Molecular dynamics simulation is a common method to help humans understand the microscopic world. The traditional general-purpose high-performance computing platforms are hindered by low computational and power efficiency, constraining practical application of large-scale long-time many-body molecular simulations. In order address these problems, novel accelerator for Tersoff potential designed...

Characterization of the computation, communication, memory, and I/O demands of current scientific applications is crucial for identifying which technologies will enable petascale scientific computing. In this paper, we present the Sequoia Toolkit for characterizing HPC applications. The Sequoia Toolkit consists of the Sequoia trace capture library and the Sequoia Event Analysis Library, or SEAL...

We present an assessment of the finitetemperature dynamical stability of discrete dislocations in graphene. In order to ascertain stability, we insert discrete dislocation quadrupole configurations into molecular dynamics calculations as initial conditions. In calculations we use Sandia National Laboratories Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and the Adaptive Int...

We extend the LAMMPS molecular dynamics program with a new, vectorized implementation of the Tersoff potential [7]. Given the well-established and well-studied mechanisms for parallelism in molecular dynamics programs [1], our efforts focus on vectorization as a further step to fully utilize available hardware. This contribution describes how our implementation achieves sustainable performance ...