When you make your own NTP server, you probably spend a lot of time trying to get it as accurate and stable as possible. To get good results, you need to connect your server to a good time reference, like an atomic clock, GPS or a GPSDO to get the PPS (Pulse Per Second) to sync your server with the reference clock.
In both Linux and BSD, there is kernel support to slave the very inaccurate CPU clock crystal to the PPS signal, continually adjusting the frequency, because the crystals of computers continuously drift due to temperature and barometric pressure differences. So most of the work is to get a crappy crystal to behave. What if you just jumped over that step, so the CPU clock gets synchronized with the same lab reference that the PPS signal uses, using a SI5351C Clock Generator?
Read on to see a simple way of doing it and get an extremely accurate NTP server for under $200.
My primary NTP Stratum-1 server is available at ntp.jacken.se, but it is also in the .se pool of ntp.org. 
So I built a pulse extender, making the pulse around 250 milliseconds instead. And now the Raspberry Pi picks up the pulse without problems. Some GPSDO units can set the pulse width by programming the unit via a serial port, but I can’t find that feature on this unit (which is poorly documented and was OEM made for some other manufacturer), so I had to do it with hardware. So how does it look when crunching the numbers on it?
The last couple of weeks I’ve been busy building a