Re: Namd benchmark problem

From: Sangamesh B (forum.san_at_gmail.com)
Date: Sun Oct 25 2009 - 01:46:29 CDT

Dear Sir,

On Sat, Oct 24, 2009 at 10:00 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, 2009-10-24 at 12:42 +0530, Sangamesh B wrote:
> >
> > Dear Namd users,
> >
> > I've installed NAMD on a Linux HPC cluster by both ways (1)
> > Downloading binaries (2) By compiling the source with Open MPI.
> >
> > To test the scaling of Namd, I downloaded the standard benchmark apoa1
> > from NAMD website. After doing the benchmark I found that its taking
> > very little time 3-4 minutes to complete(with 4 cores), but on the
> > website its shown its taking 4days to complete.
>
> please explain where it says that it takes this long?
>
> The graph shown on the following webpage

http://www.ks.uiuc.edu/Research/namd/performance.html

>From this graph I understood - 1 week for 4 processor job, 4 days for 8
processor job etc

> the input does just a few hundred steps. any benchmark
> that would need 4 days to complete is very impractical.
>
> Also the graph says, namd scales upto 256 cores. But in may case, its
taking very less time and not scaling beyond 24 cores.

> > May I know what mistake am doing here?
>
> you are must be misreading something.
>
> > On the website, there is no info provided about how to do the
> > benchmark.
>
> you just run it like any other namd input.
>
> for a bigger problem size namd input, upto what number of cores will NAMD
scale?

> axel.
>
> > Thanks
> >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>

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