RIKEN reveals the first ever petaflops computer
05 July 2006 (Volume 1 Issue 7)
A team at the RIKEN Genomic Sciences Center in Yokohama has succeeded in building a petaflops computer system called MDGRAPE-3, specially for simulating the dynamics of proteins and other biomolecules. MDGRAPE-3 was developed in collaboration with SGI Japan and Intel Japan, and is also known as “Protein Explorer.”
MDGRAPE-3 is a large system that consists of 201 units of 24 MDGRAPE-3 chips, 64 parallel servers each containing 256 of Intel’s newest Xeon 5000-series processors (codename Dempsey), and 37 parallel servers each having 74 Intel Xeon 3.2GHz processors with 2MB L2 caches. Developed by RIKEN, the MDGRAPE-3 chip is the world’s fastest LSI chip for simulation of molecular dynamics.
MDGRAPE-3 is unable to run the Linpack benchmark, which is the basis for the TOP500 supercomputer rankings. However, its nominal peak performance of one petaflops means that it is almost three times faster than IBM’s BlueGene/L, which TOP500 currently lists as the world’s fastest supercomputer.
MDGRAPE-3 can simulate and test the affinity of proteins for pharmaceutical candidate molecules at extremely high speeds. It will therefore be useful in speeding up the development of new drugs. Its ability to reveal the workings of proteins through simulations will also make it invaluable for research on the mechanisms by which some proteins cause diseases, and for development of biological nanomachines.
