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CCS Seminar
Friday - April 22, 2011
12:00 noon
Physics Research Building - Room 595
3 Cummington Street

Ron O. Dror - D.E. Shaw Research

"Overcoming Communication Latency Barriers to Enable Massively Parallel Biomolecular Dynamics Simulations on Anton"

Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This talk will describe the techniques used to reduce latency and mitigate its effects on performance in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art. Achieving this speedup required both specialized hardware mechanisms and a restructuring of the application software to reduce network latency, sender and receiver overhead, and synchronization costs. Anton delivers end-to-end inter-node latency significantly lower than any other large-scale parallel machine, and the total critical-path communication time for an Anton MD simulation is less than 3% that of the next-fastest MD platform. The resulting speedup allows Anton to capture functionally important biological events that often occur on timescales ranging from several microseconds to a millisecond, including the “folding” of proteins into their native three-dimensional shapes, the structural changes that underlie protein function, and the interactions between a protein and a drug molecule.
















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