Re: Yet another NAMD speed concerns

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Sat Apr 25 2009 - 11:43:40 CDT

I have a system of ca. 100000 atoms and I run on 32 CPUs with infiniband.
It takes 8 hours for 1 ns. I'm not sure the system scales on 256 CPUs, I
haven't tried. The more CPUs you use the more communication there will be
and this will be the bottleneck. The problem is the latency time, i.e.,
the time it takes for a message to be prepared and sent over the network.
MD uses domain decomposition where the system is subdivided into domains.
The more CPUs you use the smaller will be each subdomain and the more time
a CPU will spend in waiting until the message is sent instead of
computing.

A comment about your parameters. I think you can choose a cutoff of 12 and
you can also set "pairlistdist 14.0".

Gianluca

On Sat, 25 Apr 2009, DimitryASuplatov wrote:

> Hello,
>
> 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
> flag.
>
> My force field parameters are
> =====================
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 15.
> 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
> !!!!!!!!!!!!!!!!!!!
> ======================================================
>
> 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.
>
> 1/ Is this speed normal for namd or did i do something wrong?
> 2/ Can I use 4fs for timestep with this parameters?
> 3/ what do you do to shortcut your calculations?
>
> Thanks
> SDA
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     +1 (206) 714 4303
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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