Mercury Computer Systems, Inc. (NASDAQ: MRCY) announced preliminary results of a joint development effort with Boston University, in which the team successfully migrated a specialized biotech application to the Cell Broadband Engine(TM) (BE) processor, achieving an order of magnitude performance improvement in a smaller system footprint over the previous configuration.
“This approach to drug design has the potential to revolutionize the cost and pace of new drug development,” said Sandor Vajda, Ph.D., Professor of Biomedical Engineering at Boston University. “With Mercury’s hardware, software, and assistance in algorithm optimization, this method is more commercially viable.”
Computational fragment-based drug design (FBDD) is a promising new approach in the pharmaceutical discovery and design industry that depends heavily on computer simulation (so-called in silico experimentation). FBDD simulates the chemistry and physics of molecular interactions in order to estimate how well potential drugs bind to their target proteins.
The Structural Bioinformatics Lab of Boston University initially developed a highly regarded FBDD tool that creates a map of likely drug binding sites on the surface of proteins. This program initially took weeks to run on a departmental Linux(R) cluster. Various iterations of software development by the joint team led to significant improvements on the Linux cluster, dramatic improvements running on an IBM Blue Gene(R) cluster, and unrivalled performance on Mercury’s Cell BE processor-based hardware.
The collaboration has caused FBDD algorithms, which were primarily used for academic research, to become more commercially viable. This will enable biotech firms to use the newly created algorithms as a small molecule discovery and design platform. The team successfully migrated the FBDD computer simulation in progressive steps from a shared departmental Linux cluster running for weeks — to a single Cell BE processor running for less than three minutes. In order to accomplish this, the team ported the application to the Cell BE processor architecture, including converting the algorithm to single precision. After the initial port to the Cell BE processor and preliminary efforts to optimize the application for Cell, the average computation time for the application running on the Cell BE processor is approximately 10 times faster than the same application running on a Blue Gene processor, in a chip-to-chip comparison.
“Moving away from a shared supercomputing infrastructure on a cluster to a dedicated supercomputer on a single Cell BE processor can make a tremendous difference in productivity for a development team,” said Mirza Cifric, Director of the Biotech group at Mercury Computer Systems. “The current version of software runs in less than three minutes on a single Cell BE processor. The development team found this to be a practical and affordable alternative to running on clusters of Pentium(R) processors or clusters of Blue Gene processors.”
The Mercury MultiCore Plus SDK provides a complete, intuitive programming environment for products based on the Cell BE and other multicore processors. Combining a powerful set of software tools and libraries into a seamless package, the MultiCore Plus SDK enables users to maximize resources and application performance by taking full advantage of the multicore processor’s computation model. The efficiency achieved in the algorithm optimization and porting to the Cell BE processor is expected to enable new scientific opportunities that were unattainable with previous computational limitations.
For more information on Mercury’s Cell BE processor-based offerings, visit Mercury in Booth #1135 at Supercomputing 2006 or contact Mercury at (866) 627-6951.
Mercury Computer Systems, Inc. — Where Challenges Drive Innovation
Mercury Computer Systems is the leading provider of computing systems and software for data-intensive applications that include image processing, signal processing, and visualization. With a strong commitment to innovation, our expertise in algorithm optimization, systems development, and silicon design is blended with software application knowledge and industry-standard technologies to solve unique computing challenges. We work closely with our customers to architect solutions that have a meaningful impact on everyday life: detecting aneurysms; designing safer, more fuel-efficient aircraft; identifying security threats; discovering oil; developing new drugs; and visualizing virtually every aspect of scientific investigation. Mercury’s comprehensive, purpose-built solutions capture, process, and present data for the world’s largest medical imaging companies, 8 of the 10 top defense prime contractors, and other leading Fortune 500 and mid-market companies in semiconductor, energy, telecommunications, and other industries. Our dedication to performance excellence and collaborative innovation continues a 23-year history in enabling customers to stay at the forefront of the markets they serve. Mercury is based in Chelmsford, Massachusetts and serves customers worldwide through a broad network of direct sales offices, subsidiaries, and distributors. We are listed on the Nasdaq National Market (NASDAQ: MRCY).
Blue Gene is a registered trademark of IBM Corporation in the United States. Cell Broadband Engine is a trademark of Sony Computer Entertainment Inc. Intel and Pentium are trademarks or registered trademarks of Intel Corporation or its subsidiaries in the United States and other countries.