[gmx-users] hyperthreading

Berk Hess gmx3 at hotmail.com
Mon Aug 9 13:11:28 CEST 2010


These are nehalem Xeons I presume?
Then you get 15 to 20% more performance in Gromacs running 2 vs 1 thread or process per physical core.


> Date: Fri, 6 Aug 2010 09:24:11 -0500
> From: dmobley at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] hyperthreading
> Dear All,
> I'm putting together a new Dell Xeon cluster running ROCKS 5.3 which
> uses CENTOS (6 I believe). This is currently ~20 dual quad-cores with
> roughly 16 GB of RAM each.
> In any case, I wanted to inquire about hyperthreading. Does anyone
> have experience on similar machines with vs. without hyperthreading?
> The ROCKS users list suggests that hyperthreading ought always be off
> for HPC applications, which sounds overly simplistic to me, though I
> more or less follow the logic of this.
> So, has anyone done any benchmarking yet in a similar setting, and
> what thoughts do you have? I obviously can do some benchmarking myself
> as well but I thought I'd check in with the list first.
> Thanks so much,
> David
> -- 
> David Mobley
> dmobley at gmail.com
> 504-383-3662
> -- 
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