I was stuck with this issue for a long time for my Ubuntu 16.04. After installing a fresh copy of Ubuntu 16.04, I installed cuda 8.0 toolkit using the deb(local):
$ sudo dpkg -i cuda-repo-ubuntu1604-8-0-local-ga2_8.0.61-1_amd64.deb
$ sudo apt-get update
$ sudo apt-get install cuda
Nvidia driver is working well on my computer now. Prior to that, I was trying to install Nvidia driver using the *.run file without any luck. Give it a shot it will save your valuable time.
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Reference: Somebody liked my solution :D
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