Strong scaling of general-purpose molecular dynamics simulations on GPUs
We describe a highly optimized implementation of MPI domain decomposition in a GPU-
enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer …
enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer …
Exploring simd for molecular dynamics, using intel® xeon® processors and intel® xeon phi coprocessors
SJ Pennycook, CJ Hughes… - 2013 IEEE 27th …, 2013 - ieeexplore.ieee.org
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 …
challenges that they pose for obtaining benefits from SIMD execution. This analysis informs …
A complete and efficient CUDA-sharing solution for HPC clusters
In this paper we detail the key features, architectural design, and implementation of rCUDA,
an advanced framework to enable remote and transparent GPGPU acceleration in HPC …
an advanced framework to enable remote and transparent GPGPU acceleration in HPC …
Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology
ML Jones, E Jankowski - Molecular Simulation, 2017 - Taylor & Francis
Rationally designing roll-to-roll printed organic photovoltaics (OPVs) requires a fundamental
understanding of active layer morphologies optimised for charge separation and transport …
understanding of active layer morphologies optimised for charge separation and transport …
Implementing molecular dynamics simulation on sunway taihulight system
Molecular dynamics (MD) simulation is a common tool to study the physical movements of
atoms and molecules in many research fields. However, it is an extremely time-consuming …
atoms and molecules in many research fields. However, it is an extremely time-consuming …
Implementing molecular dynamics simulation on the Sunway TaihuLight system with heterogeneous many‐core processors
In various research of atom and molecule physical movements, molecular dynamics (MD)
simulation is a common tool to simulate and investigate the real molecular motion. However …
simulation is a common tool to simulate and investigate the real molecular motion. However …
Routine million-particle simulations of epoxy curing with dissipative particle dynamics
Mesoscale simulation techniques have helped to bridge the length scales and time scales
needed to predict the microstructures of cured epoxies, but gaps in computational cost and …
needed to predict the microstructures of cured epoxies, but gaps in computational cost and …
Structure and dynamics of B2O3 melts and glasses: from ab initio to classical molecular dynamics simulations
Abstract Boron oxide (B 2 O 3) is investigated by a combination of ab initio (DFT-based)
molecular dynamics (MD) simulations and classical MD simulations. From the trajectories of …
molecular dynamics (MD) simulations and classical MD simulations. From the trajectories of …
Developing performance-portable molecular dynamics kernels in OpenCL
SJ Pennycook, SA Jarvis - 2012 SC Companion: High …, 2012 - ieeexplore.ieee.org
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 …
portable between architectures. Using OpenCL, we develop an implementation of Sandia's …
[HTML][HTML] Perspective on coarse-graining, cognitive load, and materials simulation
E Jankowski, N Ellyson, JW Fothergill… - Computational Materials …, 2020 - Elsevier
The predictive capabilities of computational materials science today derive from overlapping
advances in simulation tools, modeling techniques, and best practices. We outline this …
advances in simulation tools, modeling techniques, and best practices. We outline this …