[gmx-developers] max cpu scale-up

Berk Hess hessb at mpip-mainz.mpg.de
Fri Sep 19 17:03:59 CEST 2008


Just try!

This depends a lot on your system.
But with 200000 atoms you should be able to scale much further on a cray 
You usually don't need to use -dd option, mdrun will optimize it for you.
If you use pme, you will get far higher performance with separate pme nodes,
mdrun will automatically select this (when you do not specify -dd).
You might need to optimize -npme.
On a xt4 you probably want to use -ddorder cartesian
No other options should be needed.

The only real disadvantage of an xt4 is that you can not get/select you 
processor blocks.
Therefore 4x4x4 might fit perfectly in a torus of the machine, but the 
with never give you such a nice assignment.


andrea spitaleri wrote:
> Hi there,
> I am using the latest cvs on hector cluster (http://www.hector.ac.uk/) 
> and normally I set the simulation to 64 cpus and -dd 4 4 4. This gives 
> to me a good performance for a simulation with ca. 200,000 atoms 
> (6ns/day with dt=2fs).
> How many cpus the new gromacs may scale-up? do you have any optimised 
> parameters? Do you think that 128 cpus can perform better in speed?
> thanks in advance
> regards
> andrea

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