We analyse gather-scatter performance bottlenecks in molecular dynamics codes and the
challenges that they pose for obtaining benefits from SIMD execution. This analysis informs …

Annotating human poses in realistic scenes is very time consuming, yet necessary for
training human pose estimators. We propose to address this problem in an active learning …

Anticipating large-scale molecular dynamics simulations (MD) in nano-fluidics, we conduct
performance and scalability studies of an optimized version of the code ls1 mardyn. We …

The numerous virtual screening (VS) methods that are used today in drug discovery
processes differ mainly by the way they model the receptor and/or ligand and by the …

The hybrid/heterogeneous nature of future microprocessors and large high-performance
computing systems will result in a reliance on two major types of components …

The historical context with regard to the origin of the DARPA High Productivity Computing
Systems (HPCS) program is important for understanding why federal government agencies …

The increasing gap between plentiful computing elements and limited memory bandwidth
makes it increasingly difficult and sometimes even infeasible for HPC community to port …

GROMACS is one of the most popular Molecular Dynamic (MD) applications and is widely
used in the field of chemical and bimolecular system study. Similar to other MD applications …

This paper investigates the development of a molecular dynamics code that is highly
portable between architectures. Using OpenCL, we develop an implementation of Sandia's …

Currently, we are facing a situation where applications exhibit increasing computational
demands and where a large variety of parallel processor systems are available. In this paper …