Quoting Paul <tic-...@bodosom.net>:
Using a PRU seems like overkill if all you want from the BBB is NTP.  The
standard pps-gpio should move the system clock precision below
system/network jitter (.5 to 1 microsecond).  The next step is using a
timer (TIMER4) which should get you into .1 microsecond offsets.

As a note to people wanting to use the timer hardware on the BBB - I have a driver for it at https://github.com/ddrown/pps-gmtimer

I wrote up the results in using it at http://blog.dan.drown.org/beaglebone-black-timer-capture-driver/

The summary of it is:

pps-gpio - 50% of the time local clock offset within +/- 0.07us, 98% within +/- 0.61us

pps-gmtimer - 50% of the time local clock offset within +/- 0.04us, 98% within +/- 0.43us

Also, if you're using pps-gpio, you might want to disable cpufreq and force your processor to 1GHz. It'll help with interrupt latency and jitter.

cpufreq ondemand, 300MHz-1GHz - http://dan.drown.org/bbb/run9/interrupt-latency.png
98% of interrupts handled 12.92us-23.21us after the event happened.

cpufreq forced 1GHz - http://dan.drown.org/bbb/run8/interrupt-latency.png
98% of interrupts handled 6.04us-8.58us after the event happened.
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