相关论文: A Comparison of the Performance of the Molecular D…

GROMACS is a widely-used molecular dynamics software package with a focus on performance, portability, and maintainability across a broad range of platforms. Thanks to its early algorithmic redesign and flexible heterogeneous…

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…

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 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,…

One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…

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…

Computational platforms for high-performance scientific applications are becoming more heterogenous, including hardware accelerators such as multiple GPUs. Applications in a wide variety of scientific fields require an efficient and careful…

A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…

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…

The heterogeneous computing paradigm has led to the need for portable and efficient programming solutions that can leverage the capabilities of various hardware devices, such as NVIDIA, Intel, and AMD GPUs. This study evaluates the…

The high-performance computing (HPC) landscape is undergoing rapid transformation, with an increasing emphasis on energy-efficient and heterogeneous computing environments. This comprehensive study extends our previous research on SYCL's…

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…

Simulations based on particle methods, such as Smoothed Particle Hydrodynamics (SPH), are known to be computationally demanding. While such methods have for long been executed in parallel on multi-core CPUs, in recent years the increasing…

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…

The first generation of exascale systems will include a variety of machine architectures, featuring GPUs from multiple vendors. As a result, many developers are interested in adopting portable programming models to avoid maintaining…

Molecular dynamics simulations are essential tools in computational biophysics, but their performance depend heavily on hardware choices and configuration. In this work, we presents a comprehensive performance analysis of four NVIDIA GPU…

Portability is critical to ensuring high productivity in developing and maintaining scientific software as the diversity in on-node hardware architectures increases. While several programming models provide portability for diverse GPU…

Neural network potentials (NNPs) are rapidly changing the landscape of state-of-the-art molecular dynamics (MD) simulations. To make full use of this development, the community needs flexible, easy-to-use interfaces firmly integrated with…

Molecular dynamics simulations are one of the methods in scientific computing that benefit from GPU acceleration. For those devices, SYCL is a promising API for writing portable codes. In this paper, we present the case study of "HAL's MD…

High-performance computing (HPC) is a major driver accelerating scientific research and discovery, from quantum simulations to medical therapeutics. While the increasing availability of HPC resources is in many cases pivotal to successful…