While working on PTP (Precision Time Protocol, IEEE 1588) with some Beaglebone Black boards, I needed a way of comparing the time on different boards with high resolution (10ns). I saw that there is no currently a PPS generator that uses GPIO pins. There is only an option to use a parallel port.
This was a good excuse to write a kernel driver. I started by modifying the parallel port PPS generator implemented in the kernel to use a GPIO pin instead. You can use this module on other boards providing you modify your device tree file accordingly. This module has been tested with kernel 3.15.3.
The source is at: https://github.com/jsln/pps-gen-gpio