Those headers come from CUDA SDK.

To update, install CUDA SDK locally:

sudo apt-get install cuda

Copy cuda.h, version.txt and libdevice.10.bc:

cp /usr/local/cuda/include/cuda.h ./include/
cp /usr/local/cuda/version.txt  .
cp /usr/local/cuda/nvvm/libdevice/libdevice.10.bc ./nvvm/libdevice/