Quoting Jakob Bohm <jb-use...@wisemo.com>:
1. Do you know if anyone has tried using the real-time coprocessors on
  the BBB to more accurately track the PPS signal?

I have a driver for the BBB's input capture timer hardware here: https://github.com/ddrown/pps-gmtimer

There's a bug in the recent BBB kernels (4.4.17-ti) that I haven't been able to track down. When you enable timer2, the ethernet hardware loses link. So this driver only works on the older 3.8.x-bone kernels.

The results were 30%-50% better offsets with pps-gmtimer vs pps-gpio. Both numbers are dwarfed by the network interface jitter for NTP clients (which is in the 15us-20us range for my environment).

There's some more info here (including a histogram comparing pps-gpio vs pps-gmtimer): https://blog.dan.drown.org/beaglebone-black-timer-capture-driver/


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