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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