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.
-Justin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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