AW: GPU workstation build

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 21 2012 - 09:33:48 CDT

Which settings for fullelectfrequency?

Norman Geist.

> -----Urspr√ľngliche Nachricht-----
> Von: chiendarret_at_gmail.com [mailto:chiendarret_at_gmail.com] Im Auftrag
> von Francesco Pietra
> Gesendet: Dienstag, 21. August 2012 15:30
> An: Norman Geist
> Betreff: Re: namd-l: GPU workstation build
>
> I believe to have recently reported on a very raw NAMD-CUDA benchmark
> for 2xGTX680 in comparison to 2xGTX580 for 200,000 atoms. What I did
> in two weeks with 580 was done in one with 680, despite pcie 2.0 of
> the gigabyte X79-UD3. Currently I am at 400,000 atoms: what I did in
> three weeks with 580 is now done in one with 680. With less energy
> consumption and heat (not requiring a conditioned room).
>
> Should I have waited for consumer pcie 3.0, a lot of money and
> /time/money would have been wasted.
>
> What now I hope is a farewell to NVIDIA-CUDA for OPENCL and AMD less
> expensive material.
>
> chiendarret
>
> On Tue, Aug 21, 2012 at 8:22 AM, Norman Geist
> <norman.geist_at_uni-greifswald.de> wrote:
> > Hi,
> >
> >
> >
> > as I see it, the 680s have 1/3 less clock rate, but therefore 3x more
> CUDA
> > cores. So for one GPU they should be faster by a factor of two.
> >
> >
> >
> > In HPC the required bandwidth of any link usually scales with the
> absolute
> > computing power of the link using/sharing units (neglecting latency
> here).
> > That means, as the 680s are two times faster, they will scale worse
> than the
> > 580s with the same bandwidth. And as we all know, the PCIE bandwidth
> is
> > already a bottleneck for namd and GPUs with PCIE2. Because of that
> reasons,
> > you should go for the PCIE3 when going with the Kepler and make sure
> you
> > have enough full occupied x16 slots with PCIE3 bandwidth and also
> keep an
> > eye on the power supply, one of these GPUs will take 195W I guess.
> >
> >
> >
> > Regards
> >
> >
> >
> > Norman Geist.
> >
> >
> >
> > Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag
> > von Aron Broom
> > Gesendet: Montag, 20. August 2012 18:21
> > An: Blake Mertz
> > Cc: namd-l_at_ks.uiuc.edu
> > Betreff: Re: namd-l: GPU workstation build
> >
> >
> >
> > In terms of the bandwidth and the integrated PCI-e bridge, I think
> you might
> > get a sense from the motherboard manual, as they will generally say
> > something like "one at 16x or two at 8x each". I guess ideally you
> want to
> > be able to tos 4 cards in there and get 16x for all of them.
> >
> > I'm also quite interested in the performance for the GTX680s. One
> thing to
> > note, although I'm not 100% certain of this, so something can correct
> me, I
> > think that without using the new PCI-e 3.0 (which the Keplers are
> capable
> > of) you'll actually have lower bandwidth with a 680 compared with a
> 580, and
> > you only get back to 580 bandwidth levels when you are using the 3.0.
> >
> > ~Aron
> >
> > On Mon, Aug 20, 2012 at 11:41 AM, Blake Mertz
> <blake.mertz_at_mail.wvu.edu>
> > wrote:
> >
> > Hello,
> >
> > I'm in the process of putting together a GPU workstation based off of
> > a Tyan S8232GM4NR motherboard -- it's a dual-socket AMD G34, with 4
> > PCI-e Gen2.0 slots that are spec'd to run at 16x
> >
> (http://tyan.com/product_SKU_spec.aspx?ProductType=MB&pid=696&SKU=60000
> 0215).
> > My two biggest concerns are:
> >
> > 1) the bandwidth on my motherboard with respect to the GPUs, and
> >
> > 2) which commercial Nvidia GPUs I should go with.
> >
> > From what I can tell by Axel Kohlmeyer's response to Matt Roark's
> > inquiry
> > (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-
> 2012/3416.html),
> > you have to look out for motherboards with integrated "PCIe bridges",
> > which I haven't been able to confirm on the S8232, either in the
> > manual or from looking online. Does anyone have experience using this
> > board for namd?
> >
> > Also, I noticed Francesco Pietra has done some testing with GTX 680s
> > (which is what I happened to initially purchase), but I haven't seen
> > much else on namd-l discussing these cards. Has anyone else had a
> > chance to compare the 680 performance over the 580s? I've had a hard
> > time judging the advantages of the new Kepler architecture over
> Fermi,
> > especially in context of namd performance. Thanks for any help you
> can
> > give.
> >
> > Blake
> >
> > --
> > Assistant Professor
> > C. Eugene Bennett Department of Chemistry
> > West Virginia University
> >
> > "Life is not easy for any of us. But what of that? We must have
> > perseverance and above all confidence in ourselves. We must believe
> > that we are gifted for something and that this thing must be
> > attained." Marie Curie
> >
> > "Start by doing what's necessary; then do what's possible; and
> > suddenly you are doing the impossible." St. Francis of Assissi
> >
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo

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