AMBER Archive (2002)

Subject: Re: question

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Nov 15 2002 - 21:22:13 CST

Hello dr. Case,

Thank you for your message. I am not sure why you are saying that amber
does not scale well after 32/64 processors. How here are some data's from
a minimization run as function of the number of processors run an origin
2000 machine with 512 processors.

#CPU's wall-time #minimization steps CPU-time
--------------------------------------------------------
16 8hours 375 127:38
64 2h:40min 500 169:11
128 1h:21min 500 170:49

So indeed the total CPU time is the same for the 64 and 128 processors
(which is what I think one would expect) however the real time run was
half if the number of processors was doubled. To me this is a pretty good
scaling.

I did not do the same test for dynamics but from the results of the
minimization procedure it seems worth increasing the maximum number of
processors allowed in amber.

Please let me know what you think. Thank you once again,
Ioana

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On Fri, 15 Nov 2002, David A. Case wrote:

> On Fri, Nov 15, 2002, Ioana Cozmuta wrote:
> >
> > Maybe this is a naive question: why is the maximum number of processors
> > that one can use in amber limited to 128?
>
> Even on the most expensive computers, amber scales poorly after about
> 32 (or certainly 64) processors.
>
> > Is it trivial to modify this limit?
>
> Should not be hard....dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
>
>