I've configured automatic shutdown as follows:
Automatic shutdown EC2 instances will be automatically terminated 300 seconds after the agent goes offline
However after a build, the instance remained running for over an hour and I had to manually stop it.
Am I missign anything?
By default, any volumes that were created when an instance launched should be automatically deleted when the instance terminates (in other words, their DeleteOnTermination flags are set to true by default). However, any volumes that are attached after the instance is running are not - this is due to that DeleteOnTermination flag are set to false.
Configure the instance to automatically delete the EBS volumes after instance shutdown by setting the DeleteOnTermination flag to true and this has to be configured on AWS side.
More details available here:
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