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

GROMACS is a de-facto standard for classical Molecular Dynamics (MD). The rise of AI-driven interatomic potentials that pursue near-quantum accuracy at MD throughput now poses a significant challenge: embedding neural-network inference into…

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…

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…

High-performance computing (HPC) applications are increasingly executed in heterogeneous environments, introducing new challenges for programming and software portability. SYCL has emerged as a leading model designed to simplify…

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.…

Structured Cartesian grids are a fundamental component in numerical simulations. Although these grids facilitate straightforward discretization schemes, their na\"{i}ve use in sparse domains leads to excessive memory overhead and…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

In the past decade, high performance compute capabilities exhibited by heterogeneous GPGPU platforms have led to the popularity of data parallel programming languages such as CUDA and OpenCL. Such languages, however, involve a steep…

GROMACS is one of the most widely used HPC software packages using the Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS parallel performance using different configurations, HPC systems, and FFT libraries…

Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…

We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate…

In recent history, GPUs became a key driver of compute performance in HPC. With the installation of the Frontier supercomputer, they became the enablers of the Exascale era; further largest-scale installations are in progress (Aurora, El…

Scientific computing in the exascale era demands increased computational power to solve complex problems across various domains. With the rise of heterogeneous computing architectures the need for vendor-agnostic, performance portability…

We assess costs and efficiency of state-of-the-art high performance cloud computing compared to a traditional on-premises compute cluster. Our use case are atomistic simulations carried out with the GROMACS molecular dynamics (MD) toolkit…

In this paper, we evaluate the portability of the SYCL programming model on some of the latest CPUs and GPUs from a wide range of vendors, utilizing the two main compilers: DPC++ and hipSYCL/OpenSYCL. Both compilers currently support GPUs…

Accelerated computing is widely used in high-performance computing. Therefore, it is crucial to experiment and discover how to better utilize GPUGPUs latest generations on relevant applications. In this paper, we present results and share…

Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…

Bioinformatics and Computational Biology are two fields that have been exploiting GPUs for more than two decades, being CUDA the most used programming language for them. However, as CUDA is an NVIDIA proprietary language, it implies a…

Over recent years heterogeneous systems have become more prevalent across HPC systems, with over 100 supercomputers in the TOP500 incorporating GPUs or other accelerators. These hardware platforms have different performance characteristics…

We present magneto-hydrodynamic simulation results for heterogeneous systems. Heterogeneous architectures combine high floating point performance many-core units hosted in conventional server nodes. Examples include Graphics Processing…