The PRUSS don't cause any CPU usage. You can reduce CPU usage by adding a 
nsleep() call to your while loop. Anyway, the max. speed of pulling the 
GPIO state (as in your while loop) is limited to approx. 140 kHz.

An alternative is to configure a GPIO interrupt

   1. Map an interrupt to any channel (except /dev/uio5, which is used by 
   libpruio).
   2. Write a callback to handle the interrupt and install it.
   3. Configure the GPIO interrupt controller.
   4. Download the configuration (pruio_config(), RB and MM mode need a 
   further start command).

As you can see this isn't trivial and needs advanced programming skills. 
You've to find a way to reset the interrupt status flag, which isn't 
supported by libpruio ATM.

Your problem description isn't very detailed. It may also be an option to 
use the General-Purpose Inputs (R31) of the free PRUSS in 28-bit shift mode 
to capture the signal at high frequencies.

BR

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