Table 5.

Computational times of the SW algorithm depending on the number of GPUs used

avg.length	# of sequences	1 GPU		2 GPUs		3 GPUs		4 GPUs
		time	speedup	time	speedup	time	speedup	time	speedup
51	4000	8,06	1,000	4,04	1,997	2,71	2,971	2,07	3,896
	8000	31,11	1,000	15,57	1,998	10,39	2,995	7,86	3,961
	12000	69,08	1,000	34,56	1,999	23,07	2,994	17,44	3,961
154	2000	17,93	1,000	9,05	1,982	6,10	2,939	4,61	3,890
	4000	67,75	1,000	34,21	1,981	22,93	2,955	17,28	3,920
	6000	149,03	1,000	74,66	1,996	50,14	2,973	37,62	3,961
257	2000	49,23	1,000	24,72	1,991	16,59	2,968	12,54	3,927
	4000	186,44	1,000	93,80	1,988	62,80	2,969	47,31	3,941
	6000	410,26	1,000	205,87	1,993	137,26	2,989	103,28	3,972
459	2000	155,63	1,000	78,16	1,991	52,45	2,967	39,48	3,942
	4000	594,14	1,000	298,50	1,990	198,57	2,992	149,54	3,973
	6000	1332,83	1,000	667,31	1,997	444,92	2,996	333,59	3,995
608	800	50,22	1,000	25,66	1,957	17,40	2,886	12,84	3,911
	1200	106,84	1,000	53,91	1,982	35,77	2,987	27,41	3,898
	1600	191,79	1,000	95,93	1,999	64,01	2,996	48,46	3,958
1103	800	164,78	1,000	83,84	1,965	56,83	2,900	41,95	3,928
	1200	359,07	1,000	179,85	1,997	119,89	2,995	89,90	3,994
	1600	628,85	1,000	314,85	1,997	209,78	2,998	158,70	3,963

Mean computational times (in seconds) of the SW algorithm depending on the number of GPUs used. The algorithm was run on Tesla S1070 in U1 rack case containing four graphics cards. The speedup refers always to the one GPU configuration.