JMeter script execution no completing even after timeout

I am executing JMeter script in AWS EC2 instance for 4000 virtual users with 60 Secs as RampUp. I have added few Requests inside the Runtime Controller and have given 20 Mins as timeout for Runtime Controller. I am running in the EC2 machine which is of 248GB. I noticed the execution will not complete even after the timeout. I noticed few virtual users have logged out or completed the execution. But for few the execution is not completing. Also, I don't see the updates in the console. I am using the below command to execute, JVM_ARGS="-Xms1g -Xmx200g" ./jmeter -n -t Load-Test-01.jmx -l TestResults4000UsersMachine1.csv

Am I doing any mistake here?

Attached is the screenshot of console,

Runtime Controller can only "ask" threads to stop, if the thread is waiting for the response from the system under test - it won't stop until it gets the response.

Looking into your screenshot I can see response times going above 2 minutes which doesn't seem acceptable to me.

So you might want to set/adjust response timeout to some reasonable value. The setting lives under "Advanced" tab of the HTTP Request sampler or in case if you have "few" requests you might want to use HTTP Request Defaults to set the timeout for all of them in one shot: