NAMD 2.4b1 on ApoA1

92,224 atoms, 12A cutoff + PME every 4 steps, periodic

Time is in seconds per step, averaged over a number of steps, after load balancing. NAMD prints this data, labeled Benchmark time, twice near the beginning of a run. Due to its measurement-based load balancing system, NAMD performance may improve dramatically after the first couple of hundred timesteps.

Download this benchmark: config, directory, 2.8M archive

DHFR Common CHARMM/AMBER Benchmark

23,558 atoms, 9A cutoff + PME every step, periodic, Origin 2000 R10000/250

		NAMD 2.2			NAMD 2.4b1			NAMD 2.5b2			AMBER 6
Procs		Time	Speedup		Time	Speedup		Time	Speedup		Time	Speedup
1		8.24	1		5.08	1		4.10	1		MAX_RSTACK
2		4.26	1.93		2.66	1.91		2.16	1.90		1.96	2
4		2.19	3.76		1.35	3.76		1.11	3.69		1.05	3.73
8		1.12	7.36		0.69	7.36		0.57	7.19		0.60	6.53
16		0.57	14.5		0.35	14.5		0.29	14.1		0.38	10.3
32		0.32	25.8		0.19	26.7		0.17	24.1		0.32	12.3
64		0.20	41.2		0.11	46.2		0.10	41.0		0.25	15.7
126		0.14	58.9		0.07	72.6		0.07	58.6		0.36	10.9
252		0.09	91.6		0.06	84.7		0.07	58.6		0.76	5.16
		config			config			config			config

Time is in seconds per step, averaged over a number of steps, after load balancing. NAMD prints this data, labeled Benchmark time, twice near the beginning of a run. Due to its measurement-based load balancing system, NAMD performance may improve dramatically after the first couple of hundred timesteps.

The NCSA Origin was chosen for this benchmark because AMBER is installed and available on the machine. The slower processors (250 MHz) and fast interconnect on this machine should demonstrate best possible AMBER scaling.