Re: Namd benchmark problem

From: Bernardo Sosa Padilla Araujo (bernardospa_at_gmail.com)
Date: Mon Oct 26 2009 - 00:10:25 CDT

Hey All,

I have a question regarding the benchmark.
NAMD scalability might be significantly different for two different systems.
Right? If it is so, why would be important to run the benchmark apoa1 if you
are going to be working with a different system? It is just to compare to
the performance that other people get with NAMD? Then if that is the case,
for any system I would have to run some kind of benchmark to see how
scalable is NAMD in that particular case. Right?
I hope someone can answer my questions.
Thanks in advance.

Best

Bernardo

2009/10/25 Axel Kohlmeyer <akohlmey_at_gmail.com>

> 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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