Gabs Ricalde is tracking this path:

On Sat, Jun 15, 2013 at 08:13:51AM +0800, Gabs Ricalde wrote:
> As an alternative to the Net4501, the AM335x in the Beaglebone has
> timers that accept an external clock up to 25 MHz (TCLKIN) and can
> timestamp events on an input pin (TIMER4-TIMER7). Both sets of pins are
> available on the headers after an appropriate pinmux configuration.
> 
> I'm finishing the clocksource driver for Linux, I'm testing it using the
> 10 MHz and PPS outputs of a LEA-6T. ntpd loopstats show +/- 0.1 us
> offsets, frequency is a flat 0.000 PPM as expected.

Edésio

On Sun, Oct 27, 2013 at 10:58:02PM -0700, Tom Van Baak wrote:
> > On most CPU architectures, the low level hardware has a register that 
> > counts on the CPU clock.
> 
> Merely counting the CPU clock is only half the requirement. Reading the clock 
> precisely when an external event occurs is the other half.
> 
> In my mind, there are three levels of NTP precision:
> 
> 1) The traditional scheme, in use for decades, where a PC uses interrupts 
> (e.g., DCD) and OS s/w acts as a crude time interval counter. This is quite 
> limiting, but Dave Mill's worked with what he had, and it's far better than 
> nothing.
> 
> 2) The external h/w capture/counter scheme, which is what any external time 
> interval or time-stamping counter can provide. By using external h/w instead 
> of internal s/w you get a precise, low-jitter time comparison at every pulse. 
> The OP was talking about the picPET, a sub-microsecond $1 time-stamping 
> counter. But you can use a $1000 HP sub-nanosecond time interval counter if 
> you prefer.
> 
> 3) An internal h/w capture/counter scheme, which is what the latest crop of 
> SBC offer. Here, not only is the counter tied to the CPU clock, but 
> timestamping is pure h/w, so all problems with s/w and latency and jitter are 
> removed from the equation. This is the ideal solution, not unlike how any 
> GPSDO is designed.
> 
> In my mind, the modern SBC architectures with single CPU clock source (could 
> be OCXO or atomic), and real GPIO pins (instead of serial or USB ports) and a 
> native h/w capture/compare register should allow NTP to work at the 10 to 100 
> ns level. If any of you could verify this, it would be time-nut worthy.
> 
> /tvb
> 
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