Re: Fwd: suitable motherboards for both graphical visualization and NAMD-CUDA computation?

From: Biff Forbush (
Date: Wed Jan 20 2010 - 20:32:06 CST

Hi Petr,

> thanks for these useful notes. I might one have more question on that.
> When I see the P6X58D board, the closest PCx16 to the connectors is PCx16
> (x8 link). I do not know what that means. Do you think that in principle
> it can be used for the video, if the other two are used for computation?
    Simple answer yes. But (a) again I emphasize the fan problem having
two dual-slot gpu cards next to one another. (b) setting this up the
way you want will probably involve fiddling with video drivers/software,
etc. (c) I only know the little bit I read, but basically the x58
chipset on your board has 40 data transfer lanes that are divided
16/16/8 for the three connectors on your board, thus you can use a pci16
device in that end slot but it will only have 8 lanes of data transfer
-- my guess is that this will not be limiting for your video.
    Now that this comes up, I see that the lower cost P7P55D that I
have (I bought this as a general purpose desktop, not an MD machine --
it does not have the x58) only supports 1x_at_16, or 2x_at_8, so that my brief
tests with the gtx295s were actually only using 8 lanes per card instead
of 16. Interestingly, the benchmarks with this machine at 2.6GHz
compared well with the performance of the 2 gtx295s in the dual-Xeon
(with full 16 bit PCI) (allowing for the processor speed difference by
interpolating between 2 GHz and 3.3G Hz Xeon results) -- this indicates
that even for the gtx295 the PCI bus at 8 lanes is not limiting in


> I
> need a quality video on 30' monitor or so. It seems that a single (not
> dual) GPU would fit here, since the other two dual GPUs might have
> conflict with the connectors.
> Thanks again,
> Petr
> From: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Petr Kral, Assistant Professor
> Department of Chemistry M/C 111
> University of Illinois at Chicago
> 845 West Taylor Street, Chicago, IL 60607
> Tel: (312)-996-6318, FAX: (312)-996-0431
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ---------------------------- Original Message ----------------------------
> Subject: Fwd: namd-l: suitable motherboards for both graphical
> visualization and NAMD-CUDA computation?
> From: "Lela Vukovic" <>
> Date: Wed, January 20, 2010 5:32 pm
> To: "Petr Kral" <>
> --------------------------------------------------------------------------
> ---------- Forwarded message ----------
> From: Biff Forbush <>
> Date: 2010/1/20
> Subject: Re: namd-l: suitable motherboards for both graphical
> visualization and NAMD-CUDA computation?
> To: Lela Vukovic <>
> Копија:
> Hi Lela,
> In theory, yes. In practice you may have difficulty with the layout.
> The P6X58D is the latest and greatest (or one of them) from Asus. It
> supports 3x PCIE-x16 (not 4 as you suggest). Yes, of course it can
> use them for different things (display, CUDA), this is a driver and
> software issue but it should be just as easy on this motherboard as on
> any other.
> However, looking at the picture of the board there is a problem with
> slot placement if you plan to use the most powerful dual-slot gpus.
> If you try to use dual-slot gpus with fans on the side (as many of
> them are), you are not going to be able to get two of them in there
> without either (a) blocking the fan on one of them, not good, or (b)
> having the 2nd gpu over top of some of the connectors (maybe this is
> just a nuisance, but depending on the case, the second gpu fan may be
> right up against the bottom of the case). The P7P55 has slots placed
> so that it is easy to fit in two dual-slot gpus with no problem. With
> either board you are not going to get 3 dual-slot gpus in there unless
> cooling is on the edges of the cards or you use water cooling. I
> discussed the same problem with regard to a Tyan Xeon board last week
> ("NAMD-CUDA benchmarks, dual GTX295, dual Xeon Nehalem system"), and I
> also used the P7P55 easily with two gtx295's.
> Regards,
> Biff
> Lela Vukovic wrote:
>> Hello,
>> We would like to purchase a machine where we could do NAMD-CUDA
>> computation and fast graphical visualization simultaneously.
>> In particular, we want to use the ASUS P6X58D Premium motherboard in
>> this hybrid mode. We have seen that a different motherboard, ASUS
>> P7P55 WS Supercomputer motherboard, seems to support this hybrid mode,
>> where we assume that the first card is for visualization and the
>> others (up to 3) for CUDA calculations. My question is whether we can
>> have the hybrid option on the above P6X58D Premium motherboard too.
>> We would like to know whether ASUS P6X58D can be used for both
>> CUDA-computation and visualization simultaneously. Any other
>> suggestions would be appreciated as well.
>> Thank you,
>> Lela

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