Kernel module timers are in the eCAP modules in the PWMSS subsystems. Three 
modules are present, but only two are wired to the big headers, the third 
is at JT or SDcard-slot (32 bit counters at 100 MHz --> maximal toggling 
time stamp = 42,9s).

Additional the TIMER[4-7] subsystems provide that feature (32 bit counters 
with divider at 24 MHz --> maximal toggling time stamp = 45812984s).

Find details and example code at

http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/ChaPins.html#sSecTimer

But as long as you synchronise both systems by an LINUX app, you'll face 
latency in a nano or even milli second range.

More accurate is the PRU-firmware I mentioned above, synchronised by a 
wired GPIO signal.  


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