[Beowulf] visualization machine

Franz Marini franz.marini at mi.infn.it
Mon Mar 31 13:40:30 PDT 2008

On Mon, 2008-03-31 at 01:17 +1100, Andrew Robbie (GMail) wrote:
> Just be aware that most of the machines designed to be number
> crunchers
> have shortcomings in board layout or bus design that make them suck
> for
> visualization.
> Not that many that will be happy with 8GB for starters. So few
> machines are
> actually ever populated with big dimms that you almost always get
> issues.
> So you end up going for machines with lots of ram slots, ecc support
> etc, which
> is all good. These are almost always at least dual socket. But many of
> those
> motherboards aren't designed to take a 16x PCIe graphics card and only
> have
> PCIe 8x buses. Also, graphics cards have an extra retaining lug which
> extends further than the PCIe slot; this is commonly blocked on server
> motherboards by some capacitor.

> High end graphics cards always take up two slots and require
> additional power; on
> the Quadro 5600 and other cards this connector enters from the top not
> the end,
> hence making it impossible to fit them in a 3U case. 

> Oh yeah -- don't think about
> one of these for under your desk unless you want to wear earmuffs in
> the office.

Only if you don't know how to choose your components.

Right now, I have (under my desk) a box with the following specs:

- Cooler Master Cosmos 1000 case
- Supermicro X7DAE+ motherboard
- 2 x Intel Xeon E5345
- Asus Extreme N8800 GTX
- 3 x WD Raptor 150GB
- 1 x WD Caviar RE2 400GB 16MB SATA-II
- 4 x Kingston KVR667D2D4F5K2/4G (2 x 2GB FB-DIMM each, for a total of
- Corsair HX620W

This is barely audible. The case has sound dampening foam on the side
panels, and silent 12cm fans to cool the components. Moreover, both the
Xeons fans and the 8800GTX one are quite quiet. The HDs are mounted on
vibration dampening staffs, with rubber grommets, this helps keeping the
sound level low, too.

It *is* possible to build a quiet workstation powerhouse. You just have
to carefully choose your components.

And by the way, that motherboard has a 16x PCIe slot. As do most
workstation-class motherboards from Supermicro. I guess you're confusing
workstation motherboards with server ones.

> Depends -- is performance critical *now*? If so, buy the fastest
> Quadro. If you want
> to maximize performance over time, just upgrade the graphics card
> every six months
> with the sweet spot on the price/performance curve. Quadros are the
> first low-yield
> parts from the fab; the same chips, with slightly slower/cheaper
> memory hierarchy,
> become mass market later.

Actually, NVidia usually puts out the "gaming" parts first, and then
follows with the Quadro class. The only difference between the two that
I can recall are the (usually) different cooling solution and hardware
support for antialiased points and lines, OpenGL logic operations,
multiple clip regions, accelerated clip planes and overlay planes.
Unless you're doing heavy (and I mean *heavy*) CAD/CAM/CAE, most of
these things won't matter to you (sure, they can result in slightly
higher speed in VMD, but not so much). The other differences (the bigger
ones) lie in the drivers, which have specific application optimizations
(for, e.g., Maya, Autocad, Softimage, Avid, etc., almost nothing, as far
as I know, for scientific applications). The Quadro FX 4600 for example
uses a G80GL chip, which is a slightly modified G80 chip (the one in the
8800 GTX). In fact, I'm quite sure it's the same chip (maybe from a
better bin), with the hardware support for the operations I mentioned
before enabled.

Should there be some engineer from NVidia reading the list, and should I
be wrong somewhere, please feel free to correct me (but spare me the
marketing crap, I said engineer, no marketing people is allowed in the
discussion ;) :D).

I use the 8800GTX for VMD, Chimera, and in-house developed applications,
and it works like a charm.


Franz Marini
Prof. R. A. Broglia Theoretical Physics of Nuclei,
      Atomic Clusters and Proteins Research Group
Dept. of Physics, University of Milan, Italy.
email : franz.marini at mi.infn.it
phone : +39 02 50317226

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