HPCwire: Iowa State Team Wins DNA Sequence Alignment Contest Using Convey Computer

Since 1986 - Covering the Fastest Computers
in the World and the People Who Run Them

Translation Disclaimer

Subscribe | Sign In

Tabor Communications
Corporate Video

Leading HPC
Solution Providers

July 13, 2012

Iowa State Team Wins DNA Sequence Alignment Contest Using Convey Computer

RICHARDSON, Texas, July 12 -- Convey Computer today announced that students at Iowa State University won first place in the 2012 MemoCODE Conference design contest with their fast exact-match short-read aligner. Using a Convey HC-1, the students' solution achieved the highest overall performance--more than 24 times faster than the second place finisher.

Experts from all segments of the commercial and academic world embarked upon the month long challenge, using a variety of design tools, hardware and software. The contest addressed a common challenge of DNA sequence alignment: efficiently map millions of 100 base pair sequences to a reference human genome of 3.1 billion base pairs, improving the performance of the reference implementation. In genomics it is necessary to map short DNA sequences (reads) generated by next generation sequencers to a reference genome in order to detect genetic variations.

Advised by Iowa State professors Phillip Jones and Joseph Zambreno, several graduate students in the Department of Electrical and Computer Engineering divided into two teams--each using a different coprocessor technology. Jones' group selected the Convey HC-1 with a field-programmable gate array (FPGA) architecture, while Zambreno's team used graphics processing units (GPUs).

Although the GPU-based team got off to a fast start, it soon became clear that the Convey FPGA solution was far superior. "This particular challenge had a big memory bandwidth issue--and having local memory was vital," explained Zambreno. "By their nature, GPUs are fairly limited to how much on-chip, easily accessible memory is available."

After a month of design planning and long hours of implementation, the students on the Convey team debuted a solution they called Shepard. "The meat of the application--doing the actual alignment--took about one second," explained Kevin Townsend, one of the grad students on the Convey team. "We won because we were able to get 80 gigabytes of memory bandwidth on Convey's coprocessor."

The team credits their success to the Convey server. "The Convey system makes it easy to develop algorithms because of its design and toolset," said Jones. "The development infrastructure is amazing compared to other FPGA solutions I have seen. And from a user's point of view, the Convey system simplifies how to get access to memory." Jones concluded, "Overall, the development infrastructure makes the HC-1 an ideal architecture for this solution."

The team sees Shepard as a potential game changer. "This type of big speed up could enable all sorts of different algorithms in bioinformatics," concluded Chad Nelson, another grad student on the Convey team. "As DNA sequencing quality improves, so will the usefulness of exact match alignment tools such as Shepard. Additionally, other application domains could also benefit from the Shepard architecture, such as data mining, social graphs, and search optimization."

The winners will be presenting their methods at the 10th ACM/IEEE International Conference on Formal Methods and Models for Codesign, Arlington, Virginia. July 16-17, 2012. http://www.memocode-conference.com.

About Convey Computer Corporation

Based in Richardson, Texas, Convey Computer breaks power, performance and programmability barriers with the world's first hybrid-core computer--a system that marries the low cost and simple programming model of a commodity system with the performance of a customized hardware architecture. Using the Convey hybrid-core systems, customers worldwide in industries such as life sciences, research, big data, and the government/military enjoy order of magnitude performance increases while reducing acquisition and operating costs.

-----

Source: Convey Computer Corp

Share Options

Subscribe

Subscribe to HPCwire

Discussion

There are 0 discussion items posted.

Join the Discussion

Become a Registered User Today!

Registered Users Log in join the Discussion

RSS Feeds

Feeds by Topic

Feeds by Industry

Feeds by Content Type

Subscribe to All Content

All

July 16, 2012

July 13, 2012

July 12, 2012

July 11, 2012

July 10, 2012

July 09, 2012

July 06, 2012

July 05, 2012

July 04, 2012

Feature Articles

Intel Expands HPC Collection with Whamcloud Buy

Intel Corporation has acquired Whamcloud, a startup devoted to supporting the open source Lustre parallel file system and its user community. The deal marks the latest in a line of high performance computing acquisitions that Intel has made over the past few years to expand its HPC footprint.
Read more...

DOE Primes Pump for Exascale Supercomputers

Intel, AMD, NVIDIA, and Whamcloud have been awarded tens of millions of dollars by the US Department of Energy (DOE) to kick-start research and development required to build exascale supercomputers. The work will be performed under the FastForward program, a joint effort run by the DOE Office of Science and the National Nuclear Security Administration (NNSA) that will focus on developing future hardware and software technologies capable of supporting such machines.
Read more...

Hybrid Memory Cube Angles for Exascale

Computer memory is currently undergoing something of an identity crisis. For the past 8 years, multicore microprocessors have been creating a performance discontinuity, the so-called memory wall. It's now fairly clear that this widening gap between compute and memory performance will not be solved with conventional DRAM products. But there is one technology under development that aims to close that gap, and its first use case will likely be in the ethereal realm of supercomputing.
Read more...

Read more HPCwire features...

Around the Web

Developing Diminutive Transitors is a Fight Against Physics

Jul 16, 2012 | EUV lithography, the technology chipmakers are counting on to keep Moore's Law alive, is behind schedule.
Read more...

New Mexico to Pull Plug on Encanto, Former Top 5 Supercomputer

Jul 12, 2012 | State says supercomputing center can’t pay bills to keep machine running.
Read more...

Computer Program Learns Games by Watching People

Jul 11, 2012 | Computer scientist builds intelligent machine with single-core laptop and some slick algorithms.
Read more...

Helix Nebula Cloud Targets European Scientific Research

Jul 10, 2012 | Science cloud in proof-of concept stage.
Read more...

Plug In and Power Down

Jul 09, 2012 | EU project offers software that makes datacenters more energy-efficient.
Read more...

Read more headlines...

Tackling the Data Deluge: File Systems and Storage Technologies

06/25/2012 | NetApp | A single hour of data collection can result in 7+ million files from just one camera. Collection opportunities are limited and must be successful every time. As defense and intelligence agencies seek to use the data collected to make mission-critical battlefield decisions, there’s greater emphasis on smart data and imagery collection, capture, storage and analysis to drive real-time intelligence. The data gathered must accurately and systematically be analyzed, integrated and disseminated to those who need it – troops on the ground. This reality leads to an inevitable challenge – warfighters swimming in sensors, drowning in data. With the millions, if not billions, of sensors providing all-seeing reports of the combat environment, managing the overload demands a file system and storage infrastructure that scales and performs while protecting the data collected. Part II of our whitepaper series highlights NetApp’s scalable, modular, and flexible storage solution to handle the demanding requirements of sophisticated ISR environments.

View the White Paper Library

Michael Wolfe Webinar: PGI Accelerator with OpenACC

Join Michael for a look at the first PGI Accelerator Fortran and C compilers to include comprehensive support for OpenACC, the new open standard for programming accelerators using compiler directives.