‘Millisecond-Scale Molecular Dynamics Simulations on Anton’ Wins SC23’s Test of Time Award

August 8, 2023

Aug. 8, 2023 — The Test of Time Award offers a way to look back at previous SC Conferences and identify a technical paper that did more than just stand out in the moment. It has to be an inspiration to high performance computing, shaping the future of computing theory or practice.

This year’s SC23 Test of Time Award recognizes a paper presented during SC09, held in Portland. Ore., “Millisecond-Scale Molecular Dynamics Simulations on Anton.”

Reflecting the effort involved in building such a complete computing system, the paper included 22 authors: David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Kenneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brannon Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. Ierardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kresten Lindorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles.

The paper described Anton, a special-purpose computing system designed and operated by D.E. Shaw Research in New York City to accelerate molecular dynamics (MD) simulations. The machine architecture and algorithms for MD were co-designed to achieve high performance on simulations where parallelism was limited by the number of molecules and high speed was required to simulate behavior over a sufficient interval.

With 512 processors, Anton demonstrated the power of hardware-software co-design to advance complex protein research. Its processors projected the movements of 50,000 atoms over time, anticipating the actions of complex molecular relationships in real time. In short, back in 2009, Anton could do in a day what it then took the world’s top supercomputers months to achieve.

In 2010, the Pittsburgh Supercomputing Center (PSC) received a grant from the National Institutes of Health and hosted an Anton machine. A long list of university and pharmaceutical researchers were excited to have access to a resource that enabled access to atomic-level details that helped inform their work in therapeutic drug design. Now, PSC is running Anton 2 for important MD simulations.

“Since 2010, PSC has provided the national research community with unique access to the remarkable Anton supercomputers,” said PSC’s Scientific Director Dr. Philip Blood. “The game-changing performance of Anton systems—orders of magnitude faster than any other resource for biomolecular simulation—continues to enable breakthrough scientific discoveries that would not have been possible through any other means.”

Beyond its influence on MD research, the Anton system exemplified what has become increasingly common: end-to-end co-design of architecture and hardware, system software, and algorithms to maximize delivered performance. With the end of Moore’s law and increasing limits to commodity hardware performance, Anton was a pathfinder for the continued evolution of high-performance computing.

Today, D.E. Shaw Research continues to develop Anton systems primarily used for internal research. However, there is an Anton system available for non-commercial research use by U.S. universities and other not-for-profit institutions.

“We feel honored to receive this award,” said Dr. David E. Shaw, chief scientist at D.E. Shaw Research and first author of the original paper released during SC09. “We regard this as an acknowledgment not only of our own work, but of the scientific contributions made by 239 research groups using Anton—time we’ve made available without cost to universities and other nonprofit institutions.”

Read More:
Shaw DE, RO Dror, JK Salmon, et al. 2009. “Millisecond-scale molecular dynamics simulations on Anton,” In Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis (SC09), Portland, OR, USA, pp. 1-11, doi: 10.1145/1654059.1654126.


Source: Bruce Loftis, SC23

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