LoBoS benchmarks, Jan/Feb 2000, c28n1

Cubic periodic molecular systems, OG = octyl glucoside:

M100 aqueous micelle of 100 OG lipids, ca. 19K atoms

M50 aqueous micelle of 50 OG lipids, ca. 17K atoms

M20 aqueous micelle of 20 OG lipids, ca. 8K atoms

bx30 aqueous sucrose, 30 A box edge, ca. 3K atoms

NEW! 5 Feb 2000 Results for 2.2.14-tcpfix

Plots are all PM Ewald tests, mostly GbNIC; spherical cutoff results are typically slightly better, except for larger systems on 100baseT. In that case, PM Ewald and spherical cutoff results are approximately equivalent.

Note that while systems of ca. 3K atoms (bx30) show little benefit at 8 processors, systems of 8K (M20) and up all show a ca. 25% reduction in elapsed time, compared to 4 processors. The relatively small gap between 2 and 1 proc/host seen at 8 processors is the smallest we've ever observed on this hardware. The M100 results for the 2.2.13 kernel (OLD) are shown to illustrate the change.

The gap between curves is significant in the above plot; it shows: (a) that there's always an advantage to using 4 procs, even for 3K atoms, (b) that systems over about 4K atoms would benefit from using 8 procs, (c) the small gap between 2 and 1 proc/host, and (d) GbNIC only offers any real advantage for large systems using 8 procs. These are all significant improvements in parallel scaling performance, especially for the 2 proc/host case. The GbNIC 8 proc results for the 2.2.13 kernel (OLD) are shown to illustrate the change.

The above shows the 8 proc results for optimizing the kernel parameter tcp_delack_strategy on Gigabit ethernet (GbNIC); note the near convergence of 2 and 1 proc/host curves, such that at 0 and 1 the times are ranked by molecular system size.

As for the previous plot, but for fast ethernet (100baseT).

Credits

EB kernel research, identification of tcp_delack_strategy kernel parameter, testbed setup, final rollout

RV benchmark suite, kernel parameter test protocol, collation and presentation (here) of results

In the following tables, the first line is the elapsed time in minutes for 100 steps of dynamics, second is estimated speedup relative to one processor, e.g.:

Nproc PM Ewald 2/host
N Time
Speedup

Nproc	PM Ewald 2/host
N	Time
	Speedup

GbNIC with kernel parameter tcp_delack_strategy set to 1

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.95	8.91	7.10	6.98
	1.94	1.95	1.94	1.97
4	4.89	4.79	3.83	3.76
	3.55	3.62	3.60	3.66
8	2.97	2.74	2.28	2.13
	5.85	6.34	6.04	6.47
		M50.dat
2	7.92	7.89	6.38	6.25
	1.94	1.95	1.94	1.98
4	4.41	4.28	3.61	3.41
	3.48	3.59	3.43	3.63
8	2.66	2.46	2.09	1.93
	5.78	6.25	5.92	6.41
		M20.dat
2	3.36	3.35	2.67	2.68
	1.94	1.95	1.94	1.93
4	1.89	1.85	1.52	1.47
	3.45	3.52	3.41	3.52
8	1.37	1.24	1.02	0.93
	4.76	5.26	5.08	5.56
		bx30.dat
2	1.74	1.75	1.47	1.46
	1.94	1.93	1.94	1.95
4	1.06	1.03	0.85	0.84
	3.18	3.28	3.34	3.40
8	0.88	0.77	0.66	0.59
	3.84	4.37	4.34	4.82

100baseT with kernel parameter tcp_delack_strategy set to 1

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.81	8.94	6.98	6.94
	1.94	1.91	1.94	1.95
4	5.06	4.96	3.88	3.80
	3.38	3.45	3.49	3.56
8	3.09	2.87	2.30	2.33
	5.53	5.96	5.89	5.81
		M50.dat
2	7.92	7.95	6.32	6.21
	1.94	1.93	1.94	1.97
4	4.43	4.38	3.50	3.48
	3.47	3.51	3.50	3.52
8	2.78	2.57	2.12	2.10
	5.53	5.98	5.78	5.84
		M20.dat
2	3.33	3.41	2.67	2.66
	1.94	1.89	1.94	1.95
4	1.95	1.89	1.52	1.47
	3.31	3.42	3.41	3.52
8	1.43	1.27	1.05	0.94
	4.52	5.09	4.93	5.50
		bx30.dat
2	1.74	1.77	1.45	1.45
	1.94	1.91	1.94	1.94
4	1.10	1.03	0.87	0.83
	3.07	3.28	3.25	3.39
8	0.92	0.79	0.68	0.59
	3.66	4.29	4.16	4.75

Results with kernel parameter tcp_delack_strategy set to 3 (default)

Kernel 2.2.14-tcpfix on GbNIC

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.83	8.84	7.01	6.92
	1.94	1.94	1.94	1.97
4	5.51	4.88	4.38	3.74
	3.11	3.51	3.10	3.64
8	5.48	3.71	3.97	2.76
	3.13	4.62	3.43	4.93
		M50.dat
2	7.83	7.92	6.29	6.22
	1.94	1.92	1.94	1.96
4	4.97	4.34	3.97	3.52
	3.06	3.50	3.07	3.47
8	5.19	3.40	3.81	2.55
	2.93	4.47	3.20	4.79
		M20.dat
2	3.35	3.35	2.68	2.65
	1.94	1.94	1.94	1.96
4	2.54	2.03	2.10	1.63
	2.56	3.20	2.48	3.19
8	4.00	2.24	2.87	1.60
	1.62	2.90	1.81	3.25

Kernel 2.2.14-tcpfix on 100baseT

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.87	8.90	6.89	6.83
	1.94	1.93	1.94	1.96
4	5.65	5.12	4.40	3.95
	3.05	3.36	3.04	3.38
8	5.35	3.69	3.94	2.77
	3.22	4.66	3.39	4.83
		M50.dat
2	7.74	7.81	6.31	6.18
	1.94	1.92	1.94	1.98
4	5.18	4.42	4.00	3.53
	2.90	3.40	3.06	3.47
8	5.29	3.33	3.77	2.64
	2.84	4.51	3.25	4.64
		M20.dat
2	3.31	3.35	2.65	2.64
	1.94	1.92	1.94	1.95
4	2.58	2.01	2.08	1.60
	2.49	3.19	2.47	3.21
8	3.85	2.26	2.70	1.60
	1.67	2.84	1.90	3.21

Previous Values, for Comparison

Kernel 2.2.13 on GbNIC

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.97	8.90	6.98	6.83
	1.94	1.96	1.94	1.98
4	6.01	5.28	4.75	4.18
	2.90	3.30	2.85	3.24
8	6.72	4.64	4.91	3.49
	2.59	3.75	2.76	3.88
		M50.dat
2	8.00	7.81	6.50	6.29
	1.94	1.99	1.94	2.00
4	5.42	4.70	4.42	3.83
	2.86	3.30	2.85	3.29
8	6.34	4.34	4.68	3.31
	2.45	3.58	2.69	3.81
		M20.dat
2	3.35	3.35	2.67	2.67
	1.94	1.94	1.94	1.94
4	3.00	2.30	2.49	1.90
	2.17	2.83	2.08	2.73
8	5.11	3.16	3.69	2.30
	1.27	2.06	1.40	2.25

Kernel 2.2.13 on 100baseT

Nproc	PM Ewald 2/host	PM Ewald 1/host	Spherical 2/host	Spherical 1/host
		M100.dat
2	8.88	9.07	7.07	6.89
	1.94	1.90	1.94	1.99
4	6.26	5.78	4.89	4.43
	2.75	2.98	2.80	3.10
8	7.10	5.35	5.15	4.22
	2.43	3.22	2.66	3.25
		M50.dat
2	7.97	8.17	6.31	6.29
	1.94	1.89	1.94	1.95
4	5.79	5.23	4.57	4.03
	2.67	2.96	2.68	3.04
8	6.77	4.93	4.92	3.89
	2.28	3.14	2.49	3.15
		M20.dat
2	3.33	3.46	2.69	2.69
	1.94	1.87	1.94	1.94
4	3.15	2.52	2.52	1.98
	2.05	2.56	2.07	2.64
8	5.18	3.42	3.75	2.57
	1.25	1.89	1.39	2.03