I am attacking the problem from another side, directly from within the OS itself:
#lspi -vvvv
tells that the link speed (= link status) "LnkSta" is at 5Gb/s, no matter whether the system is at number crunching or not. I.e., my system is at PCIe 2.0. This might explain why upgrading from sandy bridge to ivy bridge gave no speed gain of molecular dynamics. PCIe 3.0 was not achieved.
As far as I could investigate, nvidia suggests to either:
(1) Modify /etc/modprobe.d/local.conf (which does not exist on jessie) or create a new
/etc/modprobe.d/nvidia.conf, adding to that
1. options nvidia NVreg_EnablePCIeGen3=1
Actually, on my jessie, nvidia.conf reads
alias nvidia nvidia-current
remove nvidia-current rm mod nvidia
Some guys found that useless, even when both grub-efi and initramfs are edited accordingly, so that nvidia offered a different move, updating the kernel boot string, by appending this:
1. options nvidia NVreg_EnablePCIeGen3=1
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I did nothing, as I hope that the best adaptation to jessie may be suggested by those who know the OS better than me.
The kind of information about links includes:
LnkSta: the actual speed
LnkCap: the capacity of the specific port, as far as I can understand.
LnkCtl: ??
One could also run
#lspci -vt
to determine the bus where the GPU card is located, then running
# lspci -vv -s ##
where "##" is the location.
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So, it is a tricky matter, but perhaps not so much when one knows where to put the hands. At any event, being unable to go to 8GT/s, as from PCIe 3.0, means loosing time and energy (=money and pollution), at least when the GPUs are used for long number crunching.
I'll continue investigating. The above seems to be promising. Hope to get help.