[gmx-users] Hyperthreading on or off?

Andrea Carotti and.carotti at farmchim.uniba.it
Mon Feb 13 09:34:22 CET 2006

I have a similar system (4 nodes, dual xeon, gigabit ethernet, but gromacs 
3.2.1, hyperthreading off).
I was experiencing some bad performance on more that two nodes and after 
googling a bit I've found this settings I've mailed one week ago:
Let we know if this helps
----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Saturday, February 11, 2006 4:37 AM
Subject: Re: [gmx-users] Hyperthreading on or off?

> 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
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