[gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

[Mark Abraham]

> You have to
> find your optimum making some tests with your settings. To do that you can
> start your simulation and interrupt after a while to have some data logged
> in the log file. Then, from the information in that log file you can
> estimate the time that the whole task will take and compare using more or
> less number of processors until you find your optimum value.

Of course, that "while" should be at least of the order of several
minutes. There is a set-up cost borne once at the start of the calculation
which is not proportional to the length of the calculation, so you need to
run long enough to get out of the time period during which it dominates
the linear component.

Mark