Visit additional Tabor Communication Publications
January 07, 2010
Impulse C-to-FPGA DNA biotechnology algorithm leverages Pico Computing EX-500 computing platform
KIRKLAND, Wash., Jan. 7 -- Impulse Accelerated Technologies today announced that its CoDeveloper C-to-FPGA compiler has been used to develop and deploy a DNA biotechnology genome search algorithm on a new, modular FPGA acceleration platform created by Pico Computing, of Seattle, Wash. The Xilinx FPGA-accelerated bioinformatics algorithm, written in C, performs sequence analysis and pair-match scoring of DNA runs with lengths of 25 base pairs. The algorithm is inherently parallel, making it an ideal candidate for acceleration using a large number of FPGA devices. Within two days of powering up the EX-500 with the first Virtex-6 SX240T FPGA computing modules, Pico Computing engineers had successfully migrated and tested the C-language bioinformatics searching algorithm and demonstrated significant improvements in algorithm speed and throughput over previous generation FPGA products.
"This bioinformatics algorithm created by Pico Computing is a solid example of how higher-level design tools such as Impulse C can speed the development and deployment of complex algorithms," said Brian Durwood, co-founder and COO of Impulse. "Our Platform Support Package integration with multiple Pico Computing products, including the EX-500, allowed this algorithm to be moved with little difficulty onto platforms ranging from single-FPGA cards, to FPGA clusters based on Xilinx Spartan, Virtex-5 and now the new Virtex-6 FPGAs."
Using the new, modular EX-500 platform as the foundation, and Impulse C as the programming tool, Pico Computing software and firmware engineers were able to successfully deploy the bioinformatics algorithm with no significant changes needed to the algorithm source code. The Pico EX-500 supports up to six M-501 modules per PCI Express board. Each module can be configured with a range of FPGAs including the Xilinx Virtex-6 LX240T devices used in this first test application. Pico Computing will demonstrate this algorithm at the Plant and Animal Genome Conference exhibit area on Jan. 10-12, booth #426.
"The M-501 modules with Virtex-6 FPGAs satisfy demands from our customers for increasing levels of computing performance, in applications that range from data security to life sciences and financial modeling," said Mark Hur, director of sales and marketing for Pico Computing. "Our government and commercial customers depend on our ability to supply the most advanced acceleration solutions, using the most up-to-date FPGA technologies and the most advanced tools for FPGA programming. We are happy to be partnering with Impulse on this and other applications."
Impulse is also partnering with the University of Washington and other schools on Tomography, Radiology and many other medical and medical imaging projects.
Impulse provides software-to-FPGA solutions, training and design services for embedded and high performance computing. Impulse solutions are used to accelerate the development and deployment of high-throughput industrial, medical, defense, aerospace, automotive and consumer electronics applications. Impulse C is used by many government agencies, most of the worlds' auto makers and hundreds of R&D teams. For more information, visit www.ImpulseAccelerated.com.
About Pico Computing
Pico Computing, headquartered in Seattle, Wash., specializes in highly integrated development and deployment platforms based on Field Programmable Gate Array (FPGA) technologies. Applications for Pico Computing technologies include cryptography, networking, signal processing, bioinformatics, and scientific computing. Pico Computing products are used in embedded systems as well as in military, national security and high performance computing applications. For more information about Pico products and services, visit www.picocomputing.com.
Source: Impulse Accelerated Technologies
The Xeon Phi coprocessor might be the new kid on the high performance block, but out of all first-rate kickers of the Intel tires, the Texas Advanced Computing Center (TACC) got the first real jab with its new top ten Stampede system.We talk with the center's Karl Schultz about the challenges of programming for Phi--but more specifically, the optimization...
Although Horst Simon was named Deputy Director of Lawrence Berkeley National Laboratory, he maintains his strong ties to the scientific computing community as an editor of the TOP500 list and as an invited speaker at conferences.
Supercomputing veteran, Bo Ewald, has been neck-deep in bleeding edge system development since his twelve-year stint at Cray Research back in the mid-1980s, which was followed by his tenure at large organizations like SGI and startups, including Scale Eight Corporation and Linux Networx. He has put his weight behind quantum company....
May 16, 2013 |
When it comes to cloud, long distances mean unacceptably high latencies. Researchers from the University of Bonn in Germany examined those latency issues of doing CFD modeling in the cloud by utilizing a common CFD and its utilization in HPC instance types including both CPU and GPU cores of Amazon EC2.
May 15, 2013 |
Supercomputers at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC) have worked on important computational problems such as collapse of the atomic state, the optimization of chemical catalysts, and now modeling popping bubbles.
May 10, 2013 |
Program provides cash awards up to $10,000 for the best open-source end-user applications deployed on 100G network.
May 09, 2013 |
The Japanese government has revealed its plans to best its previous K Computer efforts with what they hope will be the first exascale system...
May 08, 2013 |
For engineers looking to leverage high-performance computing, the accessibility of a cloud-based approach is a powerful draw, but there are costs that may not be readily apparent.
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.