We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables multi-GPU simulation on hybrid heterogeneous clusters, using MPI for inter-node communication, CUDA kernels on the GPU for all methods working with particle data, a...

Molecular dynamics simulation should be combined with modern supercomputer technologies to obtain meaningful results in reasonable time. Widely used simulation software in MD is LAMMPS. It produces a dump with computational results of simulation, and such a large amount of data should be post-processed. However, LAMMPS does not provide ready-to-use utilities that would do it. In this paper we p...

We present a set of Python routines to perform basic tests of classical atomistic potentials and their example applications. These routines are implemented using universal Atomic Simulation Environment (ASE) and LAMMPS molecular dynamics code. ASE is utilized to create atomic configurations, to write input scripts for LAMMPS, and to read results from output files. Evaluated properties are forma...

This work details the opportunities and challenges of porting a petascale-capable, MPI-based application LAMMPS to OpenSHMEM. We investigate the major programming challenges stemming from the differences in communication semantics, address space organization, and synchronization operations between the two programming models. This work provides several approaches to solve those challenges for re...

During the last decade coarse-grained nucleotide models have emerged that allow us to DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of singleand double-stranded DNA. oxDNA was previously only available as standalone software, but has now been imp...

Molecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be simulated accurately using a longrange solver, such as PPPM. We extend the popular LAMMPS molecular dynamics code with an implementation of PPPM particularly...

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian method based on a meshless discretization of partial differential equations. I will present SPH discretization of the stochastic and deterministic Navier-Stokes and Advection-Diffusion-Reaction equations, implementation of various boundary conditions, and time integration of the SPH equations, and discuss applications of the SPH method for m...

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 issue and explain why the approach adopted might lead to inaccurate conclusions. The misleading nature of this approach is subsequently verified experimentally with a case study. Afterwards, we demonstrate how one shoul...