VMD-L Mailing List

From: Karsten Suhre (karsten.suhre_at_igs.cnrs-mrs.fr)
Date: Fri Apr 08 2005 - 07:34:04 CDT

Hi John,

thank you very much for the suggestions (and of course for VMD).

Kind regards,

Karsten.

On Wednesday 06 April 2005 23:01, John Stone wrote:
> Hi,
> One thing to be aware of is that PCI-X (not express, just "X") is
> a _significantly_ slower interconnect than AGP or PCI-Express. If you're
> using several 3-D video cards at once in such a machine, unless each of
> the video cards is in a slot that's part of a _separate_ PCI-X bus, you'll
> completely swamp the bus with graphics I/O which will bring the machine
> to its knees. High-end workstation machines like Sun and SGI boxes
> typically use several separate PCI busses, so this issue is resolved on
> the big machines, but you'll have to look VERY carefully at the design
> of PC machines to verify that they would be usable for multi-headed
> PCI-X-based graphics displays. The situation should improve dramatically
> if/when we start seeing new machines with multiple PCI-Express slots for
> graphics boards. There are already a few such motherboards, currently
> tailored towards the NVidia multi-board "SLI" configuration, those are
> what I'd probably keep an eye on in the short-term. Longer term I expect
> the workstation vendors to offer big multi-headed machines based on
> Opterons etc.
>
> Regarding CPU choice, I definitely recommend the new 64-bit CPUs for
> VMD.... There's NO reason not to buy a 64-bit processor at this point. If
> you're worried about backwards compatibility with software, you can run a
> 32-bit OS until you're comfortable going full 64-bit. Our entire research
> lab now consists of a mix of 64-bit Sun Opterons running Linux and Sun
> Sparc machines running Solaris, which are the machines we do our
> visualization on.
>
> For other programs like BLAST or NAMD, the choice is less clear.
> In the case of NAMD, the main interest is speed. NAMD doesn't use
> much memory for normal simulations, so 64-bit CPUs aren't as big of an
> advantage as they are for VMD. For BLAST I assume 64-bit would be an
> advantage due to the increased word size and resultant increase in
> pattern matching speed per clock cycle, and max process RAM use,
> but you'd need to run the 64-bit version of course.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 06, 2005 at 03:39:19PM -0500, Sabuj Pattanayek wrote:
> > Hi,
> >
> > Karsten Suhre wrote:
> > > Ideally, I would be looking for a 4-processor board, but it seems
> > > there is no such with AGP or PCI-Express support (correct?).
> >
> > You can get 4 cpu opteron (pogolinux, tyan, arima, hpc systems)
> > racks/boards or 8 cpu opteron racks (pogolinux, arima, armari, hpc
> > systems, etc) all with pci-x slots (64 bit pci this is not pci-express).
> >
> > The pci-x slots can be used with *multiple* nvidia quadro 600 pci cards
> > which have stereo support (since pci-x slots are backwards compatible
> > with pci). You can compare its specviewperf pro-e/ugs/3dsmax
> > specifications / performance with other nvidia quadro video cards on
> > their website.
> >
> > I've never seen or heard of anyone using such a configuration for a
> > visualization machine but it doesn't mean it can't be done.
> >
> > > How about the processor - is a 64-bit Opteron a good choice? Or would
> > > you stick to 32 bit for compatibility reasons?
> >
> > You can always use a 32 bit chroot for linux applications that are
> > distributed in binary only format and that don't run in a 64-bit
> > environment.
> >
> > Hope that helps,
> > Sabuj Pattanayek 

-- 
Karsten Suhre                  
Charge de Recherche CNRS (Research Scientist)  
Information Genomique & Structurale       
UPR CNRS 2589
31, chemin Joseph Aiguier            
F-13402 Marseille Cedex 20
Tel: ++33.4.91.16.46.04             
Sec: ++33.4.91.16.45.48             
Fax: ++33.4.91.16.45.49             
mailto:Karsten.Suhre_at_igs.cnrs-mrs.fr      
http://igs-server.cnrs-mrs.fr/~suhre