Ok, after removing two of the hard drives and installing the system
without RAID the problem still exists. As a test I installed the
emacs23-nox package and watched 'iotop -ako' and with the exact same
amount of data written to the disks Alpha has an IO usage of 60% for
dpkg and ~35% for jbd2 where bravo has about 5% dpkg and ~1.75% jbd2. So
it seems there is a massive overhead for Alpha to write the same amount
of data to the disk at the same rate. I will be testing this theory more
with rsync to see if the overhead ratio holds.

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https://bugs.launchpad.net/bugs/815540

Title:
  Server becomes unresponsive after spawning 16 ksoftirqd processes

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