194 citations · 532 across the 13 of their papers we have counts for
13 papers
The Tersoff many-body potential: Sustainable performance through vectorization
Markus Höhnerbach, Ahmed E. Ismail, Paolo Bientinesi
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materia…
LAMMPS' PPPM Long-Range Solver for the Second Generation Xeon Phi
William McDoniel, Markus Höhnerbach, Rodrigo Canales +2
Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the invest…
A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics
Paul Springer, Ahmed E. Ismail, Paolo Bientinesi
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we intr…
Accelerating scientific codes by performance and accuracy modeling
Diego Fabregat-Traver, Ahmed E. Ismail, Paolo Bientinesi
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly comple…
The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability
Markus Höhnerbach, Ahmed E. Ismail, Paolo Bientinesi
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around t…
A Note on Time Measurements in LAMMPS
Daniel Tameling, Paolo Bientinesi, Ahmed E. Ismail
We examine the issue of assessing the efficiency of components of a parallel program at the example of the MD package LAMMPS. In particular, we look at how LAMMPS deals with the is…