPE came into existence just a year ago with the split of Hewlett-Packard. The computer landscape, including HPC, is shifting with still unclear consequences. One wonders who’s next on the deal block following Dell’s recent merger with EMC. Read more…

By John Russell

Intel Details AI Hardware Strategy for Post-GPU Age

November 21, 2016

Last week at SC16, Intel revealed its product roadmap for embedding its processors with key capabilities and attributes needed to take artificial intelligence (AI) to the next level. Read more…

By Alex Woodie

SC Says Farewell to Salt Lake City, See You in Denver

November 18, 2016

After an intense four-day flurry of activity (and a cold snap that brought some actual snow flurries), the SC16 show floor closed yesterday (Thursday) and the always-extensive technical program wound down today. Read more…

By Tiffany Trader

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

Why 2016 Is the Most Important Year in HPC in Over Two Decades

August 23, 2016

In 1994, two NASA employees connected 16 commodity workstations together using a standard Ethernet LAN and installed open-source message passing software that allowed their number-crunching scientific application to run on the whole “cluster” of machines as if it were a single entity. Read more…

By Vincent Natoli, Stone Ridge Technology

IBM Advances Against x86 with Power9

August 30, 2016

After offering OpenPower Summit attendees a limited preview in April, IBM is unveiling further details of its next-gen CPU, Power9, which the tech mainstay is counting on to regain market share ceded to rival Intel. Read more…

By Tiffany Trader

AWS Beats Azure to K80 General Availability

September 30, 2016

Amazon Web Services has seeded its cloud with Nvidia Tesla K80 GPUs to meet the growing demand for accelerated computing across an increasingly-diverse range of workloads. The P2 instance family is a welcome addition for compute- and data-focused users who were growing frustrated with the performance limitations of Amazon's G2 instances, which are backed by three-year-old Nvidia GRID K520 graphics cards. Read more…

By Tiffany Trader

Think Fast – Is Neuromorphic Computing Set to Leap Forward?

August 15, 2016

Steadily advancing neuromorphic computing technology has created high expectations for this fundamentally different approach to computing. Read more…

By John Russell

The Exascale Computing Project Awards $39.8M to 22 Projects

September 7, 2016

The Department of Energy’s Exascale Computing Project (ECP) hit an important milestone today with the announcement of its first round of funding, moving the nation closer to its goal of reaching capable exascale computing by 2023. Read more…

By Tiffany Trader

HPE Gobbles SGI for Larger Slice of $11B HPC Pie

August 11, 2016

Hewlett Packard Enterprise (HPE) announced today that it will acquire rival HPC server maker SGI for $7.75 per share, or about $275 million, inclusive of cash and debt. The deal ends the seven-year reprieve that kept the SGI banner flying after Rackable Systems purchased the bankrupt Silicon Graphics Inc. for $25 million in 2009 and assumed the SGI brand. Bringing SGI into its fold bolsters HPE's high-performance computing and data analytics capabilities and expands its position... Read more…

By Tiffany Trader

ARM Unveils Scalable Vector Extension for HPC at Hot Chips

August 22, 2016

ARM and Fujitsu today announced a scalable vector extension (SVE) to the ARMv8-A architecture intended to enhance ARM capabilities in HPC workloads. Fujitsu is the lead silicon partner in the effort (so far) and will use ARM with SVE technology in its post K computer, Japan’s next flagship supercomputer planned for the 2020 timeframe. This is an important incremental step for ARM, which seeks to push more aggressively into mainstream and HPC server markets. Read more…

By John Russell

IBM Debuts Power8 Chip with NVLink and Three New Systems

September 8, 2016

Not long after revealing more details about its next-gen Power9 chip due in 2017, IBM today rolled out three new Power8-based Linux servers and a new version of its Power8 chip featuring Nvidia’s NVLink interconnect. Read more…

By John Russell

Leading Solution Providers

Vectors: How the Old Became New Again in Supercomputing

September 26, 2016

Vector instructions, once a powerful performance innovation of supercomputing in the 1970s and 1980s became an obsolete technology in the 1990s. But like the mythical phoenix bird, vector instructions have arisen from the ashes. Here is the history of a technology that went from new to old then back to new. Read more…

By Lynd Stringer

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

Intel Launches Silicon Photonics Chip, Previews Next-Gen Phi for AI

August 18, 2016

At the Intel Developer Forum, held in San Francisco this week, Intel Senior Vice President and General Manager Diane Bryant announced the launch of Intel's Silicon Photonics product line and teased a brand-new Phi product, codenamed "Knights Mill," aimed at machine learning workloads. Read more…

By Tiffany Trader

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

Beyond von Neumann, Neuromorphic Computing Steadily Advances

March 21, 2016

Neuromorphic computing – brain inspired computing – has long been a tantalizing goal. The human brain does with around 20 watts what supercomputers do with megawatts. And power consumption isn’t the only difference. Fundamentally, brains ‘think differently’ than the von Neumann architecture-based computers. While neuromorphic computing progress has been intriguing, it has still not proven very practical. Read more…

By John Russell

Dell EMC Engineers Strategy to Democratize HPC

September 29, 2016

The freshly minted Dell EMC division of Dell Technologies is on a mission to take HPC mainstream with a strategy that hinges on engineered solutions, beginning with a focus on three industry verticals: manufacturing, research and life sciences. "Unlike traditional HPC where everybody bought parts, assembled parts and ran the workloads and did iterative engineering, we want folks to focus on time to innovation and let us worry about the infrastructure," said Jim Ganthier, senior vice president, validated solutions organization at Dell EMC Converged Platforms Solution Division. Read more…

By Tiffany Trader

Container App ‘Singularity’ Eases Scientific Computing

October 20, 2016

HPC container platform Singularity is just six months out from its 1.0 release but already is making inroads across the HPC research landscape. It's in use at Lawrence Berkeley National Laboratory (LBNL), where Singularity founder Gregory Kurtzer has worked in the High Performance Computing Services (HPCS) group for 16 years. Read more…

By Tiffany Trader

Micron, Intel Prepare to Launch 3D XPoint Memory

August 16, 2016

Micron Technology used last week’s Flash Memory Summit to roll out its new line of 3D XPoint memory technology jointly developed with Intel while demonstrating the technology in solid-state drives. Micron claimed its Quantx line delivers PCI Express (PCIe) SSD performance with read latencies at less than 10 microseconds and writes at less than 20 microseconds. Read more…

By George Leopold

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