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NAMD, 100,000 atoms benchmarks

This is a 99,744 atom system with a PME grid of 112x108x108 (script included below). For all the tests that follow we used the NAMD 2.6 amd64 executable as provided by the NAMD developers.

NAMD script used for these tests

1 core 4 cores 8 cores 16 cores 32 cores
Days per nsec 8.35 2.50 1.40 0.89 0.60
nsec per day 0.12 0.40 0.71 1.12 1.66
Efficiency 100% 83% 75% 59% 44%

Now try the following: instead of 'filling-up' all four cores of each node, distribute the work to different nodes (applicable only if less than 32 cores are needed). The following .nodelist file is one solution:

Modified .nodelist file

Using this nodelist file and repeating the measurements, we have:

1 core 4 cores 8 cores 16 cores 32 cores
Days per nsec 8.35 2.25 1.19 0.84 0.65
nsec per day 0.12 0.44 0.84 1.19 1.54
Efficiency 100% 93% 88% 62% 21%

which means that for anything up-to and including 16 cores, you are better-off with the nodelist file shown above.

Finally, an attempt to try filling-in pairs of cores before moving to the next node (group main host 10.0.0.11 host 10.0.1.11 host 10.0.0.12 host 10.0.1.12 host 10.0.0.13 host 10.0.1.13 host 10.0.0.14 host 10.0.1.14 host 10.0.0.15 host 10.0.1.15 host 10.0.0.16 host 10.0.1.16 host 10.0.0.17 host 10.0.1.17 host 10.0.0.18 host 10.0.1.18 host 10.0.0.11 host 10.0.1.11 …) gave worst scaling than the previously mentioned solution.

about/benchmarks/namd100k.txt · Last modified: 2009/02/06 13:56 (external edit)