hi there

your project is a little mysterious, so it is hard to be specific but here are 
some thoughts based on my own recent research into using beaglebones to drive 
LEDstrips and a custom LCD array. 

from https://github.com/osresearch/LEDscape

"the beaglebone SOC has two PRUs (programmable realtime unit) which are 
designed for this sort of purpose.
the TI AM335x ARM Cortex-A8 in the BeagleBone Black has two programmable 
"microcontrollers" built into the CPU that can handle realtime tasks and also 
access the ARM's memory. This allows things that might have been delegated to 
external devices to be handled without any additional hardware, and without the 
overhead of clocking data out the USB port."

(I am actually using a fork of this library 
https://github.com/Yona-Appletree/LEDscape
for driving LED strips, and am planning to modify this code for my other 
project)

PRUs run at 200MHz and have very efficient access to some (more than the 16 
bits that you require) of the GPIO pins (these need to be pin-muxed correctly - 
that is another can of worms / kettle of fish). you read / write to pins by 
reading / writing to specific PRU registers. so you can read/write 8 (or more) 
bits simultaneously. it's much more efficient than the more traditional Linux 
sysfs approach.

there is a FAQ about using the PRUs stickied at the top of this group and lots 
more info on The internet's.

Trammell Hudson, who developed the original LEDscape code, seems to have done 
quite a bit of interfacing beaglebones to old computing hardware.

http://trmm.net/Category:Retrocomputing

eg http://trmm.net/Mac-SE_video

another example 
http://blinkenbone.com/projects/blinkenbone

I've found a logic analyser (eg https://www.saleae.com) to be very useful when 
doing this sort of stuff.

john

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