Related papers: Molecular dynamics simulations with many-body pote…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
Commercial graphics processors (GPUs) have high compute capacity at very low cost, which makes them attractive for general purpose scientific computing. In this paper we show how graphics processors can be used for N-body simulations to…
Path integral Monte Carlo (PIMC) and path integral molecular dynamics (PIMD) provide the golden standard for the ab initio simulations of identical particles. In this work, we achieved significant GPU acceleration based on PIMD, which is…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Traditional graphics processing units (GPUs) suffer from the low memory capacity and demand for high memory bandwidth. To address these challenges, we propose Ohm-GPU, a new optical network based heterogeneous memory design for GPUs.…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
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…
This paper introduces the Sheffield Magnetohydrodynamics Algorithm Using GPUs (SMAUG+), an advanced numerical code for solving magnetohydrodynamic (MHD) problems, using multi-GPU systems. Multi-GPU systems facilitate the development of…
Particle-in-Cell (PIC) Monte Carlo (MC) simulations are central to plasma physics but face increasing challenges on heterogeneous HPC systems due to excessive data movement, synchronization overheads, and inefficient utilization of multiple…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
We present a MATLAB script which can use GPU acceleration to simulate a trapped ion interacting with a low-density cloud of atoms. This script, called atomiongpu.m, can massively parallelize MD simulations of trajectories of a trapped ion…
We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in [Fan et al., Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package…
Monte Carlo (MC) simulation is commonly considered to be the most accurate dose calculation method in radiotherapy. However, its efficiency still requires improvement for many routine clinical applications. In this paper, we present our…
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…
Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering,…
We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a…
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
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…
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…
This article presents an optimized algorithm and implementation for calculating resolution-of-the-identity Hartree-Fock (RI-HF) energies and analytic gradients using multiple Graphics Processing Units (GPUs). The algorithm is especially…