MySQL (and others) very high cpu usage after leap second (June 2015)
corrspt.com
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I'd be interested in knowing which distro you were running, which NTP daemon, and which version of each.
We're running Debian 2.6.32-45, and NTP outputs this: ntpq - standard NTP query program - Ver. 4.2.6p2.
Does it answer your question?