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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)
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)
—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)
Beagle dogs and Fischer 344 rats were fed diets containing 0, 36 or 72 units Bacillus stearothermophilus alpha-amylase (Bsa)/g food or of Bacillus subtilis alpha-amylase (cBsa)/g food. The dogs (four/sex/group) received treated diets for 13 wk. For the rat studies, the parental (F0) generation (12 males and 24 females/group for the Bsa study, and 26(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 study compares the predictive power of a single measurement of CD8+CD38+, CD8+CD45RO+ or CD8+CD38+CD45RO+ subpopulations in predicting progression to AIDS in a cohort of HIV+ long-term surviving injecting drug users. The results showed that both the total CD8+ percentage, and the CD8+CD38+ and CD8+CD38+CD45RO+ subpopulations of cells all individually(More)
In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical variables to create a thermostat and a barostat, respectively. These variables generally evolve on timescales much longer than those of particle motion, but typical integrator implementations update the(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)