MBG wiki: Editing NAMD benchmarks and scaling-up

The tests were performed with a 59428-atom system, identical with the one used for the [[Molecular dynamics studies of HrcQb]]. A short (1000 steps) MD run was performed with varying number of processors and the benchmark times reported by NAMD were noted. The cluster during these tests was otherwise idle.

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<b>1,2,4,6,8 and 9 processors</b> (that is, server plus newest nodes). Note that  the 1-processor benchmark was obtained on one of the compute nodes (pc10, not the server). This explains the value of 2.18 for the 2-processor case. Also note that the 9th processor is a node located outside the cluster room which is connected with the cluster via an additional hub. The result is that for this node the network latency is higher (see [[Raw TCP performance]]).

Graphical comparison with the ideal (linear) scaling-up :

[[image:NAMD scale-up for 1,2,4,6,8,9 procs]].

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Extending the test to include the slower nodes as well gives the following table :

||Number of processors||Days per nanosecond of simulation||Scale-up||
|| 1 || 17.464 || 1.00 ||
|| 2 ||  8.013 || 2.18 ||
|| 4 ||  4.755 || 3.67 ||
|| 6 ||  3.799 || 4.60 ||
|| 8 ||  2.794 || 6.25 ||
|| 9 ||  2.616 || 6.67 ||
||10 ||  2.581 || 6.76 ||
||12 ||  2.552 || 6.84 ||
||14 ||  2.412 || 7.24 ||
||16 ||  2.327 || 7.50 ||
||18 ||  2.170 || 8.05 ||

Graphical comparison with the ideal (linear) scaling-up :

[[image:NAMD scale-up for all processors]]

Summary:

This change is a minor edit.

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