How to let cmake find CUDA

cmake mentioned CUDA_TOOLKIT_ROOT_DIR as cmake variable, not environment one. That's why it does not work when you put it into .bashrc. If you look into FindCUDA.cmake it clearly says that:

The script will prompt the user to specify CUDA_TOOLKIT_ROOT_DIR if the prefix cannot be determined by the location of nvcc in the system path and REQUIRED is specified to find_package(). To use a different installed version of the toolkit set the environment variable CUDA_BIN_PATH before running cmake (e.g. CUDA_BIN_PATH=/usr/local/cuda1.0 instead of the default /usr/local/cuda) or set CUDA_TOOLKIT_ROOT_DIR after configuring. If you change the value of CUDA_TOOLKIT_ROOT_DIR, various components that depend on the path will be relocated.

So put CUDA_BIN_PATH into .bashrc or specify CUDA_TOOLKIT_ROOT_DIR to cmake:

cmake -D CUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 ..

FindCMake.cmake looks for /usr/local/cuda. In your case, that directory might not be there. Just create a symbolic link of that name to your actual CUDA installation directory:

$ sudo ln -s /usr/local/cuda-5.5 /usr/local/cuda

Your CMake should be able to generate the Makefile for your project now.

Maybe CUDA was installed from sources (and nvcc is not in the path). Then the script can not set CUDA_TOOLKIT_ROOT_DIR because of nvcc missing. For me it worked fine after running:

sudo apt install nvidia-cuda-toolkit

(This package might require several GiB of space)