Algorithms for millisecond-scale simulation on Anton, a<br/><br/>specialized molecular Dynamics machine

Tuesday, May 19, 2009 - 3:15pm - 3:55pm
EE/CS 3-180
Ron Dror (D. E. Shaw Research)
Anton, a recently completed special-purpose machine for molecular
dynamics simulations, achieves a speedup of several orders of magnitude
over state-of-the-art general-purpose systems by mapping novel
algorithms to massively parallel application-specific hardware. This
talk will describe algorithms and numerical techniques used by Anton,
including some developed especially for Anton and others adapted to
exploit its architecture. These algorithms underlie Anton's ability to
avoid communication bottlenecks even at high levels of parallelism, to
effectively map computation onto fast, hardwired arithmetic pipelines,
and to produce accurate results efficiently and deterministically.