From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Apr 25 2009 - 09:10:14 CDT
On Sat, 2009-04-25 at 13:44 +0400, DimitryASuplatov wrote:
> I am running a simulation of my protein in water (cell = 15 angstroms
> from the protein). System contains 110349 atoms total.
> I have compiled namd 2.6 on xeon infiniband cluster uusing amd64
> installation procedure. I`ve also used icc and ifort with -xSSSE3
if you want to get the fastest execution, _particularly_
using SSE, why don't you get the 2.7 beta?? using the compiler
SSE flags is almost always a waste of effort unless the code
uses compiler intrinsics explicitly. _no_ compiler flag can
replace a good algorithm and a resourceful and smart programmer.
> My force field parameters are
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 15.
why 15 angstrom???
> switching on
> switchdist 10.
> My integrator parameters are
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 4
> stepspercycle 20
> I use
> langevin on
> langevinPiston on
> cellBasisVector1 108 0. 0.
> cellBasisVector2 0. 102 0.
> cellBasisVector3 0. 0 105.
> cellOrigin 63.87940979 13.3578186035 32.2524185181
> PME yes
> PMEGridSizeX 125
> PMEGridSizeY 125
> PMEGridSizeZ 125
> MY PROBLEM IS THAT MY SYSTEM IS TOO SLOW
> Utilization of 256 x Xeon 3Gz CPUs requires 41 hours for 10 ns
how fast is it with less CPUs? have you made a proper scaling test???
are you certain that you actually are using the infiniband network?
what kind of machine do you have _exactly_.
what kind of infiniband do you have and have you made
tests on the through put on that? i've seen quite a few
networks that were not set up correctly and thus performance
was abysmal when used with too many MPI tasks.
> I consider my system to be of a typical size. 100k atoms fro 10 ns is
> normal in our days. But it is very hard calculate with NAMD even on
> modern clusters.
it is very hard for _you_. i am certain there are a
lot of people that think very differently.
> 1/ Is this speed normal for namd or did i do something wrong?
most likely the second.
> 2/ Can I use 4fs for timestep with this parameters?
not unless you mess with the particle masses. if you
only want "approximate" results, why don't you use gromacs?
> 3/ what do you do to shortcut your calculations?
i'd rather do correct simulations.
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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