학술논문
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer
Document Type
Conference
Author
Shaw, David E.; Grossman, J.P.; Bank, Joseph A.; Batson, Brannon; Butts, J. Adam; Chao, Jack C.; Deneroff, Martin M.; Dror, Ron O.; Even, Amos; Fenton, Christopher H.; Forte, Anthony; Gagliardo, Joseph; Gill, Gennette; Greskamp, Brian; Ho, C. Richard; Ierardi, Douglas J.; Iserovich, Lev; Kuskin, Jeffrey S.; Larson, Richard H.; Layman, Timothy; Lee, Li-Siang; Lerer, Adam K.; Li, Chester; Killebrew, Daniel; Mackenzie, Kenneth M.; Mok, Shark Yeuk-Hai; Moraes, Mark A.; Mueller, Rolf; Nociolo, Lawrence J.; Peticolas, Jon L.; Quan, Terry; Ramot, Daniel; Salmon, John K.; Scarpazza, Daniele P.; Schafer, U. Ben; Siddique, Naseer; Snyder, Christopher W.; Spengler, Jochen; Tang, Ping Tak Peter; Theobald, Michael; Toma, Horia; Towles, Brian; Vitale, Benjamin; Wang, Stanley C.; Young, Cliff
Source
SC14: International Conference for High Performance Computing, Networking, Storage and Analysis High Performance Computing, Networking, Storage and Analysis, SC14: International Conference for. :41-53 Nov, 2014
Subject
Language
ISSN
2167-4329
2167-4337
2167-4337
Abstract
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations. A 512-node Anton 2 machine, currently in operation, is up to ten times faster than Anton 1 with the same number of nodes, greatly expanding the reach of all-atom bio molecular simulations. Anton 2 is the first platform to achieve simulation rates of multiple microseconds of physical time per day for systems with millions of atoms. Demonstrating strong scaling, the machine simulates a standard 23,558-atom benchmark system at a rate of 85 µs/day -- 180 times faster than any commodity hardware platform or general-purpose supercomputer.