Extending the BEAGLE library to a multi-FPGA platform

BMC Bioinformatics

Table 3 Performance results of our design

nsites	CPU(us)	GPU(us)	FPGA(us)	Memory efficiency (%)	Speedup FPGA vs. CPU	Speedup FPGA vs. GPU
128	27	93	96	2	0.28	0.97
256	41	93	101	4	0.41	0.92
512	69	94	103	7	0.67	0.91
1024	133	99	106	13	1.25	0.93
2048	225	107	107	20	2.10	1.00
4096	462	130	115	30	4.02	1.13
8192	944	167	125	28	7.55	1.34
16384	1894	240	148	28	12.80	1.62
32768	3873	385	207	28	18.71	1.86
65536	7922	672	304	29	26.06	2.21
131072	15898	1247	415	38	38.31	3.00
262144	31774	n/a	764	40	41.59	n/a
524288	63696	n/a	1240	44	51.37	n/a
1048576	127957	n/a	2280	46	56.12	n/a
8192000	1028649	n/a	15750	49	65.31	n/a

ISSN: 1471-2105