Re: improving parallel on mac cluster

From: Brian Bennion (
Date: Mon Feb 09 2004 - 12:05:09 CST

Hello Min,

Without more information on the system size I would only be guessing.
With that caveat. I don't think the ethernet connection is going to be a
problem (yet) unless it is less than 10MBs which I doubt. I have a 16 cpu
cluster running on top of a 100MBs network and for the systems I run
(~45,000 atoms) I lose effeciency with more than 8 cpus due to the
network communications. I use 11A cutoffs with switching and margins set
to zero.


 On Mon, 9 Feb 2004 wrote:

> I've managed to run my simulation in parallel on a couple of G5 mac computers
> but i've noticed that my performance does not increase after three nodes. I am
> guessing the possible reason for this to be:
> 1. simulation is bottlenecked by the ethernet connection
> 2. my molecule is not configured properly to take advantage of mutiple sys...
> i have my cutoff set to a large number(essentially no cutoff) but if i change
> it to smaller number with switching on the simulation seems to be distributed
> between the systems better.
> 3. patch size...i think this is related to reason #2. because number of
> patches namd creates seems to be dependent of the conf file and simulation
> speed seems to be dependent on the number of patches.
> could anyone provide some insight into my situation.
> Cheers
> min

**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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