Benchmarks of large biomolecular systems on HPC platforms

Here we present benchmarking results of large biomolecular molecular dynamics (MD) simulations in explicit solvent. The test systems are five protein and protein-membrane systems ranging from 20,000 to 3,000,000 atoms. The MD codes we look at are AMBER (link opens in a new window), CHARMM (link opens in a new window), DL_POLY, Gromacs (link opens in a new window), LAMMPS (link opens in a new window) and NAMD (link opens in a new window). The HPC platforms are primarily the Cray XE6 and the BlueGene/P. Some results for a GPU system are also included in the second report.

Reports

  1. First report DL-TR-2009-002 (PDF - link opens in a new window) (PDF) from 2009 and the abstract (link opens in a new window).
  2. Second report (PDF - 199kB - link opens in a new window) (December 2010).
  3. Third report (PDF - 307kB - link opens in a new window) (March 2012).
    1. Addendum (PDF - 155kB - link opens in a new window) for AMBER 12 and NAMD 2.9 with raw data (July 2012).

Data

  • The raw data from all three reports. These are in plain ASCII format with comments inside the files. The archive file also contains a spreadsheet file with the data from the third report.
  • The complete joint benchmark suite (link opens in a new window) (about 1.1 GiB, xz compressed, md5sum 5cd4c92fb8e7c13ba2ee1089648bd46c) for AMBER, CHARMM, GROMACS, NAMD and LAMMPS. Note: Neither the setup nor the runtime parameters in this suite may be suitable for actual application in scientific projects. We only provide these for the purpose of benchmark studies and do not recommend them for general use. Best practice should be gleaned from the literature, specialist books and user manuals.

Contact

If you have any questions regarding the benchmarks, ideas for further improvements, contributions, etc. feel free to contact This email address is being protected from spambots. You need JavaScript enabled to view it.