Re: Optimizing configuration option for fast calculations

From: bo liu (liubo.njuer_at_gmail.com)
Date: Thu Apr 30 2009 - 12:12:59 CDT

Hi,

Have you checked the .log and the simulation results to confirm that
everything goes ok? say, does the energy output (especially the
electrostatic energy) fluctuate too much?
In my view, some of your parameters are dicey for simulation of biological
systems. e.g. a pairlistdist of 10

Best.
Bo
2009/4/28 DimitryASuplatov <genesup_at_gmail.com>

> Hello,
>
> I have been recently writing about namd being very slow for
> calculations of my 110000 atoms system.
>
> I have received lots of suggestions and links in reply. So I was able
> to adjust my configuration options that made calculations a lot
> faster.
>
> I am writing this in case someone like me has the same speed problems
> and feels himself on the edge.
>
> 1/ # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 10.0 #(Valid with the condition of using PME)
> switching on
> switchdist 8.0 #Cutoff-2
> pairlistdist 12.0 #Cutoff+2
> stepspercycle 10
>
> 2/ # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
>
> 3/ PME yes
> PMEGridSizeX 128 # 128 = 2^7
> PMEGridSizeY 128
> PMEGridSizeZ 128
>
> Now I have the following scaling:
>
> CPUs seconds/step days per ns
> =====================================
> 4 0.4 2.31
> 16 0.117 0.68
> 32 0.062 0.36
> 64 0.038 0.22
> 128 0.031 0.18
> 256 0.018 0.105
>
> That makes it 24 hours for 10 ns on 256 CPUs. (At least 40% faster than
> before!)
>
> Thank you all for your time and help.
> SDA
>
>

-- 
-Bo Liu
----------------------------------------------------------------------------------------------------------------
Graduate Student
Theoretical and Computational Biophysics
GUCAS, CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety
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