Checking the log shows:

# [ERROR] /usr/libexec/mysqld: Sort aborted

Check the processlist on a plesk server:

# mysqladmin -u admin -p`cat /etc/psa/.psa.shadow` processlist

+---------+----------------+----------------------+----------------+---------+------+-------+------------------+
| Id      | User           | Host                 | db             | Command | Time | State | Info             |
+---------+----------------+----------------------+----------------+---------+------+-------+------------------+
| 1926335 | user           | 108.xx.xx.xxx:17599  | databasename   | Update  | 0    | Locked| select * from..' |
|         |                |                      |                |         | 0    |       |                  |
+---------+----------------+----------------------+----------------+---------+------+-------+------------------+

Kill the process:

# mysqladmin -u admin -p`cat /etc/psa/.psa.shadow` kill [thread_id]

Create an index on the table