From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 25 2009 - 15:48:23 CDT
On Sun, 2009-10-25 at 12:16 +0530, Sangamesh B wrote:
> Dear Sir,
[...]
> 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
please polish your reading glasses. this graph does not at all say so.
please check out what which lines mean. the left y-axis shows the
strong scaling performance, by multiplying the time per time step with
the number of cores, i.e. you get a horizontal line with ideal scaling.
the diagonal lines are to show you the throughput by indicating how
long it would take to generate one nanosecond of trajectory.
> From this graph I understood - 1 week for 4 processor job, 4 days for
> 8 processor job etc
to produce _1 nanosecond_ of data, not 500 femtoseconds.
> 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.
if you cannot scale beyond 24 cores, then you either must be
doing something wrong, or there is something not working well
with your hardware.
>
> > 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?
thousands. there are some tricks required. you may need a special
hardware with very low latency communication and little OS jitter.
check out the namd wiki for details.
cheers,
axel.
> axel.
>
> > Thanks
> >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
-- 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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