학술논문
Anton 3 : twenty microseconds of molecular dynamics simulation before lunch
Document Type
Conference
Author
Shaw, David E.; Adams, Peter J.; Azaria, Asaph; Bank, Joseph A.; Batson, Brannon; Bell, Alistair; Bergdorf, Michael; Bhatt, Jhanvi; Butts, J. Adam; Correia, Timothy; Dirks, Robert M.; Dror, Ron O.; Eastwood, Michael P.; Edwards, Bruce; Even, Amos; Feldmann, Peter; Fenn, Michael; Fenton, Christopher H.; Forte, Anthony; Gagliardo, Joseph; Gill, Gennette; Gorlatova, Maria; Greskamp, Brian; Grossman, J. P.; Gullingsrud, Justin; Harper, Anissa; Hasenplaugh, William; Heily, Mark; Heshmat, Benjamin Colin; Hunt, Jeremy; Ierardi, Douglas J.; Iserovich, Lev; Jackson, Bryan L.; Johnson, Nick P.; Kirk, Mollie M.; Klepeis, John L.; Kuskin, Jeffrey S.; Mackenzie, Kenneth M.; Mader, Roy J.; McGowen, Richard; McLaughlin, Adam; Moraes, Mark A.; Nasr, Mohamed H.; Nociolo, Lawrence J.; O'Donnell, Lief; Parker, Andrew; Peticolas, Jon L.; Pocina, Goran; Predescu, Cristian; Quan, Terry; Salmon, John K.; Schwink, Carl; Shim, Keun Sup; Siddique, Naseer; Spengler, Jochen; Szalay, Tamas; Tabladillo, Raymond; Tartler, Reinhard; Taube, Andrew G.; Theobald, Michael; Towles, Brian; Vick, William; Wang, Stanley C.; Wazlowski, Michael; Weingarten, Madeleine J.; Williams, John M.; Yuh, Kevin A.
Source
Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. :1-11
Subject
Language
English
Abstract
Anton 3 is the newest member in a family of supercomputers specially designed for atomic-level simulation of molecules relevant to biology (e.g., DNA, proteins, and drug molecules). Anton 3 achieves order-of-magnitude improvements in time-to-solution over its predecessor, Anton 2 (the current state of the art), and is over 100-fold faster than any other currently available supercomputer, thereby enabling broad new avenues of research on critical questions in biology and drug discovery. This speedup means that a 512-node Anton 3 simulates a million atoms at over 100 microseconds per day. Furthermore, Anton 3 attains this performance while consuming an order of magnitude less energy per simulated microsecond than any other machine. Like its predecessors, Anton 3 was designed from the ground up around a new custom chip to best exploit the capabilities offered by new technologies. We present here the main architectural and algorithmic developments that were necessary to achieve such significant advances.