(Updated November 2022)
G100
Version 2.14
Input: (http://www.ks.uiuc.edu/Research/namd/utilities/)
APOA1 - Acquaporin, (water channel) benchmark (92 224 atoms, periodic, PME)
The NAMD benchmark is the pure MPI of the large system of 93k atoms (Acquaporin in water). The Performance is shown in Graphic 1 in yellow, while in grey is the ideal curve performance.
Table 1: Performance of pure MPI run
| n nodes | n cores | Performance ns/day |
|---|---|---|
| 1 | 48 | 6.17997 |
| 2 | 96 | 11.9407 |
| 3 | 144 | 16.8295 |
| 4 | 192 | 21.6144 |
| 5 | 240 | 25.831 |
| 6 | 288 | 31.1206 |
| 7 | 336 | 32.6168 |
| 8 | 384 | 35.6982 |
| 9 | 432 | 39.7144 |
| 10 | 480 | 44.5508 |
| 12 | 576 | 51.6476 |
| 14 | 762 | 59.0734 |
| 16 | 768 | 67.7865 |
| 18 | 864 | 72.83 |
| 20 | 960 | 63.2455 |
Graphic 1: the NAMD performance (simulation time in ns/day) is reported vs. the increasing number of nodes (48 core per node). In yellow the performance of the system and in grey the ideal curve performance.
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