by 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
The ability to perform long, accurate molecular dynamics (MD) simulations involving proteins and other biological macromolecules could in principle provide answers to some of the most important currently outstanding questions in the fields of biology, chemistry, and medicine. A wide range of biologically interesting phenomena, however, occur over timescales on the order of a millisecond—several orders of magnitude beyond the duration of the longest current MD simulations.
We describe a massively parallel machine called Anton, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems. The machine, which is scheduled for completion by the end of 2008, is based on 512 identical MD-specific ASICs that interact in a tightly coupled manner using a specialized high-speed communication network. Anton has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation. The remainder of the simulation algorithm is executed by a programmable portion of each chip that achieves a substantial degree of parallelism while preserving the flexibility necessary to accommodate anticipated advances in physical models and simulation methods.
Molecular dynamics (MD) simulations can be used to model the motions of molecular systems, including proteins, cell membranes, and DNA, at an atomic level of detail. A sufficiently long and accurate MD simulation could allow scientists and drug designers to visualize for the first time many critically important biochemical phenomena that cannot currently be observed in laboratory experiments, including the “folding” of proteins into their native three-dimensional structures, the structural changes that underlie protein function, and the interactions between two proteins or between a protein and a candidate drug molecule. Such simulations could answer some of the most important open questions in the fields of biology and chemistry, and have the potential to make substantial contributions to the process of drug development.
Many of the most important biological processes occur over timescales on the order of a millisecond. MD simulations on this timescale, however, lie several orders of magnitude beyond the reach of current technology; only a few MD
runs have thus far reached even a microsecond of simulated time, and the vast majority have been limited to the nanosecond timescale. Millisecond-scale simulations of a biomolecular system containing tens of thousands of atoms will in practice require that the forces exerted by all atoms on all other atoms be calculated in just a few microseconds—a process that must be repeated on the order of 1012 times. These requirements far exceed the current capabilities of even the most powerful commodity clusters or general-purpose scientific supercomputers.
This paper describes a specialized, massively parallel machine, named Anton, that is designed to accelerate MD simulations by several orders of magnitude, bringing millisecond-scale simulations within reach for molecular systems involving tens of thousands of atoms. The machine, which is scheduled for completion by the end of 2008, will comprise 512 processing nodes in its initial configuration, each containing a specialized MD computation engine implemented as a single ASIC. The molecular system to be simulated is decomposed spatially among these processing nodes, which are connected through a specialized high-performance network to form a three-dimensional torus. Anton’s expected performance advantage stems from a combination of MD-specific hardware that achieves a very high level of arithmetic density and novel parallel algorithms that enhance scalability by reducing both intra- and inter-chip communication. Figure 1 is a photograph of one of the first Anton ASICs.
In designing Anton and its associated software, we have attempted to attack a somewhat different problem than the ones addressed by several other projects that have deployed significant computational resources for MD simulations. The Folding@Home project, 16 for example, has obtained a number of significant and interesting scientific results by using as many as 250,000 PCs (made available over the Internet by volunteers) to simulate a very large number of separate molecular trajectories, each of which is limited to the timescale accessible on a single PC. While a great deal can be learned from a large number of independent MD trajectories, many other important problems require the examination of a single, very long trajectory—the principal task for which Anton is designed. Other projects, such as FASTRUN, 6 MDGRAPE, 22 and MD Engine, 23 have produced special-purpose hardware to accelerate the most computationally expensive elements of an MD simulation. Such hardware reduces the cost of MD simulations, particularly for large molecular systems, but Amdahl’s law and communication bottlenecks prevent the efficient use of enough such chips in parallel
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