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What would be the most efficient way to compare the usage of multiple domains that are all bound to the same Apache vHost? What I want to know is which domains are used often to access the website and which are obsolete. I guess this would best be done through Apache log analysis? Which tool would be able to do that? Or would Google Analytics or Piwik be a solution (I tried Analytics but could not find any domain-usage statistics)?

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As long as you've got apache to log hostname along with the URL in the access log, just cutting out the hostname part and piping through sort | uniq -c | sort -n will give you a nice list of how many requests have been made for each domain.

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