Making PLUMED fly: a tutorial on optimizing performance

TL;DR

This paper provides a tutorial on optimizing the performance of PLUMED, a molecular dynamics analysis tool, by demonstrating benchmarking techniques and algorithmic tricks to improve computational efficiency for demanding tasks.

Contribution

It introduces a new performance measurement tool and offers detailed benchmarks and optimization strategies for enhancing PLUMED's computational efficiency.

Findings

Vector-based commands improve calculation speed for large data sets.

Benchmarking reveals key optimization points in PLUMED.

Algorithmic tricks can significantly reduce computational costs.

Abstract

PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED calculations is typically negligible compared to the molecular dynamics code's force evaluation, the software is increasingly being employed for more computationally demanding tasks where performance optimization becomes critical. In this tutorial, we describe a recently implemented tool that can be used to reliably measure code performance. We then use this tool to generate detailed performance benchmarks that show how calculations of large-numbers of distances, angles or torsions can be optimized by using vector-based commands rather than individual scalar operations. We then present benchmarks that illustrate how to optimize calculations of atomic order parameters and secondary structure variables. Throughout the tutorial and in our implementations we endeavor to explain the algorithmic tricks that are being used to optimize the calculations so others can make use of these prescriptions both when they are using PLUMED and when they are writing their own codes.