I am running Ubuntu 12.04.3 LTS. Before installing the NVIDIA driver I was running X-windows on two monitors, one connected to the motherboard and one connected to the NVIDIA card with CUDA capability.
I installed the most recent driver (Linux x64 version 331.49) but now it only sees one monitor, the one connected to the NVIDIA card. This isn’t going to work out since the CUDA-GDB debugger stops X-windows to debug the CUDA environment. How have other people configured the video drivers for X-windows in Ubuntu to avoid this problem?
reinstall linux OS, including setup of X/GUI (on the motherboard graphics device)
install the NVIDIA GPU
install the NVIDIA GPU driver using the .run file installer, selecting “no” when prompted to modify the xorg.conf file.
Or you can google for an appropriate xorg.conf to replace the existing one you have, that is appropriate for your motherboard display device. For example, googling “intel graphics xorg.conf” yielded this, which may be of interest: