[gmx-users] Hyperthreading on or off?
Mark.Abraham at anu.edu.au
Sat Feb 11 04:37:26 CET 2006
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...
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