benchmarks

The system and the simulation conditions used in this benchmark are:

  • Protein: Ubiquitin
  • Number of atoms: 1231
  • 1 fs time step, 10000 steps
  • Berendsen thermostat. Temperature: 330 K
  • Cutoffs 10, 12 and 14 Angstroms
  • Force field: CHARMM Param 22 (almost, NAMD), OPLSAA (GROMACS).

single processor benchmarks

Program Time (s)
almost 96.38
GROMACS 3.3.2 97.84
NAMD 2.6 116.63

Note: almost and GROMACS where compiled locally with GCC 4.0.1. The NAMD executable was downloaded from the NAMD site.

Platform: Mac Pro 2 x 3.0 GHz Dual-Core Intel Xeon. 4 GB 667 MHz DDR2 FB-DIMM memory.

parallel benchmarks

Program Time (s) NP 1 Time (s) NP 2 Time (s) NP 3 Time (s) NP 4
almost
96.39
50.02
34.56
27.86
GROMACS 3.3.2
97.84
51.00
38.00
29.00
NAMD 2.6
118.63
75.04
58.91
72.21

Note: The parallel versions of almost and GROMACS where compiled with GCC 4.0.1 and MPICH2. The parallel version of NAMD 2.6 was downloaded from the NAMD site.

Platform: Mac Pro 2 x 3.0 GHz Dual-Core Intel Xeon. 4 GB 667 MHz DDR2 FB-DIMM memory. All processes where local.


Andrea Cavalli
Last modified: Wed Dec 5 18:13:00 CET 2007

Copyright © 1999-2009 Andrea Cavalli