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Table 1 Performance evaluation of the optimized SIMT and partitioned vectorized algorithms on GTX 280

From: CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Query Sequences

Partitioned

SIMT

  

10-2 k

20-2 k

40-3 k

10-2 k

Query

Length

Time

GCUPS

Time

GCUPS

Time

GCUPS

Time

GCUPS

P02232

144

1.58

13.3

1.41

14.9

1.40

15.0

1.38

15.2

P05013

189

1.80

15.4

1.66

16.7

1.65

16.8

1.75

15.8

P14942

222

2.01

16.1

1.84

17.6

1.82

17.8

2.00

16.2

P07327

375

3.97

13.8

3.64

15.1

3.51

15.6

3.35

16.4

P01008

464

4.57

14.8

4.20

16.1

4.03

16.8

4.05

16.7

P03435

567

5.87

14.1

5.38

15.4

5.28

15.7

4.94

16.4

P42357

657

6.64

14.5

6.16

15.6

5.97

16.1

5.00

16.6

P21177

729

6.92

15.4

6.40

16.6

6.24

17.1

5.77

16.6

Q38941

850

7.98

15.6

7.37

16.9

7.35

16.9

6.35

16.8

P27895

1000

10.27

14.2

9.29

15.7

8.74

16.7

7.44

16.7

P07756

1500

15.07

14.5

14.08

15.6

13.43

16.3

8.64

16.9

P04775

2005

19.30

15.2

18.05

16.2

17.36

16.9

13.04

16.8

P19096

2504

22.89

16.0

21.49

17.0

21.19

17.3

17.50

16.7

P28167

3005

28.54

15.4

26.08

16.8

25.53

17.2

21.89

16.7

P0C6B8

3564

32.44

16.1

30.56

17.0

29.60

17.6

26.41

16.6

P20930

4061

40.47

14.7

36.07

16.5

34.31

17.3

31.35

16.6

P08519

4548

42.41

15.7

39.89

16.7

38.86

17.1

35.84

16.6

Q7TMA5

4743

42.44

16.3

39.36

17.6

39.30

17.6

40.18

16.5

P33450

5147

50.91

14.8

47.74

15.8

44.20

17.0

41.92

16.5

Q9UKN1

5478

55.46

14.4

49.49

16.2

46.66

17.2

45.62

16.5