By configuring 8 GT/s PCIE 3.0 for the Nvidia driver, I got a 10% speedup on Gromacs md_run. 45 ns/day -> 50 ns/day (1AKI protein).
This posting is just informational, my findings on how to do this, so others can possibly also exploit this if they desire so. There is no question that i'm asking here. Config: Intel Ivytown (Ivybridge family processor (i7-4960X). Nvidia GeForce GTX670. Single GPU card installed. ASUS X79 Deluxe Motherboard. Single socket system. Fedora 19 Nvidia driver: 331.20 Application: md_run Gromacs 4.6.4 1AKI protein from tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html To measure PCIe Link Speed, do either of: 1. nvidia-settings (from cmd-line, this is part of the Nvidia drivers package). Look under PowerMizer to see what PCIe Link Speed is presently used (will change under load). run md_run to generate a load. If 8GT/s is not enabled then expect to see 5 GT/s during an md_run. 2. lspci -vv | grep -i nvidia Use the device PCI reg address to get details (needs root privileges): lspci -vv -s 01:00.0 You would see something like: LnkCap: Port #0, Speed 8GT/s, Width x16 => PCIE Capability is set to 8 GT/s here (this is after applying below settings). LnkSta: Speed 2.5GT/s, Width x16 => PCIE Link State presently low speed as md_run is not running (to save power). If the capability shows 5 GT/s (or speed is just 5 GT/s under md_run load) then you can try below setting to elevate to 8 GT/s. I'm using the parameter NVreg_EnablePCIeGen3=1 as provided by the Nvidia driver. 1. I tried it first during a single Fedora boot and ran md_run (a 30 mins wall-time example) to determine whether it's stable. During boot, when the boot options show up for the images: Press 'e' to edit the cmd line. Add to the cmd line: nvidia.NVreg_EnablePCIeGen3=1 Then 'Ctrl-X' to boot with the cmd-line (note: this option will be forgotten on the next boot). Run md_run or some other tests that heavily exercise the graphics card to gauge the stability. 2. To make the change permanent (as root): edit /etc/default/grub and add to the GRUB_CMDLINE_LINUX option: nvidia.NVreg_EnablePCIeGen3=1 grub2-mkconfig -o /boot/grub2/grub.cfg Now reboot and the setting will take effect from then onwards (for every boot). FYI: Note that I'm using an Intel i7-4960X (Ivybridge family: 15MB, 6 Cores). It seems to support PCIE 3.0 with 8 GT/s (I'm not speaking for Intel). Disclaimer: Nvidia does not guarantee link/system stability when doing this. I don't either. It works for me. Your mileage may vary. I only have a single GPU card on the PCIE bus. -- Henk Neefs Gromacs User Computer Architect (Ivytown chip architect at Intel). Not speaking for Intel, these are all personal opinions. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.