[gmx-users] gigabit scaling, DPPC benchmark

[David]

> Diego, I don't think hyperthreading was used on these runs since there
> were only two processes running on each node. Is there a way to easily
> toggle hyperthreading? I'd rather not go into the BIOS or reboot the
> system. To estimate the effect of hyperthreading I usually just make
> sure there are 4 processes per node (e.g. for -np 2, run two copies
> simultaneously). For example I get 109,209,354 for 1-,2-,4-thread jobs
> as compared to 158,404,517 for real cpus.
I don't understand the numbers above. 

If you run two jobs per processor that will kill the cache.
Hyperthreading is a real pain because you can have two processes on one
CPU and the other CPU idle. Best to turn it off completely.

On our Quad Opteron box you can see that we have significant super-
scaling, 226% on 2 CPUs and 427% on four CPUs, so GROMACS can scale on
good hardware (see benchmarks on www.gromacs.org).

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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