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Anton is a massively parallel supercomputer designed and built by D. E. Shaw Research in New York. It is a special-purpose system for molecular dynamics (MD) simulations of proteins and other biological macromolecules. An Anton machine consists of a substantial number of application-specific integrated circuits (ASICs), interconnected by a specialized high-speed, three-dimensional torus network.
Unlike earlier special-purpose systems for MD simulations, such as MDGRAPE-3 developed by RIKEN in Japan, Anton runs its computations entirely on specialized ASICs, instead of dividing the computation between specialized ASICs and general-purpose host processors.
Each Anton ASIC contains two computational subsystems. Most of the calculation of electrostatic and van der Waals forces is performed by the high-throughput interaction subsystem (HTIS). This subsystem contains 32 deeply pipelined modules running at 800 MHz arranged much like a systolic array. The remaining calculations, including the bond forces and the fast Fourier transforms (used for long-range electrostatics), are performed by the flexible subsystem. This subsystem contains four general-purpose Tensilica cores (each with cache and scratchpad memory) and eight specialized but programmable SIMD cores called geometry cores. The flexible subsystem runs at 400 MHz.
Anton's network is a 3D torus and thus each chip has 6 inter-node links with a total in+out bandwidth of 607.2 Gbit/s. An inter-node link is composed of two equal one-way links (one traveling in each direction), with each one-way link having 50.6 Gbit/s of bandwidth. Each one-way link is composed of 11 lanes, where a lane is a differential pair of wires signaling at 4.6 Gbit/s. The per-hop latency in Anton's network is 50 ns. Each ASIC is also attached to its own DRAM bank, enabling large simulations.
The performance of a 512-node Anton machine is over 17,000 nanoseconds of simulated time per day for a protein-water system consisting of 23,558 atoms. In comparison, MD codes running on general-purpose parallel computers with hundreds or thousands of processor cores achieve simulation rates of up to a few hundred nanoseconds per day on the same chemical system. The first 512-node Anton machine became operational in October 2008. The multiple petaFLOP-per-second, distributed-computing project Folding@home has achieved similar aggregate ensemble simulation timescales, compared to those of Anton, specifically achieving the 1.5-millisecond range in January 2010.
The Anton supercomputer is named after Anton van Leeuwenhoek, who is often referred to as "the father of microscopy" because he built high-precision optical instruments and used them to visualize a wide variety of organisms and cell types for the first time.
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- Jeffrey S. Kuskin, Cliff Young, J.P. Grossman, Brannon Batson, Martin M. Deneroff, Ron O. Dror, and David E. Shaw (2009). "Incorporating Flexibility in Anton, a Specialized Machine for Molecular Dynamics Simulation" (PDF). Proceedings of the 14th Annual International Symposium on High-Performance Computer Architecture (HPCA '08), Salt Lake City, Utah, February 16–20, 2008 (IEEE). ISBN 978-1-4244-2070-4.
- Cliff Young, Joseph A Bank. Ron O. Dror, J. P. Grossman, John K. Salmon, and Shaw, David E. (2009). "A 32x32x32, spatially distributed 3D FFT in four microseconds on Anton" (PORTLAND, OREGON). SC '09: Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis (New York, NY, USA: ACM): 1–11. doi:10.1145/1654059.1654083. ISBN 978-1-60558-744-8.
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