English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations

Gecht, M., Siggel, M., Linke, M., Hummer, G., & Köfinger, J. (2020). MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics, 153(14): 144105. doi:10.1063/5.0019045.

Item is

Basic

show hide
Genre: Journal Article

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Gecht, Michael1, Author              
Siggel, Marc1, Author              
Linke, Max1, Author              
Hummer, Gerhard1, 2, Author              
Köfinger, Jürgen1, Author              
Affiliations:
1Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068292              
2Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany, ou_persistent22              

Content

show
hide
Free keywords: -
 Abstract: Despite the impending flattening of Moore's law, the system size, complexity, and length of molecular dynamics (MD) simulations keep on increasing, thanks to effective code parallelization and optimization combined with algorithmic developments. Going forward, exascale computing poses new challenges to the efficient execution and management of MD simulations. The diversity and rapid developments of hardware architectures, software environments, and MD engines make it necessary that users can easily run benchmarks to optimally set up simulations, both with respect to time-to-solution and overall efficiency. To this end, we have developed the software MDBenchmark to streamline the setup, submission, and analysis of simulation benchmarks and scaling studies. The software design is open and as such not restricted to any specific MD engine or job queuing system. To illustrate the necessity and benefits of running benchmarks and the capabilities of MDBenchmark, we measure the performance of a diverse set of 23 MD simulation systems using GROMACS 2018. We compare the scaling of simulations with the number of nodes for central processing unit (CPU)-only and mixed CPU-graphics processing unit (GPU) nodes and study the performance that can be achieved when running multiple simulations on a single node. In all these cases, we optimize the numbers of message passing interface (MPI) ranks and open multi-processing (OpenMP) threads, which is crucial to maximizing performance. Our results demonstrate the importance of benchmarking for finding the optimal system and hardware specific simulation parameters. Running MD simulations with optimized settings leads to a significant performance increase that reduces the monetary, energetic, and environmental costs of MD simulations.

Details

show
hide
Language(s): eng - English
 Dates: 2020-06-222020-09-042020-10-092020-10
 Publication Status: Published in print
 Pages: 17
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1063/5.0019045
BibTex Citekey: gecht_mdbenchmark_2020
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: The Journal of Chemical Physics
  Other : J. Chem. Phys.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Woodbury, N.Y. : American Institute of Physics
Pages: - Volume / Issue: 153 (14) Sequence Number: 144105 Start / End Page: - Identifier: ISSN: 0021-9606
CoNE: https://pure.mpg.de/cone/journals/resource/954922836226