This issue is caused due to the size of "~/.beeline/history" file in user's home directory. While we run big queries, it will flood the history file and slow down beeline on start up and shutdown. To resolve this issue, please move "~/.beeline/history" file and retry beeline.
In the lower versions (below 2.1.0), we can have a cron job to delete "history" file periodically. This issue has been fixed in latest Hive versions by adding "--maxHistoryRows". Please check the below JIRA for more details.