[gmx-developers] max cpu scale-up
hessb at mpip-mainz.mpg.de
Fri Sep 19 17:03:59 CEST 2008
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
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
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