Table 1.

Computation Performance. Computation performance in each method. Analyzed haplotype window types were consecutive window haplotypes (ConsWH) and combinational window haplotypes (CombWH). Fold acceleration is defined as actual elapsed time divided by accumulated time for each process. Acceleration linearity is defined as fold acceleration divided by number of used compute-nodes. 22 nodes are used for analysis except five nodes for the Unphased CombWH analysis.

program	option	analyzed haplotype	window size	elapsed time	accumulated time	fold acceleration	acceleration linearity
FBAT	-e	ConsWH	1–26	2.2 min	31.7 min	14.4	65.5%
FBAT	-e	CombWH	1–5	1.9 min	30.3 min	15.9	72.3%
Unphased	-uncertain	ConsWH	1–17	69.9 day	909.0 day	13.0	59.1%
Unphased	-certain	ConsWH	1–26	13.8 min	256.1 min	18.6	84.5%
Unphased	-certain	CombWH	1–5	6.5 day	7.2 day	1.1	22.0%