mysql> show variables like 'slow_query%';
+---------------------+------------------------------------+
| Variable_name    | Value               |
+---------------------+------------------------------------+
| slow_query_log   | OFF                |
| slow_query_log_file | /var/lib/mysql/instance-1-slow.log |
+---------------------+------------------------------------+
2 rows in set (0.01 sec)

mysql> show variables like 'long_query_time';
+-----------------+-----------+
| Variable_name  | Value   |
+-----------------+-----------+
| long_query_time | 10.000000 |
+-----------------+-----------+
1 row in set (0.00 sec)

mysql> set global slow_query_log='ON';
Query OK, 0 rows affected (0.00 sec)
 
mysql> set global slow_query_log_file='/var/lib/mysql/instance-1-slow.log';
Query OK, 0 rows affected (0.00 sec)
 
mysql> set global long_query_time=2;
Query OK, 0 rows affected (0.00 sec)

/etc/mysql/conf.d/mysql.cnf
[mysqld]
slow_query_log = ON
slow_query_log_file = /var/lib/mysql/instance-1-slow.log
long_query_time = 2

mysql> select sleep(2);
+----------+
| sleep(2) |
+----------+
|    0 |
+----------+
1 row in set (2.00 sec)

$ cat /var/lib/mysql/instance-1-slow.log
/usr/sbin/mysqld, Version: 8.0.13 (MySQL Community Server - GPL). started with:
Tcp port: 3306 Unix socket: /var/run/mysqld/mysqld.sock
Time         Id Command  Argument
/usr/sbin/mysqld, Version: 8.0.13 (MySQL Community Server - GPL). started with:
Tcp port: 3306 Unix socket: /var/run/mysqld/mysqld.sock
Time         Id Command  Argument
# Time: 2018-12-18T05:55:15.941477Z
# User@Host: root[root] @ localhost [] Id:  53
# Query_time: 2.000479 Lock_time: 0.000000 Rows_sent: 1 Rows_examined: 0
SET timestamp=1545112515;
select sleep(2);