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2024-03-29
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2024-03-28
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. ----- <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]]). ||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 || Graphical comparison with the ideal (linear) scaling-up : [[image:NAMD scale-up for 1,2,4,6,8,9 procs]]. ----- 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]]
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