Benchmarking hierarchical network architecture with CHARMM
Data
First number is timing in seconds (lower number is better)
Second number in () is speedup from previous number of CPUs
number in brackets <> is speedup over single CPU timing
OS is GNU/Linux-2.6.11-gentoo-r6, Gentoo distribution
CHARMM is unmodified c32a2
pref.dat was used
AMD Opteron (x86_64): 2 X Opteron 242 (1.6GHz) per box, gigE,
inexpensive 24 port switch
| CPUs | sequential order | hierarchical order |
| | 276483 atoms | 276483 atoms |
| 1 | 1049.2 | 1049.2 |
| 2 | 552.5(1.90)<1.90> | 552.5(1.90)<1.90> |
| 4 | 313.2(1.76)<3.35> | 301.9(1.83)<3.48> |
| 8 | 198.6(1.58)<5.28> | 176.3(1.71)<5.95> |
| 16 | 140.7(1.41)<7.46> | 115.0(1.53)<9.12> | >
| 32 | 111.6(1.26)<9.40> | 84.1(1.37)<12.48> |
Notes:
For details see this reference: Borstnik U, Hodoscek M, Janezic D,
'Improving the performance of molecular dynamics simulations on parallel clusters',
J. Chem. Inf. Comp. Sci., 44 (2), 2004, pp 359-364.
Compile options:
- gcc-x86_64-3.4.3:g77 -O3 -mcmodel=medium -ffast-math -fno-backslash -fugly-complex -fno-globals -Wno-globals
See also other tables: Spatial decomposition, More performance benchmarks,
Milan Hodoscek
Last modified: Fri July 15 09:47:27 CEST 2005