There is still only one kernel, the host if you will. Since graphics drivers are kernel mode, it has to be loaded into the kernel. So VM style pass-through of PCI devices doesn't really make sense.

However, GPUs are increasingly supporting virtualisation and multiprocessing. For example, nVidia supports multiplexing a single GPU across multiple VMs for VMWare View. I'm not sure if there is special driver paravirtualisation magic happening but I suspect so. But there is at least some GPU process control and resource scheduling now, and I expect this technique will be accessible to linux in the near future.

At present you can map through the host devices created by kernel drivers into the container, and then access them via userland libraries. You are still dependent on the library versions and the driver version matching. This works for CUDA and OpenGL. https://blog.simos.info/how-to-run-graphics-accelerated-gui-...