From: Lane, William (William.Lane_at_cshs.org)
Date: Fri Nov 15 2013 - 02:22:53 CST
Francesco,
On my x79 motherboard (an Asrock x79 Extreme 4) in the UEFI BIOS
settings advanced --> North Bridge Configuration there are options for
PCIe 1 Link Speed, PCIe 2 Link Speed and PCIe 3 Link Speed. They all
default to Gen2 or PCIe 2.0. The BIOS won't auto-detect a PCIe 3.0
capable graphics adapter.
I do remember Nvidia had a blurb about enabling PCIe 3.0 on LGA2011
motherboards on Windows. It stated that the default behavior of the
drivers was to disable PCIe 3.0. Nvidia had a fix to override this behavior --
at least on Windows.
William
________________________________
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 11:46 PM
To: NAMD
Subject: Fwd: RE: namd-l: PCIexpress 3.0 for MD with NAMD on GPUs
sorry, i forgot the forum
---------- Forwarded message ----------
From: "Francesco Pietra" <chiendarret_at_gmail.com<mailto: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<mailto:William.Lane_at_cshs.org>>
Cc:
William:
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.
thanks
francesco pietra
On Nov 12, 2013 12:42 AM, "Lane, William" <William.Lane_at_cshs.org<mailto: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<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of Francesco Pietra [chiendarret_at_gmail.com<mailto: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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