Related papers: Optimizing the Performance of Reactive Molecular D…
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…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
As fusion energy devices advance, plasma simulations are crucial for reactor design. Our work extends BIT1 hybrid parallelization by integrating MPI with OpenMP and OpenACC, focusing on asynchronous multi-GPU programming. Results show…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Modern HPC systems are increasingly relying on greater core counts and wider vector registers. Thus, applications need to be adapted to fully utilize these hardware capabilities. One class of applications that can benefit from this increase…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
The two main thrusts of computational science are more accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g.…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
Molecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Applications to process seismic data employ scalable parallel systems to produce timely results. To fully exploit emerging processor architectures, application will need to employ threaded parallelism within a node and message passing…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations…
Efficient simulation of complex plasma dynamics is crucial for advancing fusion energy research. Particle-in-Cell (PIC) Monte Carlo (MC) simulations provide insights into plasma behavior, including turbulence and confinement, which are…
Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…
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 materials science and computational chemistry. We present…