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If a hardware issue was affecting availability of the EC2 service then it should also be noted here https://health.aws.amazon.com/health/home#/account/dashboard/open-issues In which region is your instance?
Is this just a normal on-demand instance that you've spun up, not a spot instance that could have been shutdown by AWS at short notice?
It sounds like resource exhaustion issue, and would be worthwhile setting up CloudWatch agent to collect more detailed system logs https://docs.aws.amazon.com/AmazonCloudWatch/latest/monitoring/Install-CloudWatch-Agent.html
Appreciate the following may be time-consuming, but as an exercise (to see if this is repeatable) would you be able to install CloudWatch agent on a fresh EC2 instance and then go through the software installation & setup that you were doing? This may point to where the bottleneck is.
have you seen the ec2 status from Management Console during connection issue happen, and maybe you could try SSM and same thing happen on session.
fyi, if something under-lay (base infra level/lower than OS) outage happen AWS usually let you know about this outage ahead or sometimes after.
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Could you be more specific about "pretty big instance". What instance type and size is it?