So far  I think we've established that it is not a rouge CPU hog that is
blocking the system. Having to restart the system rather the session,
also lends credence to that it is not a simple userspace or even gfx
driver issue.

On the theory that the GPU goes nuts, download and build
http://cgit.freedesktop.org/xorg/app/intel-gpu-tools/ (maybe apt-get
install intel-gpu-tools if you feel lucky), then run intel_gpu_top.
Except for running gtkperf etc, the GPU should be lightly loaded.

On the theory that the CPU goes nuts, apt-get install powertop
latencytop, and run the pair of those looking for abnormalities. For
powertop, the CPU should be waking up and hitting max frequency when
busy and hitting C6+ when idle. latencytop should help identify what is
taking time (not necessarily cpu cycles) to complete.

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https://bugs.launchpad.net/bugs/1189645

Title:
  General lag under desktop environments

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