How to automatically kill slow MySQL queries after N seconds?

If you have MySQL where the processlist is in the INFORMATION_SCHEMA, you can do this to generate the KILL QUERY commands in bulk from within the mysql client for query running longer than 20 minutes (1200 seconds):

SELECT GROUP_CONCAT(CONCAT('KILL QUERY ',id,';') SEPARATOR ' ') KillQuery
FROM information_schema.processlist WHERE user<>'system user'
AND time >= 1200\G

You can do WHERE clauses against the INFO field to look for a specific query, the TIME field against long running queries, or the DB field against a specific database.

If you are root@localhost, you should have full privileges to run this as follows

SECONDS_TOO_LONG=1200
KILLPROC_SQLSTMT="SELECT GROUP_CONCAT(CONCAT('KILL QUERY ',id,';') SEPARATOR ' ') KillQuery FROM information_schema.processlist WHERE user<>'system user' AND time >= ${SECONDS_TOO_LONG}"
mysql -uroot -ppassword -ANe"${KILLPROC_SQLSTMT}" | mysql -uroot -ppassword

You can crontab this as follows:

SECONDS_TOO_LONG=1200
QUERIES_RUNNING_TOO_LONG=`mysql -uroot -ppassword -ANe"SELECT COUNT(1) FROM information_schema.processlist WHERE user<>'system user' AND time >= ${SECONDS_TOO_LONG}"`
if [ ${QUERIES_RUNNING_TOO_LONG} -gt 0 ]
then
    KILLPROC_SQLSTMT="SELECT GROUP_CONCAT(CONCAT('KILL QUERY ',id,';') SEPARATOR ' ') KillQuery FROM information_schema.processlist WHERE user<>'system user' AND time >= ${SECONDS_TOO_LONG}"
    mysql -uroot -ppassword -ANe"${KILLPROC_SQLSTMT}" | mysql -uroot -ppassword
fi

Here is another variation:

SECONDS_TOO_LONG=1200
QUERIES_RUNNING_TOO_LONG=`mysql -uroot -ppassword -ANe"SELECT COUNT(1) FROM information_schema.processlist WHERE user<>'system user' AND time >= ${SECONDS_TOO_LONG}"`
if [ ${QUERIES_RUNNING_TOO_LONG} -gt 0 ]
then
    KILLPROC_SQLSTMT="SELECT CONCAT('KILL QUERY ',id,';') KillQuery FROM information_schema.processlist WHERE user<>'system user' AND time >= ${SECONDS_TOO_LONG}"
    mysql -uroot -ppassword -ANe"${KILLPROC_SQLSTMT}" > /tmp/kill_log_queries.sql
    mysql -uroot -ppassword < /tmp/kill_log_queries.sql
fi

BTW You do not have specify a myDB since I explicit read from information_schema.processlist as a fully qualified tablename.

Here is a demonstration of what you should see. For this example, I will echo the KILL command of all processes whose time > 20000 seconds:

[root@***** ~]# mysql `lwdba_connect` -ANe"SELECT GROUP_CONCAT('KILL ',id,'; ' SEPARATOR ' ') FROM information_schema.processlist WHERE time > 25000 AND user<>'system user';"
+----------------------------------------------------+
| KILL 180186;  KILL 180141;  KILL 176419;  KILL 3;  |
+----------------------------------------------------+
[root@***** ~]#

I have been doing this technique for the last 5 years.