Related papers: Performance Analysis of CP2K Code for Ab Initio Mo…
High-performance computing, together with a neural network model trained from data generated with first-principles methods, has greatly boosted applications of \textit{ab initio} molecular dynamics in terms of spatial and temporal scales on…
We present a scalable dissipative particle dynamics simulation code, fully implemented on the Graphics Processing Units (GPUs) using a hybrid CUDA/MPI programming model, which achieves 10-30 times speedup on a single GPU over 16 CPU cores…
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…
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…
No area of computing is hungrier for performance than High Performance Computing (HPC), the demands of which continue to be a major driver for processor performance and adoption of accelerators, and also advances in memory, storage, and…
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling…
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…
iPIC3D is a widely used massively parallel Particle-in-Cell code for the simulation of space plasmas. However, its current implementation does not support execution on multiple GPUs. In this paper, we describe the porting of iPIC3D particle…
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 is focused on improving multi-GPU performance of a research CFD code on structured grids. MPI and OpenACC directives are used to scale the code up to 16 GPUs. This paper shows that using 16 P100 GPUs and 16 V100 GPUs can be…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
Performance optimization can be a daunting task especially as the hardware architecture becomes more and more complex. This paper takes a kernel from the Materials Science code BerkeleyGW, and demonstrates a few performance analysis and…
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…
Cycle-level simulators such as gem5 are widely used in microarchitecture design, but they are prohibitively slow for large-scale design space explorations. We present Concorde, a new methodology for learning fast and accurate performance…
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 non-orthogonal local submatrix method applied to electronic-structure based molecular dynamics simulations is shown to exceed 1.1 EFLOP/s in FP16/FP32 mixed floating-point arithmetic when using 4,400 NVIDIA A100 GPUs of the Perlmutter…
For computational fluid dynamics (CFD) applications with a large number of grid points/cells, parallel computing is a common efficient strategy to reduce the computational time. How to achieve the best performance in the modern…
VPIC is a general purpose Particle-in-Cell simulation code for modeling plasma phenomena such as magnetic reconnection, fusion, solar weather, and laser-plasma interaction in three dimensions using large numbers of particles. VPIC's…
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…