We found what's causing this - opcache was being loaded twice (both in
cli and in php5-fpm):

# php -m
(...)
[Zend Modules]
Zend OPcache
Zend OPcache

# ls -l |grep opcache
lrwxrwxrwx 1 root root 32 Dec  3 07:15 05-opcache.ini -> 
../../mods-available/opcache.ini
lrwxrwxrwx 1 root root 32 Apr 22 12:55 20-opcache.ini -> 
../../mods-available/opcache.ini


The update created an extra opcache.ini symlink, opcache was being loaded 
twice, and it caused extremely poor performance.

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https://bugs.launchpad.net/bugs/1573625

Title:
  very high system load after upgrading to 5.5.9+dfsg-1ubuntu4.16

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