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%

Mishima et al. BMC Bioinformatics 2008 9(Suppl 6):S10   doi:10.1186/1471-2105-9-S6-S10