Fwd: RE: PCIexpress 3.0 for MD with NAMD on GPUs

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Nov 12 2013 - 01:46:45 CST

sorry, i forgot the forum
---------- Forwarded message ----------
From: "Francesco Pietra" <chiendarret_at_gmail.com>
Date: Nov 12, 2013 6:45 AM
Subject: RE: namd-l: PCIexpress 3.0 for MD with NAMD on GPUs
To: "Lane, William" <William.Lane_at_cshs.org>

This is Gigabyte X79-UD3, BIOS F16 (the last one available), i7-4930K

BIOS frequencies are set to AUTO

BCLK 100
CPU clock ratio 34 (i.e., 3400GHx, no overclock)

I can't see any setting for PCIe, except in "advanced settings... CPU base
clock... Host/PCIe clock frequency, which is set to 100MHz. Don't see any
setting for PCIe 2.0 or 3.0, unless this requires to use manual settings.

Most unfortunately no one was able (here and on Debian amd64 forum) to
indicate which nVidia driver enables PCIe 3.0 (if at all, since it is well
known that nVidia is favoring Windows, Mac, and android at the detriment of
linux. They disregard that supercomputers are driven by linux and that
Windows has no journaling, and that both mac and android are what they
are). At any event, the nVidia driver 3.04.xx present on amd64 wheezy is
known to activate PCIe 2.0 only). I'll try with upgrading to jessie,
although for MD a stable system like wheezy is preferable.

francesco pietra
On Nov 12, 2013 12:42 AM, "Lane, William" <William.Lane_at_cshs.org> wrote:

> Did you switch the PCIe to 3.0 in the BIOS? It defaults to 2.0 on my
> motherboard.
> ------------------------------
> *From:* owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> Francesco Pietra [chiendarret_at_gmail.com]
> *Sent:* Monday, November 11, 2013 1:51 AM
> *To:* NAMD
> *Subject:* namd-l: PCIexpress 3.0 for MD with NAMD on GPUs
> Hello:
> Which version of the nvidia driver is needed to activate PCIexpress 3.0
> between the GPUs and RAM for MD with NAMD2.9 or NAMD2.10? As far as I can
> remember, nvidia deactivated PCIe 3.0 for linux from version 295.xx until
> at least 310.xx. Is that correct?
> With a PCIe 3.0 certified consumer motherboard, on replacing sandy bridge
> i7-3930 with ivy bridge i7-4930, with two GTX-680 cards, under nvidia
> 304.88, such as with Debian stable wheezy, PCIe was left to 2.0, instead of
> the expected 3.0. Even with a heavy job, half a million atoms, while
> replacing 1066MHz with 1866MHz RAM, speed increase was of only a few
> percent.
> I wonder whether nvidia 319.xx, available with Debian testing (jessie)
> could open the bottleneck between the GPUs and RAM.
> Thanks a lot for advice
> francesco pietra
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