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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. Achieving this speedup required a combination...
Exhaled breath contains more than 1000 constituents at trace level concentrations, with a wide variety of these compounds potentially serving as biomarkers for specific diseases, physiologic status, or therapeutic progress. Some of the compounds in exhaled breath (EB) are well studied, and their relationship with disease pathologies is well established. However, molecularly specific analysis of such...
An effective special-purpose supercomputer for molecular dynamics (MD) requires much more than high-performance acceleration of computational kernels: such accelerators must be balanced with general-purpose computation and communication resources. Achieving this balance was a significant challenge in the design of Anton, a parallel machine that will accelerate MD simulations by several orders of magnitude...
Anton is a massively parallel special-purpose supercomputer designed to accelerate molecular dynamics (MD) simulations by several orders of magnitude, making possible for the first time the atomic-level simulation of many biologically important phenomena that take place over microsecond to millisecond time scales. The majority of the computation required for MD simulations involves the calculation...
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