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| Anton (computer) | |
|---|---|
| Name | Anton |
| Developer | D. E. Shaw Research |
| Released | 2008 (first-generation) |
| Type | Special-purpose supercomputer |
| Purpose | Molecular dynamics simulation |
| Cpu | Custom ASICs |
| Memory | On-chip and FPGA-linked DRAM |
| Os | Custom microkernel |
| Predecessor | General-purpose clusters |
| Successor | Anton 2 |
| Website | D. E. Shaw Research |
Anton (computer) is a family of special-purpose supercomputers developed by D. E. Shaw Research for high-throughput, long-timescale molecular dynamics simulations of proteins, nucleic acids, and biomolecular assemblies. Anton systems integrate custom application-specific integrated circuits with novel networking and software to accelerate classical force-field dynamics, enabling studies that complement experiments at institutions such as Harvard University, Stanford University, Massachusetts Institute of Technology, University of Cambridge, and Max Planck Society. The project intersects communities across computational chemistry, structural biology, biophysics, and pharmaceutical discovery involving groups like National Institutes of Health, Roche, Novartis, and GlaxoSmithKline.
Anton was conceived to address limitations encountered by researchers at Columbia University and Princeton University working with general-purpose clusters and massively parallel systems such as those at Oak Ridge National Laboratory and Lawrence Berkeley National Laboratory. Designed for molecular dynamics similar to methods developed by Martin Karplus, Arieh Warshel, and Michael Levitt, Anton emphasizes long continuous trajectories, rare-event sampling, and accurate treatment of long-range electrostatics relevant to studies of enzymes like HIV-1 protease and receptors such as G protein-coupled receptors. The machines supported collaborative programs with academic labs at University of California, San Francisco, Yale University, and University of Chicago as well as industrial research at Pfizer and Merck.
Anton’s hardware centers on custom ASIC chips developed by D. E. Shaw Research and fabricated with processes similar to those used by companies such as Intel, AMD, and NVIDIA. Each chip implements specialized force-evaluation pipelines and pair-list engines informed by algorithms from groups at University of Illinois Urbana–Champaign and Swiss Federal Institute of Technology in Zurich. The system’s interconnect topology draws on principles used in machines like Cray XT5 and research into low-latency networks from Lawrence Livermore National Laboratory. Memory subsystems incorporate DRAM and on-chip buffers analogous to designs by Micron Technology and Samsung Electronics. Cooling and rack design reflect practices used at facilities like Argonne National Laboratory and corporate data centers such as Google and Amazon Web Services.
Anton runs a custom software stack and microkernel tailored to tightly couple with its ASICs, drawing on algorithmic advances from molecular dynamics packages such as CHARMM, AMBER, GROMACS, and NAMD. Algorithms implemented include optimized integration schemes related to work by Berk Hess and Mark Spoel, long-range electrostatics strategies comparable to particle-mesh Ewald refinements from Tom Darden and Shankar Subramaniam, and multiple time-stepping inspired by methods by Linda Verlet and Harold T. Davis. Anton’s scheduler and load-balancing incorporate concepts from parallel computing research at Massachusetts Institute of Technology and University of Toronto. Software tools interface with structural data formats used by Protein Data Bank and visualization programs such as VMD and PyMOL.
Anton demonstrated orders-of-magnitude improvements in achievable simulation time scales compared with contemporaneous general-purpose clusters used by groups at Los Alamos National Laboratory and Sandia National Laboratories. Benchmarks reported trajectories of hundreds of microseconds to milliseconds for proteins like Hen Egg-White Lysozyme and kinases studied at University of Pennsylvania and University of Washington. Performance comparisons frequently referenced systems built with processors from IBM and accelerators from NVIDIA, and were discussed in venues including Supercomputing Conference and journals linked to American Chemical Society and Nature Publishing Group.
Development began within D. E. Shaw Research under leadership linked to entrepreneurs and researchers with ties to Columbia University and Princeton University. Early prototype work drew on collaborations with fabrication and design partners similar to those working with Cadence Design Systems and Synopsys. First-generation Anton installed at institutions such as Pittsburgh Supercomputing Center and academic centers led to second-generation Anton 2, which incorporated lessons from chip designers at ARM Holdings and interconnect engineers associated with Mellanox Technologies. Public presentations and papers emerged through conferences like Gordon Research Conferences and meetings of the Biophysical Society.
Anton enabled studies of protein folding, ligand-binding kinetics, conformational landscapes of enzymes like RNA polymerase and transporters such as ATP synthase, and investigations into viral proteins including those of Influenza A virus and HIV. Work on binding unbinding pathways informed efforts at pharmaceutical companies including AstraZeneca and Bristol-Myers Squibb. Findings facilitated by Anton were published alongside contributions from labs at University of California, Berkeley, University of Oxford, and Technical University of Munich, and influenced methods taught in courses at Imperial College London and ETH Zurich.
Critiques of Anton echoed themes raised by computational scientists at Princeton University and Caltech regarding specialization trade-offs: while enabling unprecedented timescales, Anton’s architecture is less flexible for non-classical simulations used in quantum chemistry approaches championed by researchers such as John Pople and Walter Kohn. Cost and access considerations paralleled debates about large instrumentation at European Organization for Nuclear Research and synchrotron facilities like SLAC National Accelerator Laboratory. Concerns also touched on reproducibility and comparability relative to established packages from groups at University of Groningen and Ecole Polytechnique Federale de Lausanne.
Category:Supercomputers Category:Molecular dynamics Category:Computer hardware