Kenneth M. Mackenzie

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Anton is a recently completed special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine's specialized hardware dramatically increases the speed of MD calculations, making possible for the first time the simulation of biological molecules at an atomic level of detail for periods on the order of a(More)
—Emerging application domains such as interactive vision, animation, and multimedia collaboration display dynamic scalable parallelism and high-computational requirements, making them good candidates for executing on parallel architectures such as SMPs and clusters of SMPs. Stampede is a programming system that has many of the needed functionalities such as(More)
Anton 2 is a second-generation special-purpose supercomputer for molecular dynamics simulations that achieves significant gains in performance, programmability, and capacity compared to its predecessor, Anton 1. The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of(More)
A software cache implements instruction and data caching entirely in software. Dynamic binary rewriting offers a means to specialize the software cache miss checks at cache miss time. We describe a software cache system implemented using dynamic binary rewriting and observe that the combination is particularly appropriate for the scenario of a simple(More)
This paper explores the energy and delay issues that occur when some or all of the local storage is moved out of the embedded device , and into a remote network server. We demonstrate using the network to access remote storage in lieu of local DRAM results in significant power savings. Mobile applications continually demand additional memory, with(More)
Strong scaling of scientific applications on parallel architectures is increasingly limited by communication latency. This paper describes the techniques used to mitigate latency in Anton, a massively parallel special-purpose machine that accelerates molecular dynamics (MD) simulations by orders of magnitude compared with the previous state of the art.(More)
—Special-purpose computing hardware can provide significantly better performance and power efficiency for certain applications than general-purpose processors. Even within a single application area, however, a special-purpose machine can be far more valuable if it is capable of efficiently supporting a number of different computational methods that, taken(More)
Anton, a special-purpose parallel machine currently under construction, is the result of a significant hardware-software codesign effort that relied heavily on an architectural simulator. One of this simulator's many important roles is to support the development of <i>embedded software</i> (software that runs on Anton's ASICs), which is challenging for(More)