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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/ip-10-244-207-161.pid' (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 skip-external-locking

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

/etc/mysql/my.cnf

# # 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 # http://dev.mysql.com/doc/mysql/en/server-system-variables.html # 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. [client] 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. [mysqld_safe] socket = /var/run/mysqld/mysqld.sock nice = 0 [mysqld] # # * Basic Settings # # # * IMPORTANT # 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 skip-external-locking # # Instead of skip-networking the default is now to listen only on # localhost which is more compatible and is not less secure. bind-address = 127.0.0.1 # # * 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 #log-queries-not-using-indexes # # 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 [mysqldump] quick quote-names max_allowed_packet = 16M [mysql] #no-auto-rehash # faster start of mysql but no tab completition [isamchk] 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/
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    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? Commented Apr 12, 2011 at 12:42
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    @BMDan - Good suggestions, it all passes. This issue is becoming increasingly confusing to me. Gha. Commented Apr 12, 2011 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)? Commented Apr 12, 2011 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. Commented Apr 12, 2011 at 15:47

5 Answers 5

Reset to default
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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.

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    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 :) Commented Apr 13, 2011 at 7:52
  • I would've but I can't for 2 days after answering. Commented Apr 13, 2011 at 8:28
  • Glad you figured it out. In unrelated news, based on the log, you should really run mysql_upgrade. :) Commented Apr 14, 2011 at 11:29
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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
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  • 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). Commented Apr 12, 2011 at 12:01
  • @Kit: updated my answer. Can you post the relevant part of the output of mount and df -h? Commented Apr 12, 2011 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 :( Commented Apr 12, 2011 at 14:13
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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 ?

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  • Added to the question. Commented Apr 12, 2011 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. Commented Apr 12, 2011 at 16:03
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Check SELinux. If SELinux is on, you will need to re-label or turn it off. This would give a permissions error message.

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  • sestatus says disabled. Commented Apr 12, 2011 at 15:40
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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
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  • 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. Commented Apr 12, 2011 at 14:15

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