[gmx-users] Gromacs on Gigabit Ethernet Dual Opteron Cluster
lindahl at csb.stanford.edu
Mon Oct 6 19:01:02 CEST 2003
It depends on the type of interaction, but water-water calculations can
sometime be as cheap as 50% of normal interactions.
(Because we have special optimized loops for them, and there is only
one LJ interaction site per molecule).
On Monday, October 6, 2003, at 02:26 AM, Ghermes Chilov wrote:
> Hello Anton,
> Monday, October 6, 2003, 11:59:40 AM, you wrote:
> AF> Ghermes Chilov wrote:
>>> The system (dummified protein in water)is big enough:~ 107.000 atoms,
>>> -shuffle -sort were used.
> AF> If your protein is big w/r the number of waters, it will become
> AF> as soon as it fills a whole processor, i.e. CPU0 will be
> overloaded with
> AF> protein, and the others are doing water with time to spare...
> No, it's not big: ~ 7-8% of the system... khmm, it becomes sufficient
> for 100%/8%=12 CPU's, isn't it? Or even for a smaller number, if
> water-water interactions are in principle more easy to calculate.
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