[gmx-users] Hyperthreading on or off?

[Mark Abraham]

Hector Mtz-Seara wrote:
> 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.

The low CPU usage suggests that there's a non-compute bottleneck - 
probably MPI communication or disk I/O. What benchmark systems are you 
using? The ones on the gromacs web page are recommended and scale 
reasonably on Xeon+gigabit. How does non-parallel compare with parallel 
with 1 and 2 processors? I can't think why hyperthreading would have a 
significant impact, but it can't hurt to try turning it off...

Mark