Re: improving parallel on mac cluster

From: yu275197_at_yorku.ca
Date: Tue Feb 10 2004 - 16:47:34 CST

Hi Brian
You are right. I don't think it's my network because i loose efficiency after
the third machine. Do you know of any other reason why my simulation won't run
any faster. It's very frustruating that i can't take advatage of the 100 plus
systems i have here.

Cheers
Min

Quoting Brian Bennion <brian_at_youkai.llnl.gov>:
> 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.
>
> Brian
>
>
>
> On Mon, 9 Feb 2004 yu275197_at_yorku.ca 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 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>
>

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