>due to multitasking nature of Linux, the GPIO manipulation is constantly interrupted for short periods when the CPU is doing something else, such as receiving or sending data over network, writing log files, etc.

With a few simple tweaks (isolcpus + irqbalance + setting cpu affinity), you can get rid of the overwhelming majority of interruptions a specific userland program running on a Linux machine could encounter.

If this quote is talking about kernel context switches, choice of I/O scheduler and tick rate in the kernel could be tweaked for better performance.

You could probably use an Arduino for this, they connect to a computer using serial-over-USB.

You can do GPIO bit-twiddling pretty fast: http://skpang.co.uk/blog/archives/323

The new raspberry pi zero can be run as a device, so you could use that.

O.o this $5 puppy could essentially replace the 1.5K National Instruments DAQ I'm using right now. Even better, I won't have to deal with their horrendous API documentation anymore.

Of course that would require a Linux kernel, so not bare metal anymore, but there might be a way to make this work!

Now I just need to get my hands on one, it's out of stock everywhere within a radius of 300km...

They haven't committed to making more, or if they do, to the $5 price point.

They are making more, but they sell them faster than they can make them.

Really?? Then the zero was a really shitty marketing move...