Native C libraries to GPIO pins?

For a native C library, I suggest using libMRAA:
https://github.com/intel-iot-devkit/mraa
We added support there for the UP board. It provides a C library, and also offers Python and Javascript and Java bindings on top.

Regarding speed, however, the GPIO pins on the UP board cannot be toggled very quickly, even with C code. This is a hardware limitation that we've observed in the GPIO controller used in this Intel SoC. GPIO performance is about 10x slower, compared to Raspberry Pi 2.

Also, something else to be aware of is that the C libraries for RPi that offer very fast GPIO access typically bypass the kernel driver and access the GPIO registers directly. Something like this could be implemented for UP - it still doesn't get around the fact that the GPIO hardware is 10x slower, but it can at least get around some of the inefficiencies inherent in access the GPIOs via the kernel sysfs interface. But this is not straightforward because there are 2 hardware components to be aware of - the GPIO controller in the SoC, and the CPLD on the board in between the SoC and the GPIO pins. The latter needs to be configured correctly according to the desired pin mode and direction. When you access the GPIOs via sysfs, in the range 0-27, the kernel drivers are taking care of this for you.