Table 2. Time (in seconds) and Speedup (S) for end-to-end all-to-all analysis of the Proteus_300 dataset using pyMCPSC on a multi-core PC with Intel i7 CPU having 8 cores (16 threads), 32 GB RAM, running at 3.0 GHz, under Ubuntu 14.04 Linux.
GRALIGN already uses all the CPU cores by default.
| 1 Thread | 4 Threads | 8 Threads | 12 Threads | 16 Threads | |||||
|---|---|---|---|---|---|---|---|---|---|
| Time | Time | S | Time | S | Time | S | Time | S | |
| Pairwise scores generation | |||||||||
| GRALIGN | 86 | 86 | 1.00 | 86 | 1.00 | 86 | 1.00 | 86 | 1.00 |
| USM | 139 | 46 | 3.02 | 20 | 6.95 | 17 | 8.18 | 15 | 9.27 |
| FAST | 4100 | 1035 | 3.96 | 412 | 9.95 | 329 | 12.46 | 313 | 13.10 |
| TM-align | 3601 | 1032 | 3.49 | 423 | 8.51 | 333 | 10.81 | 299 | 12.04 |
| CE | 16776 | 4022 | 4.17 | 1858 | 9.03 | 1420 | 11.81 | 1213 | 13.83 |
| Consensus scores | 28 | 28 | 1.00 | 28 | 1.00 | 28 | 1.00 | 28 | 1.00 |
| Block level | |||||||||
| Scores Generation | 24730 | 6249 | 3.96 | 2827 | 8.75 | 2213 | 11.17 | 1954 | 12.66 |
| Dataset Analysis | 843 | 849 | 0.99 | 844 | 1.00 | 846 | 1.00 | 847 | 1.00 |
| End to End | |||||||||
| End to End | 25573 | 7098 | 3.60 | 3671 | 6.97 | 3059 | 8.36 | 2801 | 9.13 |