[gmx-users] Re: MPI scaling (was RE: MPI tips)
lubos.vrbka at gmail.com
Thu Feb 2 09:25:30 CET 2006
David Mathog wrote:
>>You are running an extremely short number of timesteps, but increasing the
>>system *size* to make the simulations take longer. That most likely means
>>you're *mostly* increasing the overhead involved in setting up the system.
>>So of course scaling is abysmal -- you're still running trivially short
>>calculations, just *really big* trivially short calculations. Try running
>>reasonable sized calculations that are long (MORE STEPS) and then
> I don't really understand your reasoning for increasing the number
> of steps since the nodes have to do some sort of communication at
> each step, and whatever the ratio of that time to computation time
> per step is, it shouldn't vary with the number of steps.
in my opinion, the overhead mentioned above is the problem. imagine the
1) simulation setup
takes 30 seconds (allocation of resources, initial creation of pair
lists, fft optimization, lincs initialization, or whatever else might
2) simulation itself
takes 30 seconds on 1 processor
takes 15 seconds on 2 processors
total 4:3 (30+30)/(30+15) instead of 'real' scaling 2:1 (30:15). if you
increase the simulation by order of magnitude you get (since setup takes
the same time) 330:180 that is much closer to the 'real' scaling 2:1.
making the simulation longer by 2 orders of magnitude gives you even
this example is an exxageration, but it should illustrate why you should
make the test simulation longer...
_ at _"
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