Cyclic Data Streaming on GPUs for Short Range Stencils Applied to Molecular Dynamics

TL;DR

This paper introduces a GPU-based cyclic data streaming framework for short-range stencils in molecular dynamics, achieving scalable performance through high-bandwidth communication and parallel-in-time processing.

Contribution

The paper presents a novel GPU framework enabling linear scaling for explicit algorithms using ring-based data propagation, simplifying parallelization for scientific computing applications.

Findings

Framework achieves linear scaling limited only by dataset size and GPU count

Outperforms LAMMPS in strong scaling scenarios on single node

Demonstrates effective parallel-in-time parallelization for molecular dynamics

Abstract

In the quest for highest performance in scientific computing, we present a novel framework that relies on high-bandwidth communication between GPUs in a compute cluster. The framework offers linear scaling of performance for explicit algorithms that is only limited by the size of the dataset and the number of GPUs. Slices of the dataset propagate in a ring of processes (GPUs) from one GPU, where they are processed, to the next, which results in a parallel-in-time parallelization. The user of the framework has to write GPU kernels that implement the algorithm and provide slices of the dataset. Knowledge about the underlying parallelization strategy is not required because the communication between processes is carried out by the framework. As a case study, molecular dynamics simulation based on the Lennard-Jones potential is implemented to measure the performance for a homogeneous fluid. Single node performance and strong scaling behavior of this framework is compared to LAMMPS, which is outperformed in the strong scaling case.