Actually the NAMD double precision thing is not entirely true. I also
thought that initially, but what in fact happens is that the GPU performs
all the individiaul non-bonded force calculations in single precision, and
then the summation is done in double precision.
Personally I think there are advantages and disadvantages to both NAMD and
AMBER, but I suppose it depends largely on what questions you are trying to
answer. In either case though, a fast CPU with a GTX580 will produce
excellent results for a moderate price.
~Aron
On Tue, Jan 10, 2012 at 6:29 PM, filip fratev <filipfratev.yahoo.com> wrote:
> >For instance quad core Xenon2.66Ghz and GTX580 3GB.....
> I mean a pair of GTX580:)
>
>
> ________________________________
> From: filip fratev <filipfratev.yahoo.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wednesday, January 11, 2012 1:24 AM
> Subject: Re: [AMBER] i7 extreme for Amber GPU computing?
>
> Hi Raik,
> i7 will be much
> better than some middle class Xenon's. The speed of the CPU, and of course
> many
> other factors, are important for the GPU scale. For instance quad core
> Xenon
> 2.66Ghz and GTX580 3GB perform 48ns/day on JAC against more than 57ns/day
> with i72600K.4.6Ghz.
> That's the reality..
> If I am not
> wrong NAMD uses only double precision, thus Tesla will be better but why to
> spend money when you can use Amber. Moreover the NAMD GPU version is
> somewhat
> basic and Amber GPU is much much better!
>
> My advice at the
> moment is i7+few GTX580 3GB. In fact a good configuration is listed on the
> Amber website:
> http://ambermd.org/gpus/
> Paragraph: Building
> your own System
>
> Keep in mined
> that Kepler will be realized after few months.
>
> All the best
>
>
> ________________________________
> From: Aron Broom <broomsday.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Wednesday, January 11, 2012 12:39 AM
> Subject: Re: [AMBER] i7 extreme for Amber GPU computing?
>
> I've used the M2070 cards with the Xeon 6-core processors, and also the
> GTX570/580 with 2-core intel or 6-core AMD. If you are wanting to
> potentially run NAMD also, then I would highly suggest going with the
> 6-core CPU (I didn't see an advantage for the intel over the AMD in my
> benchmarks), but if you are just doing AMBER then keep in mind that AMBER
> under GPU acceleration only uses 1 cpu per gpu.
>
> Also, you can see from the AMBER benchmarks page that additional GPUs don't
> scale all that well past 2 GPUs. In particular you need to consider your
> motherboard, if you have a single 16x and putting two cards in reduces each
> to 8x, then it really isn't worth your money to put two cards in. I'd
> suggest either making sure you get a motherboard with 2 separate 16x slots,
> or just build multiple cheaper systems (unless there is some massive system
> you need to simulate).
>
> In terms of the expensive M2070 cards versus the GTX570 or 580 (~1/5 the
> price), the GTX cards are faster because the memory clocks are actually
> higher. The main draw-back is memory. For NAMD this isn't much of an
> issue as its memory usage is rather small on the GPU, but for AMBER you
> want to make sure you have enough memory. You can buy 3GB GTX580 cards
> though. There are some guidelines on the amber page concerning how much
> memory will allow you to simulate a certain system size, so unless you need
> more than 3GB (the M2070s have 6GB for instance) then I would save the cash
> and go for the cheaper and faster GTX580. Of course there is also the ECC
> on the M2070, but (and if others have a different opinion I'd love to hear
> it) if you are talking about molecular dynamics only, then the occasional
> extremely rare error isn't going to be an issue at all.
>
> That's my two cents,
>
> ~Aron
>
> On Tue, Jan 10, 2012 at 3:34 PM, Raik Grünberg <raik.gruenberg.gmail.com
> >wrote:
>
> > Hi there,
> >
> > I am trying to configure a new desktop / workstation for GPU
> > accelerated Amber simulations. The top-notch high-end configuration
> > seems to be based on dual Xeon with two or four NVidia Tesla. Does
> > anyone have experience with a system built around the (cheaper but
> > supposedly faster) Intel i7 extreme processor?
> >
> > Thanks in advance!
> > Raik
> >
> > --
> > ___________________________________
> > Raik Grünberg
> > http://www.raiks.de/contact.html
> > ___________________________________
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Tue Jan 10 2012 - 21:30:02 PST
