Skip to main content

Table 5 Computational times of the SW algorithm depending on the number of GPUs used

From: Protein alignment algorithms with an efficient backtracking routine on multiple GPUs

avg.length # of sequences 1 GPU 2 GPUs 3 GPUs 4 GPUs
   time speedup time speedup time speedup time speedup
51 4000 8,06 1,000 4,04 1,997 2,71 2,971 2,07 3,896
  8000 31,11 1,000 15,57 1,998 10,39 2,995 7,86 3,961
  12000 69,08 1,000 34,56 1,999 23,07 2,994 17,44 3,961
154 2000 17,93 1,000 9,05 1,982 6,10 2,939 4,61 3,890
  4000 67,75 1,000 34,21 1,981 22,93 2,955 17,28 3,920
  6000 149,03 1,000 74,66 1,996 50,14 2,973 37,62 3,961
257 2000 49,23 1,000 24,72 1,991 16,59 2,968 12,54 3,927
  4000 186,44 1,000 93,80 1,988 62,80 2,969 47,31 3,941
  6000 410,26 1,000 205,87 1,993 137,26 2,989 103,28 3,972
459 2000 155,63 1,000 78,16 1,991 52,45 2,967 39,48 3,942
  4000 594,14 1,000 298,50 1,990 198,57 2,992 149,54 3,973
  6000 1332,83 1,000 667,31 1,997 444,92 2,996 333,59 3,995
608 800 50,22 1,000 25,66 1,957 17,40 2,886 12,84 3,911
  1200 106,84 1,000 53,91 1,982 35,77 2,987 27,41 3,898
  1600 191,79 1,000 95,93 1,999 64,01 2,996 48,46 3,958
1103 800 164,78 1,000 83,84 1,965 56,83 2,900 41,95 3,928
  1200 359,07 1,000 179,85 1,997 119,89 2,995 89,90 3,994
  1600 628,85 1,000 314,85 1,997 209,78 2,998 158,70 3,963
  1. Mean computational times (in seconds) of the SW algorithm depending on the number of GPUs used. The algorithm was run on Tesla S1070 in U1 rack case containing four graphics cards. The speedup refers always to the one GPU configuration.