I wrote a kernel driver for the BBB timer hardware. It produces pps events for 
things like ntpd to consume. The source for it is at 
https://github.com/ddrown/pps-gmtimer

A side effect of this driver is it measures the interrupt latency and jitter on 
the BBB hardware. The attached file interrupt-latency.png contains an interrupt 
latency histogram and cumulative distribution function. This interrupt latency 
should be similar to what the pps-gpio driver experiences on this hardware. The 
difference is the timer hardware driver can remove the effects of the interrupt 
latency. 

The graphs of offset over 7 days worth of samples don't show a huge difference. 
The *-timer.png file is from pps-gmtimer and the *-gpio.png file is from 
pps-gpio.  The stddev of the offsets are 244ns from the gpio run and 143ns from 
the timer run. 

The BBB hardware supports hardware IEEE1588/PTP timestamps, so people might be 
interested in that as well. The driver for it is already in Linux, but not 
enabled in the default BBB kernel config. 

Let me know if you have any questions. 

Unrelated to the PPS driver: all the feedback on the software frequency 
temperature compensation has been useful. 90% of the time, the local clock is 
within 173ppb. 98% of the time, it's within 218ppb. I think I can narrow this 
range even further with a temperature rate of change variable. All the graphs 
are at http://dan.drown.org/bbb/latest/
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