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Podcast: ECP EXAALT Program Extends the Reach of Molecular Dynamics

Computationally, EXAALT’s goal is to develop a comprehensive molecular dynamics capability for exascale. “The user should be able to say, ‘I’m interested in this kind of system size, timescale, and accuracy,’ and directly access the regime without being constrained by the usual scaling paths of current codes,” said Danny Perez of Los Alamos National Laboratory (LANL) and the EXAALT team.

BioScience gets a Boost Through Order-of-Magnitude Computing Gains

Intel is working with leaders in the field to eliminate today’s data processing bottlenecks. In this guest post from Intel, the company explores how BioScience is getting a leg up from order-of-magnitude computing progress. “Intel’s framework is designed to make HPC simpler, more affordable, and more powerful.”

Amber Molecular Dynamics Optimization on Intel Xeon Phi

“The Amber Molecular Dynamics software is a well known and understood application for the structural dynamics of large biological molecules. With modern computer systems, a speedup in the computations can lead to studying events that occur on longer timescales, as well as statistical convergences. By incorporating the Intel Xeon Phi coprocessor into the workflow on a compute server, additional speedups can be obtained.”

Gather Scatter Operations

Gather and scatter operations are used in many domains. However, to use these types of functions on an SIMD architecture creates some programming challenges.

Video: GPU-Accelerated Analysis of Large Biomolecular Complexes

“This presentation will highlight the use of GPU ray tracing for visualizing the process of photosynthesis, and GPU accelerated analysis of results of hybrid structure determination methods that combine data from cryo-electron microscopy and X-ray crystallography atom molecular dynamics with all- simulations.”