How can I stop a running MySQL query?

Use mysqladmin to kill the runaway query:

Run the following commands:

mysqladmin -uusername -ppassword pr

Then note down the process id.

mysqladmin -uusername -ppassword kill pid

The runaway query should no longer be consuming resources.

mysql> show processlist;
+----+------+-----------+-----+---------+------+---------------------+------------------------------+----------+
| Id | User | Host      | db  | Command | Time | State               | Info                         | Progress |
+----+------+-----------+-----+---------+------+---------------------+------------------------------+----------+
| 14 | usr1 | localhost | db1 | Query   |    0 | starting            | show processlist             |    0.000 |
| 16 | usr1 | localhost | db1 | Query   |   94 | Creating sort index | SELECT  `tbl1`.* FROM `tbl1` |    0.000 |
+----+------+-----------+-----+---------+------+---------------------+------------------------------+----------+
2 rows in set (0.000 sec)

mysql> kill 16;
Query OK, 0 rows affected (0.004 sec)

mysql> show processlist;
+----+------+-----------+-----+---------+------+----------+------------------+----------+
| Id | User | Host      | db  | Command | Time | State    | Info             | Progress |
+----+------+-----------+-----+---------+------+----------+------------------+----------+
| 14 | usr1 | localhost | db1 | Query   |    0 | starting | show processlist |    0.000 |
+----+------+-----------+-----+---------+------+----------+------------------+----------+
1 row in set (0.000 sec)

Just to add

KILL QUERY **Id** where Id is connection id from show processlist

is more preferable if you are do not want to kill the connection usually when running from some application.

For more details you can read mysql doc here

Connect to mysql

mysql -uusername -p  -hhostname

show full processlist:

mysql> show full processlist;
+---------+--------+-------------------+---------+---------+------+-------+------------------+
| Id      | User   | Host              | db      | Command | Time | State | Info             |
+---------+--------+-------------------+---------+---------+------+-------+------------------+
| 9255451 | logreg | dmin001.ops:37651 | logdata | Query   |    0 | NULL  | show processlist |
+---------+--------+-------------------+---------+---------+------+-------+------------------+

Kill the specific query. Here id=9255451

mysql> kill 9255451;

If you get permission denied, try this SQL:

CALL mysql.rds_kill(9255451)