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I attempted to move my database to a different mount on my Ubuntu installation on an amazon EC2 instance, because it was filling up the root directory. I think I've borked something up. When I run:

$ sudo mysqld --datadir=/var/lib/mysql --user mysql
110412 11:36:44 [Warning] Can't create test file /mnt/var/lib/mysql/ip-10-244-207-161.lower-test
110412 11:36:44 [Warning] Can't create test file /mnt/var/lib/mysql/ip-10-244-207-161.lower-test

In /var/log/mysql/error.log:

110412 16:01:27 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Can't find file: './mysql/plugin.frm' (errno: 13)
110412 16:01:27 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
/usr/sbin/mysqld: Can't create/write to file '/mnt/tmp/ibRTnZix' (Errcode: 13)
110412 16:01:27  InnoDB: Error: unable to create temporary file; errno: 13
110412 16:01:27 [ERROR] Plugin 'InnoDB' init function returned error.
110412 16:01:27 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
110412 16:01:27 [ERROR] /usr/sbin/mysqld: Can't create/write to file '/mnt/var/lib/mysql/' (Errcode: 13)
110412 16:01:27 [ERROR] Can't start server: can't create PID file: Permission denied

The file ip-10-244-207-161.lower-test does not already exist:

ls -l /mnt/var/lib/mysql
total 20532
-rwxr-xr-x 1 mysql root         0 2011-02-28 22:23 debian-5.1.flag
-rwxr-xr-x 1 mysql mysql 10485760 2011-04-12 07:31 ibdata1
-rwxr-xr-x 1 mysql mysql  5242880 2011-04-12 07:31 ib_logfile0
-rwxr-xr-x 1 mysql mysql  5242880 2011-02-28 22:23 ib_logfile1
drwxr-xr-x 2 mysql root      4096 2011-02-28 22:23 mysql
-rwxr-xr-x 1 mysql root         6 2011-02-28 22:23 mysql_upgrade_info
drwxr-xr-x 2 mysql mysql     4096 2011-04-11 08:22 scrapy_cache

The directories seem to be accessable:

$ ls -l /mnt/var/lib/ | grep mysql
drwxr-xr-x 4 mysql mysql 4096 2011-04-12 07:31 mysql

$ ls -l /var/lib/ | grep mysql
lrwxrwxrwx 1 mysql     root      18 2011-04-12 09:05 mysql -> /mnt/var/lib/mysql

ls -ld /mnt/{,var/{,lib/{,mysql}}}
drwxr-xr-x 5 root  root   4096 2011-04-12 07:27 /mnt/
drwxr-xr-x 3 mysql root   4096 2011-04-12 07:29 /mnt/var/
drwxr-xr-x 3 mysql ubuntu 4096 2011-04-12 07:33 /mnt/var/lib/
drwxr-xr-x 4 mysql mysql  4096 2011-04-12 07:31 /mnt/var/lib/mysql

The parts I changed in my.cnf:

user            = mysql
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /mnt/var/lib/mysql
tmpdir          = /mnt/tmp

I would really appreciate some help on this as I've failed miserable while trying to debug it.

I did a sudo chown -R mysql /mnt/var/lib/mysql so everything should be owned by the mysql server. /mnt is most certainly writable as I ran mv /var/lib/mysql /mnt/var/lib/ when I migrated. Mount confirms this:

$ mount | grep /mnt
/dev/sda2 on /mnt type ext3 (rw)

The disk is not full in space and it hasn't run out of inodes, disk quota don't seem to be active I installed repquota but it outputted absolutely nothing:

$ df -h /dev/sda2
Filesystem            Size  Used Avail Use% Mounted on
/dev/sda2             335G  2.0G  316G   1% /mnt

$ df -i /dev/sda2
Filesystem            Inodes   IUsed   IFree IUse% Mounted on
/dev/sda2            44564480     104 44564376    1% /mnt

Creating things as the MySQL user works, as suggested in the comments:

$ su -s /bin/bash - mysql

$ touch /mnt/var/lib/mysql/ip-10-244-207-161.lower-test

$ ls -ld /mnt/var/lib/mysql/ip-10-244-207-161.lower-test
-rw-r--r-- 1 mysql mysql 0 2011-04-12 14:10 /mnt/var/lib/mysql/ip-10-244-207-161.lower-test

$ rm -f /mnt/var/lib/mysql/ip-10-244-207-161.lower-test
$ ls -ld /mnt/var/lib/mysql/ip-10-244-207-161.lower-test
ls: cannot access /mnt/var/lib/mysql/ip-10-244-207-161.lower-test: No such file or directory

MySql isn't running.

$ ps aux | grep mysql
ubuntu   20825  0.0  0.0   3700   776 pts/1    S+   15:40   0:00 grep --color=auto mysql


# The MySQL database server configuration file.
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
# For explanations see

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

# * Basic Settings

#   If you make changes to these settings and your system uses apparmor, you may
#   also need to also adjust /etc/apparmor.d/usr.sbin.mysqld.

user        = mysql
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /mnt/var/lib/mysql
tmpdir      = /mnt/tmp
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        =
# * Fine Tuning
key_buffer      = 16M
max_allowed_packet  = 16M
thread_stack        = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
# * Query Cache Configuration
query_cache_limit   = 1M
query_cache_size        = 16M
# * Logging and Replication
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1

log_error                = /var/log/mysql/error.log

# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
# * InnoDB
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
# * Security Features
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem

max_allowed_packet  = 16M

#no-auto-rehash # faster start of mysql but no tab completition

key_buffer      = 16M

# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
!includedir /etc/mysql/conf.d/
share|improve this question
Let's test! su -s /bin/bash - mysql, then touch /mnt/var/lib/mysql/ip-10-244-207-161.lower-test. Does it succeed? Next, still as "mysql", ls -ld /mnt/var/lib/mysql/ip-10-244-207-161.lower-test. Does that work? Lastly, as mysql, rm -f /mnt/var/lib/mysql/ip-10-244-207-161.lower-test, followed by an ls: is it really gone? – BMDan Apr 12 '11 at 12:42
@BMDan - Good suggestions, it all passes. This issue is becoming increasingly confusing to me. Gha. – Kit Sunde Apr 12 '11 at 14:13
Can you post the output of ps aux | grep mysql and the contents of the configuration files (/etc/my.cnf or /etc/mysql/my.cnf)? – Lekensteyn Apr 12 '11 at 15:36
@Lensteyn - Here you go. MySql isn't running (this was the first thing I checked). I've posted the full config file. – Kit Sunde Apr 12 '11 at 15:47

Does the file /mnt/var/lib/mysql/ip-10-244-207-161.lower-test exist? If yes, is it owned by mysql? All files an directories in /mnt/var/lib/mysql should be owned by the MySQL user.

Is /mnt mounted as rw (read-write), and not ro (read-only)? You can check that by running mount (without arguments).

MySQL has a page in their documentation on this error. It basically means that the data directory or filesystem is write-protected.

Are disk quota's active? You can check the current quota status (if installed) with:

sudo repquote -a

Is the disk full? Check the current disk usage with:

df -h
share|improve this answer
The file does not exist no. I did a sudo chown -R mysql /mnt/var/lib/mysql so they are. /mnt must be rw because I ran mv /var/lib/mysql /mnt/var/lib/ when I migrated (checking mount confirms tihs). – Kit Sunde Apr 12 '11 at 12:01
@Kit: updated my answer. Can you post the relevant part of the output of mount and df -h? – Lekensteyn Apr 12 '11 at 12:09
Thanks for updating, I've updated the post with mount and df -h as you suggested. Everything seems to be in order :( – Kit Sunde Apr 12 '11 at 14:13

It smells like the problem might be due to insufficient permissions on the parent-directories of /mnt/var/lib/mysql, and probably /mnt/var in particular. Can you post the output of ls -ld /mnt/{,var/{,lib/{,mysql}}}?

EDIT: Ok, thought about this some more. You say you changed the location of the socket in my.cnf - could it be that the server is successfully starting (check with ps ax | grep mysql) but the mysql client you're using is looking for the socket somewhere else e.g. an old location? What's the full error message you get from running mysql ?

share|improve this answer
Added to the question. – Kit Sunde Apr 12 '11 at 11:58
No the MySQL server isn't starting. I stupidly realized that there should be an error log somewhere since mysql was only echoing [Warnings]. Editing in the error log. – Kit Sunde Apr 12 '11 at 16:03
up vote 3 down vote accepted

I finally figured out what the problem was. I had on the instance running (installed by default). To make its stop complaining I did:

sudo aa-complain /usr/sbin/mysqld

Now starts like expected and I can query my data. I feel bad for taking up so much time for such a trivial issue and I really appreciate how helpful everyone has been. I wouldn't have figured out the problems with without user78151 asking about .

An alternative solution can be to configure to allow you to use those directories (I don't care either way) which was described in a blog post I found.

share|improve this answer
If this answer solves your problem, mark it as accepted. I was about to post the same after I've read the line before the configuration about apparmor. Lesson for the next time: do not ignore comments :) – Lekensteyn Apr 13 '11 at 7:52
I would've but I can't for 2 days after answering. – Kit Sunde Apr 13 '11 at 8:28
Glad you figured it out. In unrelated news, based on the log, you should really run mysql_upgrade. :) – BMDan Apr 14 '11 at 11:29

Check SELinux. If SELinux is on, you will need to re-label or turn it off. This would give a permissions error message.

share|improve this answer
sestatus says disabled. – Kit Sunde Apr 12 '11 at 15:40

Did you mistype the data directory?

You wrote:

$ sudo mysqld --datadir=/var/lib/mysql --user mysql

but should be:

$ sudo mysqld --datadir=/mnt/var/lib/mysql --user mysql
share|improve this answer
I'm afraid not, /var/lib/mysql is a symbolic link to /mnt/var/lib/mysql. It made no difference when I tried running that instead. – Kit Sunde Apr 12 '11 at 14:15

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