RightScale founder and CTO Thorsten Von Eicken says it seems clear AWS is patching a critical security update. "As usual, AWS is totally tight-lipped about the underlying cause. It seems obvious that the company is patching a security vulnerability, but it will not disclose which one until October 1 -- that is, after they have patched all hosts."
An AWS official responded to a commenter in the company's Forum page apologizing for the impact and short notice, but saying that its actions involve "very timely security and operational patches."
AWS has instructions here on how to reboot instances. In the EC2 console there is a tab named "Instances" -- from there, navigate to "actions" and click "reboot." AWS says when an instance is rebooted, it remains on the same physical host and keeps its public DNS name, private IP address, and any data on its instance store volumes. It does not start a new billing cycle.
AWS has not yet formally issued a broader public statement than sending notifications to its customers. AWS officials did not immediately respond to questions about the issue.
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