Re: Namd benchmark problem

From: Axel Kohlmeyer (
Date: Sat Oct 24 2009 - 11:30:45 CDT

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 input does just a few hundred steps. any benchmark
that would need 4 days to complete is very impractical.

> 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.


> Thanks

Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.

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