Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations

Toyoda, Shinjiro; Miyagawa, Hiroh; Kïtamura, Kazuo; Amisaki, Takashi; Hashimoto, Eiri; Ikeda, Hitoshi; Kusumi, Akihiro; Miyakawa, Nobuaki

doi:10.1002/(sici)1096-987x(19990130)20:2<185::aid-jcc1>3.0.co;2-l

Cited by 63 publications

(45 citation statements)

References 20 publications

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“…The velocity and position of individual particles can be calculated by motion integration techniques. Some of the worldwide computation systems that are adaptable to FPGA boards, such as GROMACS, 161 MD-GRAPE, 162 MDGRAPE-2, 163 NAMD 164 and MODEL, 165 have succeeded in processing the computationally complex LJ force and Coulombic force. In order to accelerate the force computation, lookup table storing the LJ potential as a function of r ij might be used instead of direct computation of LJ potential by putting interatomic distances into Eq.…”

Section: Recon¯gurable Computingmentioning

confidence: 99%

Molecular Dynamics Simulation of Iron — A Review

Chui

Liu

et al. 2015

SPIN

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Molecular dynamics (MD) is a technique of atomistic simulation which has facilitated scienti¯c discovery of interactions among particles since its advent in the late 1950s. Its merit lies in incorporating statistical mechanics to allow for examination of varying atomic con¯gurations at nite temperatures. Its contributions to materials science from modeling pure metal properties to designing nanowires is also remarkable. This review paper focuses on the progress of MD in understanding the behavior of iron -in pure metal form, in alloys, and in composite nanomaterials. It also discusses the interatomic potentials and the integration algorithms used for simulating iron in the literature. Furthermore, it reveals the current progress of MD in simulating iron by exhibiting some results in the literature. Finally, the review paper brie°y mentions the development of the hardware and software tools for such large-scale computations.

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Section: Recon¯gurable Computingmentioning

confidence: 99%

Molecular Dynamics Simulation of Iron — A Review

Chui

Liu

et al. 2015

SPIN

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“…A naive calculation of the interactions at all target particles takes O(N 2 ) arithmetic operations. Existing accelerators include GRAPE (GRAvity PipE) project [18], MD-GRAPE [19], [20], MD Engine [21], [22]. All these hardware systems are specialized ASIC based solutions for specific N-body applications.…”

Section: Scientific Application: N-body Problemsmentioning

confidence: 99%

An Automated Framework for Accelerating Numerical Algorithms on Reconfigurable Platforms Using Algorithmic/Architectural Optimization

Kim

Deng

Mangalagiri

et al. 2009

IEEE Trans. Comput.

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Abstract-This paper describes TANOR, an automated framework for designing hardware accelerators for numerical computation on reconfigurable platforms. Applications utilizing numerical algorithms on large-size data sets require high-throughput computation platforms. The focus is on N-body interaction problems which have a wide range of applications spanning from astrophysics to molecular dynamics. The TANOR design flow starts with a MATLAB description of a particular interaction function, its parameters, and certain architectural constraints specified through a graphical user interface. Subsequently, TANOR automatically generates a configuration bitstream for a target FPGA along with associated drivers and control software necessary to direct the application from a host PC. Architectural exploration is facilitated through support for fully custom fixed-point and floating point representations in addition to standard number representations such as single precision floating point. Moreover, TANOR enables joint exploration of algorithmic and architectural variations in realizing efficient hardware accelerators. TANOR's capabilities have been demonstrated for three different N-body interaction applications: the calculation of gravitational potential in astrophysics, the diffusion or convolution with Gaussian kernel common in image processing applications, and the force calculation with vector-valued kernel function in molecular dynamics simulation. Experimental results show that TANOR-generated hardware accelerators achieve lower resource utilization without compromising numerical accuracy, in comparison to other existing custom accelerators.

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“…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 [13], MDGRAPE [31], and MD Engine [32], 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 to extend individual simulations beyond microsecond time scales.…”

Section: Introductionmentioning

confidence: 99%

Anton, a special-purpose machine for molecular dynamics simulation

Shaw

Deneroff

Dror

et al. 2007

SIGARCH Comput. Archit. News

154

105

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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 time scales on the order of a millisecond-about three orders of magnitude beyond the duration of the longest current MD simulations.In this paper, we describe a massively parallel machine called Anton, which should be capable of executing millisecondscale 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.

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Development of MD Engine: High-speed accelerator with parallel processor design for molecular dynamics simulations

Cited by 63 publications

References 20 publications

Molecular Dynamics Simulation of Iron — A Review

Molecular Dynamics Simulation of Iron — A Review

An Automated Framework for Accelerating Numerical Algorithms on Reconfigurable Platforms Using Algorithmic/Architectural Optimization

Anton, a special-purpose machine for molecular dynamics simulation

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