Anton 3: twenty microseconds of molecular dynamics simulation before lunch

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...

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Main Authors: 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.
Format: Conference Proceeding
Language:English
Subjects:
Analytical models
Biological system modeling
Computational modeling
Computer systems organization
Computer systems organization > Architectures
Computer systems organization > Architectures > Distributed architectures
Computer systems organization > Architectures > Distributed architectures > Grid computing
Computer systems organization > Architectures > Parallel architectures
Computer systems organization > Architectures > Serial architectures
Computer systems organization > Architectures > Serial architectures > Superscalar architectures
Computing methodologies
Computing methodologies > Modeling and simulation
Computing methodologies > Modeling and simulation > Simulation types and techniques
Computing methodologies > Modeling and simulation > Simulation types and techniques > Massively parallel and high-performance simulations
Drugs
Heuristic algorithms
High performance computing
Proteins
Software and its engineering
Software and its engineering > Software organization and properties
Software and its engineering > Software organization and properties > Software system structures
Software and its engineering > Software organization and properties > Software system structures > Distributed systems organizing principles
Software and its engineering > Software organization and properties > Software system structures > Distributed systems organizing principles > Grid computing
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Summary: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.
ISSN:2167-4337
DOI:10.1145/3458817.3487397