[gmx-users] Hyperthreading on or off?

[Hector Mtz-Seara]

Dear users,

I have a short question. I've bought 5 nodes of dual Xeon 3.2 for 
running gromacs connected by a gigabit switch. I have  been performing 
some benchmarks using PME & Gromacs-3.3 & Lam-7.1.1 and the performance 
is very poor when using more than 2 nodes ( in fact 3 or more nodes 
perform nearly equal than 2 nodes that performs quite well). Looking at 
CPU consuming mean value during calculation its around 20%. I have 
hiperthreading on. Can it be the cause of this poor performance? do you 
recommend to switch it off?. Any other suggestion to improve the 
performance, because with this results I can't send any job using more 
than 4 CPU's what is terrible for the system I want to simulate.

Any help will be fantastic,

Hector