Related papers: Enhanced molecular dynamics performance with a pro…
A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, together with extensions to more complex systems. New measurements include the…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
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…
This paper discusses the potential of graphics processing units (GPUs) in high-dimensional optimization problems. A single GPU card with hundreds of arithmetic cores can be inserted in a personal computer and dramatically accelerates many…
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 use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing…
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…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
Massive data sets have radically changed our understanding of how to design efficient algorithms; the streaming paradigm, whether it in terms of number of passes of an external memory algorithm, or the single pass and limited memory of a…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
We present a single-node, multi-GPU programmable graph processing library that allows programmers to easily extend single-GPU graph algorithms to achieve scalable performance on large graphs with billions of edges. Directly using the…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
Graphics processing units (GPUs) are recently being used to an increasing degree for general computational purposes. This development is motivated by their theoretical peak performance, which significantly exceeds that of broadly available…
The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…
Elegant is an accelerator physics and particle-beam dynamics code widely used for modeling and design of a variety of high-energy particle accelerators and accelerator-based systems. In this paper we discuss a recently developed version of…
Hard spheres are arguably one of the most fundamental model systems in soft matter physics, and hence a common topic of simulation studies. Event-driven simulation methods provide an efficient method for studying the phase behavior and…
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…