Skip to main content

Table 3 Comparison between EMS1 and three implementations of EMS2

From: Efficient sequential and parallel algorithms for finding edit distance based motifs

Instance Metric EMS1 EMS2 EMS2M EMS2P threads
      1 2 4 8 16
(8,1) time 0.11 s 0.13 s 0.12 s 0.09 s 0.08 s 0.06 s 0.05 s 0.06 s
  memory 2.69 MB 4.25 MB 3.17 MB 2.67 MB 3.20 MB 3.55 MB 6.02 MB 7.99 MB
(12,2) time 19.87 s 15.60 s 16.62 s 2.71 s 1.94 s 1.44 s 0.89 s 0.55 s
  memory 34.28 MB 210.47 MB 126.91 MB 84.98 MB 104.60 MB 125.18 MB 142.82 MB 150.23 MB
(16,3) time 1.74 h 23.73 m 26.79 m 3.73 m 2.32 m 1.38 m 48.58 s 36.93 s
  memory 8.39 GB 11.62 GB 6.97 GB 8.55 GB 10.21 GB 10.53 GB 9.84 GB 9.91 GB
(9,2) time 10.84 s 1.72 s 3.02 s 1.12 s 0.96 s 0.78 s 0.49 s 0.35 s
  memory 3.44 MB 26.67 MB 17.04 MB 42.86 MB 57.76 MB 54.77 MB 59.85 MB 66.53 MB
(11,3) time 33.48 m 1.91 m 3.57 m 45.85 s 30.78 s 19.68 s 13.49 s 9.78 s
  memory 92.86 MB 477.12 MB 313.33 MB 2.27 GB 2.63 GB 2.65 GB 2.55 GB 2.60 GB
(13,4) time - 1.08 h 1.76 h 44.03 m 26.16 m 14.51 m 8.62 m 6.82 m
  memory - 8.26 GB 5.58 GB 149.60 GB 179.66 GB 180.13 GB 168.80 GB 172.74 GB
  1. Time is in seconds (s), minutes (m) or hours (h). An empty cell implies the algorithm did not complete in the stipulated 72 h