Table D.5.

Results for parallel Nullspace Algorithm on Intel Xeon (Clovertown) machine for E. coli metabolic networks.

			Time (s)								#EM
			1p	2p	4p	8p	16p	32p	64p	128p
E. coli	Original	Gen. cand.	13.45	7.12	3.73	1.92	1.28	1.21	1.17	0.81	92,594
	49 × 64(19)a	sorting	0.84	0.42	0.33	0.10	0.05	0.05	0.02	0.01
	Compressed	rank tests	2.55	1.98	1.35	0.89	0.55	0.39	0.30	0.10
	26 × 41(12)b	comm.	0.00	0.01	0.01	0.01	0.01	0.02	0.04	0.08
		merge	0.00	0.02	0.05	0.05	0.05	0.06	0.06	0.07
		Total	17.10	9.72	5.65	3.09	2.16	2.01	1.92	1.39
E. coli	Original	Gen. cand.	46.99	23.86	11.95	6.39	3.73	2.37	1.32	0.73	188,729
	50 × 66(19)	sorting	2.94	1.48	0.82	0.55	0.27	0.11	0.06	0.03
	Compressed	rank tests	8.15	6.27	4.27	2.74	1.54	0.90	0.69	0.47
	27 × 43(13)	comm.	0.00	0.01	0.02	0.05	0.05	0.06	0.06	0.08
		merge	0.00	0.05	0.08	0.09	0.10	0.11	0.11	0.12
		Total	58.90	32.35	17.71	10.31	6.57	3.91	2.31	1.63
E. coli	Original	Gen. cand.	2189.32	1077.90	538.30	268.93	135.53	67.48	37.35	21.25	1,224,785
	50 × 66(28)	sorting	84.58	26.60	14.07	10.84	5.55	1.99	1.35	1.32
	Compressed	rank tests	91.60	70.40	48.58	30.57	17.89	10.06	5.27	2.85
	29 × 45(19)	comm.	0	0.06	0.14	0.3	0.27	0.28	0.31	0.4
		merge	0	0.80	1.26	1.42	1.47	1.56	1.67	1.79
		Total	2381.49	1185.06	609.42	318.80	166.29	86.30	50.97	36.16

^aDimensions of stoichiometry matrix of the metabolic network; number of reversible reactions given in parentheses.

^bDimensions of stoichiometry matrix of the reduced metabolic network.