A MapReduce Accelerator to Tackle Molecular Dynamics
Novel architectures are born out of necessity and for some applications, including molecular dynamics, there have been endless attempts to push parallel performance.
In this area, there are already numerous approaches to acceleration. At the highest end is the custom ASIC-driven Anton machine from D.E. Shaw, which is the fastest system, but certainly not the cheapest. On the more accessible accelerators side are Tesla GPUs for accelerating highly parallel parts of the workload—and increasingly, FPGAs are being considered for boosting the performance of major molecular dynamics applications, most notably GROMACS as well as general purpose, high-end CPUs (Knights Landing …
A MapReduce Accelerator to Tackle Molecular Dynamics was written by Nicole Hemsoth at The Next Platform.