Re: TclForces and efficient PBC corrections

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 12 2013 - 01:37:53 CST

two comments:

a) there is plenty of information about using Tcl efficiently on the
Tcl/Tk wiki and in the Tcl tutorials on www.tcl.tk.

b) the major drawback of TclForces is that it is executed in serial on
rank 0 only. this can seriously impact your parallel performance, just
have a look at Amdahl's law... ;-)

axel.

On Mon, Nov 11, 2013 at 7:02 PM, Morgan, Brittany
<Brittany.Morgan_at_umassmed.edu> wrote:
> Hi All,
>
> I use TclForces and I need to correct for periodic boundary conditions. I
> have procedures which correct for PBC brute force, but I'm having serious
> performance issues when I turn them on (the time required more than
> doubles).
>
> Can anyone tell me if:
> 1. For the scalar distance, does "getbond <coor1> <coor2>" return a distance
> corrected for periodic boundary conditions?
>
> 2. Is there a built-in way to obtain the vector distance between two
> positions, corrected for periodic boundary conditions? Or does anyone know
> of a resource for doing more efficient calculations in Tcl?
>
> 3. Is the IBVERBS version of charmrun faster when using TclForces?
>
> I didn't have serious performance issues with my PBC corrections previously,
> but I've recently started working on a new cluster and this problem has
> appeared. Previously, I was using NAMD 2.9b2, but IBVERBS is not currently
> working on the new cluster. I've been using NAMD 2.9-multicore instead.
>
>
>
>
>
> Any suggestions would be much appreciated.
>
>
>
> Brittany Morgan
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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