[gmx-users] Updating GTX670 PCIE speed from 5GT/s to 8GT/s resulted in about 10% speedup of md_run.

Henk Neefs henk.neefs at gmail.com
Wed Dec 4 08:29:28 CET 2013

Below information might be of interest to the Gromacs
development/optimization team.

What can we derive from the 10% md_run speedup when PCIE3.0 speed increases
from 5GT/s->8GT/s?

A 60% PCIE speed increase results in a 10% run time reduction. 
Hence about 10/60=17% of the run time gets spent in (non-overlapping) PCIE
bus communication for this particular configuration and for this particular
simulated molecular system.
I'm refering to the "non-overlapping" part as this is the part that is not
hidden by (not overlapped with) calculations.

So changing the PCIE speed provides a (non-user-friendly) knob to the
gromacs developers to estimate the part of the run time that is determined
by the (non-overlapping) PCIE bus communication.

Not sure whether the Nvidia CUDA profiling environment provides a better way
to quantify this. In case there isn't a better way, above method is a poor
man's flow (for which you likely need root access) to provide this
Henk Neefs
Gromacs user

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