AW: LES very slow

From: Norman Geist (
Date: Wed Feb 27 2013 - 01:19:51 CST

Hi Siri,


so far, I couldn’t find a reason for your problem in your hardware. I don’t
know what LES is actually doing, but the manual tells that NAMD only
supports up to 15 copies.

Nevertheless, I can’t see a reason why this kind of computation should harm
the good scaling of namd. Does “normal” md scale better, so we can identify
if it is a general problem of your setup, or if it is due LES.



Norman Geist.


Von: Siri Søndergaard []
Gesendet: Mittwoch, 27. Februar 2013 00:11
An: Norman Geist
Betreff: Re: namd-l: LES very slow


I've attached the files... I hope this is what you were looking for.


2013/2/26 Norman Geist <>

Hi Siri,


to help you we could use some information about the hardware you use.
Approximating you use linux, please supply the output of the following


1. cat /proc/cpuinfo

2. lspci


This should be enough for the beginning.


PS: If not using linux, please give otherwise information about the hardware
you use.


Norman Geist.


Von: [] Im Auftrag
von Siri Søndergaard
Gesendet: Dienstag, 26. Februar 2013 01:00
Betreff: namd-l: LES very slow




I'm trying to run LES on a system of ~30.000 atoms. I'm using 20 copies of
each of two dyes attached to DNA. The problem is when I extend the
simulation to more than one cpu the scaling does not increase accordingly.
An increase from one to 12 cpus only gives a decrease in simulation time
from ~9 days to ~4 days pr. ns. Does anybody know how to solve this?


Best regards, Siri


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