Any tips for code to do the actual writing?

I don't really understand how writing to a file creates pulses to a pump.

Is this a real file that you're writing to? Or some kind of memory mapped IO?

if the latter, I'd probably drop into Inline::C for this. On windows, I'd write the whole timing and writing loop in C and run it in a system thread. But I don't know enough about Linux to know if this makes sense there.