How can I use an Nvidia GPU with an open-source embedded board?
You need the following components:


An nVidia GPU, which has a PCIe interface generally
The necessary support components for power supply and heat management
Drivers that know how to send commands to the GPU and retrieve results
A compiler that translates CUDA to the internal binary format


The latter two are available as closed source programs for Windows and Linux running on Intel/AMD processors.

The GPUs are sold standalone only to companies that buy several thousand units, as interfacing the IC is difficult and close to undoable without support from nVidia, so they won't bother for a few units only.

If it really has to be CUDA, your best bet is to take a standard graphics card and interface it through PCIe.

If OpenCL is fine, then I'd go with an FPGA based solution, e.g. from Xilinx or Altera -- interfacing FPGAs is a bit better documented as there are several people using low- to midrange FPGAs and writing articles about it. Building a stable and spec-compliant power supply for a high-end FPGA is still nontrivial, but at least the documentation is available, and ICs are sold separately.