Fwd: GPU workstation build

From: Francesco Pietra (francesco.pietra_at_accademialucchese.it)
Date: Tue Aug 21 2012 - 08:44:09 CDT

---------- Forwarded message ----------
From: Francesco Pietra <francesco.pietra_at_accademialucchese.it>
Date: Tue, Aug 21, 2012 at 3:30 PM
Subject: Re: namd-l: GPU workstation build
To: Norman Geist <norman.geist_at_uni-greifswald.de>

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.


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=600000215).
> 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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