Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

TL;DR

This paper introduces a novel heterogeneous domain decomposition method for molecular simulations, improving scalability and speed by optimizing parallelization schemes for complex multiscale and inhomogeneous systems.

Contribution

The paper presents a new heterogeneous domain decomposition approach that combines spatial decomposition with a priori subdomain rearrangement, enhancing parallel efficiency in molecular simulations.

Findings

Theoretical models for force computation scaling laws are developed.

The new method outperforms static and dynamic load balancing schemes.

Validated on biomolecular and phase-separated fluid systems.

Abstract

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid.