On 16.04, the version of aufs looks correct, maybe it's a different bug. Did 
you also try with Docker 1.12 on 16.04?
Looking at the other bug, there is a Docker container than can help diagnose if 
you are encountering the aufs issue:
docker run -it --rm akihirosuda/test18180

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https://bugs.launchpad.net/bugs/1633223

Title:
  rcu_sched detected stalls with kernel 3.19.0-58, NVIDIA driver, and
  docker

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