[gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 30 17:51:35 CET 2009

Dimitris Dellis wrote:
> Hi.
> I run the same  (exactly) simulations with v3.3.3 and v4.0.3, on the 
> same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2.
> I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 
> (30% higher hours/ns), for few systems (512 molecules of 5-15 sites, 
> nstlist=10) I tried.
> This happens with single precision serial and parallel, np=2,4 (openmpi  
> 1.3) versions and only when electrostatics (PME) are present.
> With Simple LJ potentials the performance is exactly the same.
> Is there any speed comparison 3.3.3 vs 4.0.3 available ?
> D.D.

Can you show us your .mdp file?  What did grompp report about the relative PME 
load?  These topics have been discussed a few times; you'll find lots of 
pointers on optimizing performance in the list archive.


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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