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2024-05-13
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2024-05-12
Editing revision 6 of NAMD benchmarks and scaling-up
Editing old revision 6. Saving this page will replace the latest revision with this text.
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. ||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 || Graphically : [[NAMD scale-up for 1,2,4,6,8,9 procs]]
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