APPLICATIONS

Cray today announced that the Cray XD1 supercomputer is now available bundled with Smith-Waterman bioinformatics software, the most precise algorithm for comparing gene and protein sequences. Life sciences researchers can now use the Cray XD1 system equipped with Smith-Waterman cores to significantly reduce the time required for genomic data analysis, a critical step in many life science and biotechnology research areas. The Cray XD1 Smith-Waterman solution has performed 28 times faster when tested against other 64-bit AMD/Opteron processor-based solutions running the same application -- shortening analysis times from days to hours. The Cray solution combines the Cray XD1 high-performance supercomputer platform, field-programmable gate arrays (FPGAs) and Smith-Waterman software to provide a complete, out-of-the-box Smith-Waterman analysis tool. The Cray XD1 FPGAs act as specialized processors that accelerate a small, time-consuming portion of the Smith-Waterman algorithm, shortening the analyses many times over. The changes made to invoke the FPGAs are being released back into the open-source community, so researchers can always run the latest version of this popular open-source tool. Furthermore, because the Cray XD1 runs standard Linux/MPI applications, users enjoy the flexibility of an open platform, while gaining the performance of a dedicated hardware appliance. "The Cray XD1 supercomputer gives Smith-Waterman users a production-ready computing solution that delivers exceptional functionality and performance," said Amar Shan, product manager for the Cray XD1 system. "The bundle provides processing speed and precision that conventional systems cannot match. Researchers can dramatically accelerate the Smith-Waterman algorithm and get accurate results up to 28 times faster than with off-the-shelf processing. What's more, the system is versatile enough to run additional life sciences applications as well as other scientific work, allowing customers to leverage their computing investment."