Anton (computer)

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.[1]

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).[2] 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.[3]

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.[4]

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.[5] 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.[6] The multiple petaFLOP,[7] 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.[8]

The Anton supercomputer is named after Anton van Leeuwenhoek,[9] 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.

See also

References

  1. ↑ David E. Shaw, Martin M. Deneroff, Ron O. Dror, Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J.P. Grossman, C. Richard Ho, Douglas J. Ierardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine McLeavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, and Stanley C. Wang (July 2008). "Anton, A Special-Purpose Machine for Molecular Dynamics Simulation". Communications of the ACM (ACM) 51 (7): 91–97. doi:10.1145/1364782.1364802. ISBN 978-1-59593-706-3. (Related paper published in Proceedings of the 34th Annual International Symposium on Computer Architecture (ISCA '07), San Diego, California, June 9–13, 2007).
  2. ↑ Richard H. Larson, John K. Salmon, Ron O. Dror, Martin M. Deneroff, Cliff Young, J.P. Grossman, Yibing Shan, John L. Klepeis, and David E. Shaw (2009). "High-Throughput Pairwise Point Interactions 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.
  3. ↑ 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.
  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.
  5. ↑ "National Resource for Biomedical Supercomputing". Retrieved May 14, 2010.
  6. ↑ 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 (2009). "Millisecond-Scale Molecular Dynamics Simulations on Anton" (Portland, Oregon). Proceedings of the ACM/IEEE Conference on Supercomputing (SC09) (New York, NY, USA: ACM): 1–11. doi:10.1145/1654059.1654099. ISBN 978-1-60558-744-8.
  7. ↑ Pande Group (updated automatically). "Client Statistics by OS". Stanford University. Retrieved February 3, 2012. Check date values in: |date= (help)
  8. ↑ Vijay Pande (January 17, 2010). "Folding@home: Paper #72: Major new result for Folding@home: Simulation of the millisecond timescale". Retrieved September 22, 2011.
  9. ↑ John Markoff (July 8, 2008). "Herculean Device for Molecular Mysteries". The New York Times, July 8, 2008 (NY Times). Retrieved April 25, 2010.

External links

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