AMBER Archive (2009)

Subject: Re: [AMBER] Use of Amber in distributed calculations

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Sat Jan 17 2009 - 08:01:36 CST

On Sat, Jan 17, 2009 at 07:48:42AM -0600, M. L. Dodson wrote:
> On Sat, Jan 17, 2009 at 10:33:55AM +0300, drugdesign wrote:
> > Dear Amber users, I am making a review on molecular dynamics software, which can be used for distributed calculations for the project like FOLDING_at_HOME.
> > I wonder whether there is Amber client version which can be used for the
> > distributed calculations like boinc or F_at_Home software?
> > Don't you by chance know some @home projects which use amber client for
> > molecular dynamics?
> >
> > Best regards,
> > Andrew
> >
>
> The Amber developers will probably have something to say about this,
> but this kind of parallelism won't work with Amber (at least as it is
> generally used). Folding_at_home works because each calculation
> "quantum" is almost completely independent. Only the final results
> need to be communicated back to a central location. The parallelism
> in Amber is MUCH, MUCH, MUCH tighter. Even a dedicated Gbit ethernet
> interconnect is not fast enough to get good scaling given the speed of
> modern "PC" computers. There has been an enormous amount of
> discussion on this list about this issue. Use the archive at the
> Amber web site to search for the threads.
>
> Bud Dodson
>
> PS, This situation is unfortunate for those of us that would like to
> use networks of cheap PC workstations to speed up our calculations.
> Others may have things to say about this, or know of special
> situations where distributed calculations DO speed things up using
> Amber. Obviously, I'm not aware of any.

Apologies for replying to myself. I may have misunderstood your
question. If you meant: "Are there projects similar to folding_at_home
that use Amber to do the standalone MD jobs?", again I would say no.
But this is not due to technical issues, rather the Amber license
might prohibit many from running such project software. If there were
enough interest, the developers of such s/w should contact the Amber
administration (again, see the web site).

Bud Dodson 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one

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