Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

• Published in: Journal of computational chemistry Vol. 36; no. 26; pp. 1990 - 2008
• Main Authors: Kutzner, Carsten, Páll, Szilárd, Fechner, Martin, Esztermann, Ansgar, de Groot, Bert L., Grubmüller, Helmut
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 05.10.2015; Wiley Subscription Services, Inc; John Wiley and Sons Inc
• Subjects: Analytical chemistry; benchmark; Benchmarking; Benchmarks; Central processing units; Computer Simulation; CPUs; energy efficiency; GPU; hybrid parallelization; Molecular chemistry; molecular dynamics; Molecular Dynamics Simulation; parallel computing; Simulation; Software; Software and Updates; MD; energy efficiency; hybrid parallelization; molecular dynamics; GPU; parallel computing; benchmark
• ISSN: 0192-8651; 1096-987X; 1096-987X
• DOI: 10.1002/jcc.24030

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well‐exploited with a combination of single instruction multiple data, multithreading, and message passing interface (MPI)‐based single program multiple data/multiple program multiple data parallelism while graphics processing units (GPUs) can be used as accelerators to compute interactions off‐loaded from the CPU. Here, we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance‐to‐price ratio, energy efficiency, and several other criteria. Although hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer‐class GPUs this improvement equally reflects in the performance‐to‐price ratio. Although memory issues in consumer‐class GPUs could pass unnoticed as these cards do not support error checking and correction memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost‐efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well‐balanced ratio of CPU and consumer‐class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Molecular dynamics (MD) simulation is a crucial tool for the study of (bio)molecules. MD simulations typically run for weeks or months even on modern computer clusters. Choosing the optimal hardware for carrying out these simulations can increase the trajectory output twofold or threefold. With GROMACS, the maximum amount of MD trajectory for a fixed budget is produced using nodes with a well‐balanced ratio of CPU and consumer‐class GPU resources.