[gmx-users] gigabit scaling, DPPC benchmark

Christian Burisch burisch at bph.ruhr-uni-bochum.de
Mon Jun 6 19:47:17 CEST 2005

Diego Enry wrote:

Hi everyone!

> Jason, I don't know if that's the problem but when I use a P4EE 3Ghz,
> Gromacs runs  faster without hyperthreading.

Are you using kernel 2.6 (if you are using Linux at all...)? We are 
just now upgrading our cluster, and the effect of HT with kernel 2.6 
on Gromacs was one thing I wanted to benchmark. But if you - or anyone 
else reading this - have done so already I would be very glad if you 
could share the info!

@Jason: Another way to decrease network latency - which is probably 
the limiting factor in your case - may be GAMMA (it was mentioned a 
long time ago on this list):


We never tried it ourselves since we are using Myrinet in most of our 
nodes, but it sounds very interesting!



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