Is it possible to stop all running processing using the GPU via CUDA, without restarting the machine?
The lsof utility will help with this. You can get a list of processes accessing your NVIDIA cards with:
lsof /dev/nvidia*
Then use kill or pkill to terminate the processes you want. Note that you may not want to kill X if it's running. On my desktop system, both X and kwin are also accessing the GPU.