Sun Blade X6275 Blade Cluster Delivers Fast and Efficient NAMD Performance
(As of Tuesday, 17 November 2009)
Oracle’s Sun Blade 6048 chassis with 48 of Oracle’s Sun Blade X6275 server modules (768 cores) was tested in this benchmark using NAMD molecular dynamics applications software. Interconnected via Quad Data Rate InfiniBand (QDR IB), the cluster delivered the best published result for this benchmark, with up to 95 percent better performance than double data rate (DDR) IB, a scalability efficiency of nearly 80 percent.
NAMD is a parallel molecular dynamics code designed for high-performance simulations of large biomolecular systems. It was developed by the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. NAMD is driven by major trends in computing and structural biology and received a 2002 Gordon Bell Award.
Molecular dynamics simulation is important to biological and materials science research. Molecular dynamics is used to determine the low energy conformations or shapes of a molecule. These conformations are presumed to be the biologically active conformations