A simple way to change runtime variables wihtout restarting mysql server.

First check the running value:

mysql> show variables like 'long_query%';
+-----------------+-------+
| Variable_name | Value |
+-----------------+-------+
| long_query_time | 10 |
+-----------------+-------+

Change the value:

mysql> set @@long_query_time=2;

Check again:

mysql> show variables like 'long_query%';
+-----------------+-------+
| Variable_name | Value |
+-----------------+-------+
| long_query_time | 2 |
+-----------------+-------+

Success!

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