Changes to my.cnf don't take effect (Ubuntu 16.04, mysql 5.6)

Question

Changes I make to my.cnf don't seem to have any effect on the mysql environment. Here's a summary of what's happened...

I installed mysql 5.7 on Ubuntu 16.04 but then realized I needed to downgrade to mysql 5.6 due to incompatibility issues.

I apt purged the related applications and then removed any remaining directories such at /etc/mysql and /var/lib/mysql

I then installed mysql-5.6 (server and client) and related packages.

I was able to load one database from a dump from a server also running mysql 5.6 but when I tried to load a second database from a second dump from that same server, I got this error:

ERROR 2006 (HY000) at line 1721: MySQL server has gone away

When I Googled that, I saw results saying to set various options via the my.cnf file.

When I run...

updatedb && locate my.cnf

...I only see four results which are all links back to the same file: /etc/mysql/my.cnf.fallback. E.g. /etc/mysql/my.cnf.fallback == /etc/mysql/my.cnf

There are no .my.cnf files in either the root home directory or my user's home directory. I put a typo into the my.cnf file and reloaded mysql just to see the expected error and know the file was being loaded. I then removed the erroneous code and added the following:

[mysqld]
max_allowed_packet=1073741824

I then reloaded mysql by running in various ways:

service mysql restart

or

service mysql stop
service mysql start

or

/etc/init.d/mysql stop
/etc/init.d/mysql start

I then kept getting this default value indicating that it was not getting set from my.cnf:

mysql> SHOW VARIABLES LIKE 'max_allowed_packet';
+--------------------+---------+
| Variable_name      | Value   |
+--------------------+---------+
| max_allowed_packet | 4194304 |
+--------------------+---------+

If I do this:

mysql> SET GLOBAL max_allowed_packet=1073741824;

and log out and back into the mysql client, I see the correct value:

mysql> SHOW VARIABLES LIKE 'max_allowed_packet';
+--------------------+------------+
| Variable_name      | Value      |
+--------------------+------------+
| max_allowed_packet | 1073741824 |
+--------------------+------------+

But of course, if I restart the mysql server, the value reverts.

I've exhausted my search ability. What can I possibly be doing wrong?

Answer 1

The config files are fine. The root cause is a bug in the MySQL 5.6 packaging for Ubuntu 16.04.

If you check your /var/log/syslog you'll probably see a line like this:

Sep 15 18:56:09 ip-172-31-18-162 kernel: [  383.840275] audit: type=1400 audit(1505501769.234:50): apparmor="DENIED" operation="open" profile="/usr/sbin/mysqld" name="/etc/mysql/my.cnf.fallback" pid=25701 comm="mysqld" requested_mask="r" denied_mask="r" fsuid=0 ouid=0

A security tool called AppArmor is denying access to a symlinked file (/etc/mysql/my.cnf.fallback).

Try this workaround, which will allow symlinks to be read by mysqld.

echo '/etc/mysql/** lr,' >> /etc/apparmor.d/local/usr.sbin.mysqld
systemctl reload apparmor

Now mysqld should see your custom config.

This bug appears to be fixed in the MySQL 5.7 Ubuntu package.