Debugging Central

This page is part of the debugging series — pages with debugging details for a variety of Ubuntu packages.


The MySQL installation document is pretty thorough for generic linux installs. Recent Ubuntu releases have an additional step (or two) that must be followed to install the MySQL components in a non-standard location.

The most germane aspect is running two or more MySQL databases on a single server, administered by different people.

Failure Symptoms

Cannot create database files in a non-standard location

The mysqld works during the standard install (apt-get will start the server automatically) but has the following error when creating a database at a location other than the standard /var/lib/mysql directory.

sudo mysql_install_db --user=mysql --datadir=/opt/mysql/data
Installing MySQL system tables...
091029 10:31:02 [Warning] Can't create test file /opt/mysql/data/pookey.lower-test
091029 10:31:02 [Warning] Can't create test file /opt/mysql/data/pookey.lower-test
ERROR: 1005  Can't create table 'db' (errno: 13)

There are probably two problems.

The first, and most significant, problem is almost certainly a problem with apparmor permissions. Go to /etc/apparmour.d/usr.sbin.mysqld and add the following lines at the bottom of the /usr/sbin/mysqld clause

 /opt/mysql/ r,
 /opt/mysql/** rwk,

Note that the trailing slash is important.

Restart apparmor after the change.

The second problem is the default mysql option file residing in /etc/mysql/my.cnf, which has default-install definitions. Copy this file to a new location and edit it for the new datadir

How to file

Thank you for taking the time to report this bug and helping to make Ubuntu better. 

Could you please provide the following information:
 * content of /var/log/daemon.log related to mysql processes:
 * apparmor audit messages related to mysqld. The output of the command:
   grep audit /var/log/kern.log
 * mysqld apparmor profile and abstraction:
 * list of mysqld apparmor profiles:
    ls -l /etc/apparmor.d/usr.sbin.mysqld*
 * mysql configuration stripped of private information (such as password):
 * extra mysql configuration from the conf.d directory:
 * directory listing of mysql datadir (by default /var/lib/mysql):
    sudo ls -l /var/lib/mysql

Relevant error messages

Debugging procedure

1. Look in /var/log/daemon.log for error messages about mysqld and mysqld_safe failing to start or stop.

2. If mysqld is not able to open files (permission denied errors) or doesn't find files, it may be related to an incorrect mysqld apparmor profile.

  1. Check whether there are audit messages related to mysqld (acces denied) in the kernel.log file.
  2. Check if mysql is configured with a custom datadir (/etc/mysql/my.cnf and files in /etc/mysql/conf.d/*).
  3. Check if the mysqld apparmor profile has been updated to include the custom datadir in it. If not the problem is related to an incorrect mysqld apparmor profile (/etc/apparmor.d/usr.sbin.mysqld). It needs to be updated.
  4. Reply with the AppArmor stock reply.

How to Triage

Stock Reply

Update mysqld AppArmor profile

Mark the bug as Invalid using the following stock reply:

Thank you for taking the time to report this bug and helping to make Ubuntu better. It seems that you're using a non-standard location for your data directory (datadir option in my.cnf). However mysqld apparmor profile (in /etc/apparmor.d/usr.sbin.mysqld) hasn't been updated to allow access to the custom directory.

See for more information on how to update mysqld apparmor profile.

How to Forward

Known bugs

  • The debian-sys-maint user is not available and thus the status script reports a failure from mysqld.
  • Mysql configuration uses non-standard location for its data files and thus mysqld apparmor profile needs to be updated.


CategoryBugSquad CategoryDebugging

DebuggingMySQL (last edited 2010-07-09 22:01:04 by pool-71-252-251-234)