Your target seems to be possible. The PRU clock is very stable.

Start with example code at pruss_toggle 
<http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/ChaExamples.html#sSecExaPruToggle>.
 
Adapt the pinmuxing and the PRU firmware:

   1. PRU generates your desired 1 Hz pulse train
   2. PRU starts first, waits for the first PRU-1 pulse on a GPIO input, 
   and then sends synchronised pulses on a GPIO output.

The only problem is to get PRU-1 starting at the obtained timestamp by the 
ARM (linux) process.

-- 
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