Murat and Abd,
What you are observing is just simply that the application (AMBER)
doesn't scale in the environment that you tried. This can be due to
many reasons, including: libraries, interconnect, memory, etc..
'top' may give some indication, but it will not give the full picture
(eg: is the CPU stalling, or is the interconnect is stalling?)
You need to run a profiler on the job to get a better idea of the root
of scalability issue.
Kenneth Tan
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News: OptimaNumerics Enhances Performance on SGI Altix Supercomputers
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C. J. Kenneth Tan, Ph.D.
OptimaNumerics Ltd. Telephone: +44 798 941 7838
E-mail: cjtan.OptimaNumerics.com Telephone: +44 871 504 3328
Web: http://www.OptimaNumerics.com Facsimile: +44 289 066 3015
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On 2005-05-13 23:42 -0700 Abd Ghani Abd Aziz (ghaniee.yahoo.com) wrote:
> Date: Fri, 13 May 2005 23:42:49 -0700 (PDT)
> From: Abd Ghani Abd Aziz <ghaniee.yahoo.com>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: Re: AMBER: maximum number of processors
>
> Dear MURAT CETINKAYA,
>
> Dear MURAT CETINKAYA,
>
> I think that your connection already achieved maximum
> peak. you can rsh to your nodes and do "top" to see
> whether your sander run using 100% of your cpu speed.
>
> Abd Ghani Abd Aziz
> Unievrsiti Putra Malaysia
>
> --- MURAT CETINKAYA <cetinkayam.psu.edu> wrote:
> > Hi Amber users,
> >
> > I normally run sander with 16 nodes (dual processor
> > in each) and I know the
> > speed of the run. This time I tried using 32 nodes,
> > but the speed seems just
> > the same as 16 node runs. The system I simulate is
> > completely the same as
> > before. Is there a limit for the number of nodes
> > that AMBER can use? Or is
> > there another point I cannot figure out?
> >
> > Thanks.
> >
> > PS: I use amber7 and all nodes are functioning well.
> > Murat CETINKAYA
> > Biomolecular Materials Lab,
> > Dept. of Engr. Science and Mechanics,
> > The Pennsylvania State University,
> > University Park, PA 16802
> > office: (814) 863 9967
> > web: www.personal.psu.edu/muc176
> >
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> >
>
>
>
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Received on Sat May 14 2005 - 16:53:00 PDT
