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I'm starting a Windows stock image via Bamboo. The instance starts up relatively quickly, but the elastic agent hangs and then shuts down 40 minutes later. This has happened multiple times - it always shuts down after 40 minutes. Take a look at the log:

Apr 21, 2015 10:12:11 AM Requested that new elastic instance be created for configuration: Windows stock image / ami-6697dd0e
Apr 21, 2015 10:12:11 AM Elastic instance [i-f3118c0e] transitioned from STARTING to IDENTIFIED.
Apr 21, 2015 10:12:32 AM Elastic instance [i-f3118c0e] transitioned from IDENTIFIED to RUNNING.
Apr 21, 2015 10:52:55 AM Elastic instance [i-f3118c0e] transitioned from RUNNING to SHUTTING_DOWN.
Apr 21, 2015 10:53:35 AM Elastic instance [i-f3118c0e] transitioned from SHUTTING_DOWN to TERMINATED.
Apr 21, 2015 10:53:35 AM Detected that the elastic instance [i-f3118c0e] has been terminated.

I have edited the Bamboo Elastic Configuration variable "Idle agent shutdown delay" to be 1000 minutes. It was previously 40. I saw no indication that the Bamboo server needed to be restarted to apply this.

Why does it shut down consistently after 40 minutes?

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This is an issue that will be fixed in Bamboo 5.9. Refer to this bug. You will need to make a custom image configuration using the AMI appropriate to your region. Here are the fixed AMIs from a comment in the bug:

image.ASIA_PACIFIC_SE_1.EBS.x86_64.windows.Windows=ami-1cb0824e
image.SOUTH_AMERICA_1.EBS.x86_64.windows.Windows=ami-31ec692c
image.US_EAST_1.EBS.x86_64.windows.Windows=ami-04ccf46c
image.EU_CENTRAL_1.EBS.x86_64.windows.Windows=ami-22033f3f
image.EU_WEST_1.EBS.x86_64.windows.Windows=ami-3f503148
image.US_WEST_2.EBS.x86_64.windows.Windows=ami-e93b11d9
image.ASIA_PACIFIC_NE_1.EBS.x86_64.windows.Windows=ami-28ae5428
image.ASIA_PACIFIC_SE_2.EBS.x86_64.windows.Windows=ami-e3374ad9
image.US_WEST_1.EBS.x86_64.windows.Windows=ami-79c1233d
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