Table 6 Docking calculation time results for the protein complex (PDB ID: [PDB:1JK9]) for each process (in seconds).
From: Protein-protein docking on hardware accelerators: comparison of GPU and MIC architectures
| Â | 1CPU | 8CPUs | GPU | MICoffload | MICnative | ||||
|---|---|---|---|---|---|---|---|---|---|
P1. Initialization | 0.0 | 0.0 | Â | 0.8 | Â | 4.0 | Â | 0.7 | Â |
P2. Receptor voxel | 0.3 | 0.3 | (1.1×) | 0.3 | (1.1×) | 0.3 | (1.1×) | 4.4 | (0.1×) |
P3. Receptor FFT | 0.1 | 0.1 | (1.0×) | 0.0 | (1.7×) | 1.0 | (0.1×) | 0.3 | (0.2×) |
P4. Ligand rot & voxel | 12.9 | 3.4 | (3.8×) | 2.3 | (5.5×) | 7.4 | (1.7×) | 1.2 | (11.1×) |
P5. Ligand FFT | 69.8 | 14.2 | (4.9×) | 2.2 | (31.1×) | 15.1 | (4.6×) | 7.9 | (8.9×) |
P6. Convolution | 27.4 | 4.6 | (5.9×) | 1.1 | (25.6×) | 13.9 | (2.0×) | 3.6 | (7.7×) |
P7. Inverse FFT | 71.5 | 14.1 | (5.1×) | 2.2 | (31.8×) | 15.2 | (4.7×) | 8.3 | (8.6×) |
P8. Identifying the bests | 4.3 | 1.7 | (2.5×) | 1.7 | (2.5×) | 9.8 | (0.4×) | 0.3 | (12.5×) |
P9. Post processes | 0.0 | 0.0 | Â | 0.0 | Â | 0.0 | Â | 0.0 | Â |
Data transfer | Â | Â | Â | 0.6 | Â | 10.1 | Â | Â | Â |
Total | 186.4 | 38.5 | (4.8×) | 10.8 | (17.3×) | 77.0 | (2.4×) | 26.8 | (7.0×) |