Table 5 Performance comparison among SW implementations using the small and medium sets
From: SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences
Implementation | SWIFOLD | SWAPHI-LS | SW# | CUDAlign | SW# | CUDAlign |
|---|---|---|---|---|---|---|
Accelerator | Intel Arria 10 GX | Intel Xeon Phi 3120P | NVIDIA GTX980 | NVIDIA GTX1080 | ||
Matrix size (cells) | Performance (GCUPS) | |||||
100K | 49.81 (56.92) | 0.42 | 0.3 | 0.03 | 0.23 | 0.03 |
3M | 105.14 (223.1) | 7.69 | 7.62 | 1.08 | 7.55 | 1.08 |
28M | 122.91 (255.49) | 21.24 | 33.33 | 8.18 | 41.47 | 8.63 |
291M | 126.95 (268.83) | 30.67 | 64.53 | 45.89 | 111.60 | 58.24 |
1G | 129.44 | 32.84 | 75.24 | 79.21 | 144.97 | 117.97 |
9G | 131.45 (202.56) | 33.9 | 69.54 | 84.05 | 143.50 | 152.63 |
25G | 131.96 | 34.16 | 120.92 | 160.79 | 255.89 | 295.43 |
35G | 131.98 (203.51) | 34.38 | 68.84 | 84.43 | 142.12 | 155.19 |
100G | 132.15 | 33.19 | 118.81 | 163.77 | 253.13 | 297.05 |
575G | 132.33 (204.06) | 30.36 | 67.55 | 84.84 | 143.51 | 158.13 |