Thank you! Was banging my head against the wall on RHEL6's tomcat. Went on Hacker News to stop thinking about it for a few minutes. Son of a bitch, the solution was right on the front page.
I didn't really think about it at the time, but right about then (I'm in GMT+10) a Minecraft server (OpenJDK 64-bit, Ubuntu 11.10) I had running got rather upset ...
2012-07-01 09:59:59 [WARNING] Time ran backwards! Did the system time change?
2012-07-01 10:01:14 [WARNING] Can't keep up! Did the system time change, or is the server overloaded?
... and stuck on 100% CPU until I noticed it and restarted it this morning. Thankfully no other issues that I've noticed.
I saw the same across all of our Ubuntu servers. Some running Tomcat others running SmartFox Server (a java based game server). A reboot + app restart fixed it.
Even if you're not running java in your stack, it's worth a quick check on your servers. Our SoftLayer servers use an Adaptec RAID card and the monitoring software uses the JVM and will suck up all of your CPU. All of our MySQL/Cassandra/Redis/Kestrel servers needed to be bounced because they had RAID cards. Frustrating.
I also use Softlayer and have a pair of servers with Adaptec RAID cards. Checking up on them they were not affected.
Having looked in to it, it seems our server admin decided to install OpenNTP to replace the standard NTP daemon. I'm not sure why he did that, but it seems OpenNTP just ignores leap seconds and compensates after the fact just as if your clock had drifted a second out of sync in the usual way.
Even if you don't have java installed but you're running on shared infrastructure that might be running MySQL/Java elsewhere it's a crazy day. My inbox is full of performance-below-acceptable-levels/high-load alerts.
Yes, this happened on my development MySQL instance and also one of my production instances of MySQL -- but not another one that I have. I'm not sure why it only affected one, maybe different versions of MySQL?
I saw this on my Fedora 17 laptop. Chrome started eating up 100% CPU and my laptop started getting really hot. I tried restarting Chrome, updating Chrome, etc. Nothing worked. Rebooting fixed the problem.
Surprisingly, none of my servers have had problems, but I don't run Java anywhere.
/etc/init.d/ntp stop; date; date `date +"%m%d%H%M%C%y.%S"`; date;
-- then restart java