AW: LES very slow

From: Norman Geist (
Date: Tue Feb 26 2013 - 00:42:30 CST

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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