. Author manuscript; available in PMC: 2016 Apr 21.

Published in final edited form as: J Chem Inf Model. 2011 Sep 7;51(9):2345–2351. doi: 10.1021/ci200235e

Table 1.

Similarity matrix construction throughput for CPU (SSE4 population count algorithm with row-major and Morton-order) vs GPU (GeForce GTX 480), 1024-bit fingerprints. Similarity matrix for N molecules had shape N×N.

# molecules	Method	Time (s)	Throughput (Tan/s * 10⁶)
	SSE4	6.36	174.3
32,768	SSE4-Morton	5.2	214.8
	GPU	1.19	1088
	SSE4	124.1	139.4
131,072	SSE4-Morton	79.98	217.0
	GPU	15.6	1157