Table 8. Benchmarking SmartMap software.
| Pre-algorithm alignment and processing | Read allocation algorithm | |||||||
|---|---|---|---|---|---|---|---|---|
| Read Alignment | Processing Alignments | Reading alignments | ||||||
| Algorithm | CPU Time | Wall Time | CPU Time | Proc. File Size | CPU Time | Max. Memory | Algorithm Time | Avg. MAE |
| SmartMap | 317:30:25 | 6:39:46 | 1:34:29 | 59 GB | 0:16:49 | 53 GB | 0:42:38 | 4.04 |
| BM-Map | 317:30:25 | 6:39:46 | N/A | 820 GB | 6:25:09 | 146 GB | ERROR | – |
| Iteration 0 | 317:30:25 | 6:39:46 | 1:34:29 | 59 GB | 0:16:10 | 53 GB | 0:35:16 | 4.12 |
| Random | 317:30:25 | 6:39:46 | 2:15:12 | 15 GB | 0:03:58 | 39 GB | 0:15:46 | 5.48 |
| Uniread | 36:08:04 | 0:45:34 | 0:17:07 | 13 GB | 0:03:19 | 39 GB | 0:14:43 | 6.50 |
Benchmarking conducted on computer with Ubuntu 20.04.1 LTS with 224 GB of RAM and dual Intel Xeon CPU E5-2690 v3 @ 2.60GHz processors, running on one thread except the read alignment, which used 48 threads. All times are represented in hours:minutes:seconds.
Alignment conditions are identical for all but Uniread. Parsing reads is typically conducted in parallel with alignment. File size represents the size of the required file after read parsing needed for the algorithm in question. Reading alignments is part of each algorithm and is included in the Algorithm Total Time.