Bug #80254 ERROR: The partition with /var/lib/mysql is too full!
Submitted: 3 Feb 2016 14:18 Modified: 21 Jun 2016 8:53
Reporter: George Salt Email Updates:
Status: Open Impact on me:
None 
Category:MySQL Server Severity:S3 (Non-critical)
Version:5.5.47-0ubuntu0.14.04.1 OS:Ubuntu (Mint 17.2 64-bit)
Assigned to: Lars Tangvald CPU Architecture:Any

[3 Feb 2016 14:18] George Salt
Description:
/etc/init.d/mysql: ERROR: The partition with /var/lib/mysql is too full!

How to repeat:
sudo /etc/init.d/mysql start
 * Starting MySQL database server mysqld                                 [fail]
[3 Feb 2016 16:38] Lars Tangvald
Could you try running:
LC_ALL=C BLOCKSIZE= df --portability $datadir/. | tail -n 1 

This is the command the init script runs to check for minimum available space (4MB)
[5 Mar 2016 1:00] Bugs System
No feedback was provided for this bug for over a month, so it is
being suspended automatically. If you are able to provide the
information that was originally requested, please do so and change
the status of the bug back to "Open".
[21 Jun 2016 8:53] Stéphane Lambert
I have the same problem.

LC_ALL=C BLOCKSIZE= df --portability $datadir/. | tail -n 1 

answers : 
/dev/sdb1        955118356 620849288 285728756      69% /
[21 Jun 2016 8:59] Lars Tangvald
Hi,

Did you set the datadir variable before running the command?

Try replacing $datadir with /var/lib/mysql
[21 Jun 2016 9:19] Stéphane Lambert
it is. 

Please note I just run an upgrade and the server was perfectly well for years...

#
# 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
#
user		= mysql
default-storage-engine          = InnoDB
pid-file	= /var/run/mysqld/mysqld.pid
socket		= /var/run/mysqld/mysqld.sock
port		= 3306
basedir		= /usr
datadir		= /var/lib/mysql
tmpdir		= /tmp
lc-messages-dir	= /usr/share/mysql
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
#
# Error log - should be very few entries.
#
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/
[21 Jun 2016 9:37] Lars Tangvald
Can you try running:
/usr/sbin/mysqld --print-defaults | tr " " "\n" | grep -- "--datadir" 

And see what the output is?
[21 Jun 2016 9:51] Stéphane Lambert
/usr/sbin/mysqld --print-defaults | tr " " "\n" | grep -- "--datadir" 

=> 

--datadir=/var/lib/mysql
[21 Jun 2016 10:00] Stéphane Lambert
Can it be linked to something around ubuntu's open-files-limit ?
[21 Jun 2016 10:04] Lars Tangvald
Can you add
 set -x
to the start of /etc/init.d/mysql

Then try to start up the server again?
Should print out more data from the startup.
[21 Jun 2016 10:22] Lars Tangvald
Just noticed that if you run /etc/init.d/mysql as a regular user (not mysql or root) it will trigger this exact error.

Are you starting the service as non-root? If so, try just adding a sudo
[21 Jun 2016 10:31] Stéphane Lambert
/etc/init.d/mysql  start set -x

=> 

df: '/var/lib/mysql/.': Permission denied
 * /etc/init.d/mysql: ERROR: The partition with /var/lib/mysql is too full!

and 

sudo /etc/init.d/mysql  start set -x
[sudo] password for slambert: 

=>

 * Starting MySQL database server mysqld                                                                                                         No directory, logging in with HOME=/
                                                                                                                                          [fail]
[21 Jun 2016 10:55] Lars Tangvald
If you just run 
sudo /etc/init.d/mysql start

The server won't be started? Or does it give the error, but still start.

Which distro version are you running on?
[21 Jun 2016 10:55] Lars Tangvald
And just to note: The service must be started with sudo
[21 Jun 2016 12:15] Stéphane Lambert
No it doesn't ; 
sudo /etc/init.d/mysql  start set -x
[sudo] password for slambert: 

=>

 * Starting MySQL database server mysqld
No directory, logging in with HOME=/
[fail]

I'm under 
Distributor ID:	LinuxMint
Description:	Linux Mint 17.2 Rafaela
Release:	17.2
Codename:	rafaela
slambert@smongdee02 ~ $ 

Thanks for your help, it's big headache hear...
[21 Jun 2016 12:29] Lars Tangvald
It still fails without set -x?

Can you check if there's anything in mysql error logs?

Also, can you check the output from 
 getent passwd mysql
?
[21 Jun 2016 12:39] Stéphane Lambert
Start without set -x gives same result

I have 2 errors in logs :
.............
[ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
............
[ERROR] Fatal error: Can't open and lock privilege tables: Incorrect file format 'user'
.............

getent passwd mysql
=>
mysql:x:115:125:MySQL Server,,,:/var/lib/mysql/:/bin/false
[22 Jun 2016 6:14] Lars Tangvald
You upgraded from a previous 5.5 to a newer 5.5?

Can you try running:
 mysqld --verbose --help 2>&1 >/dev/null
and see if there's any output? It should print out any errors that are preventing the server from starting
[22 Jun 2016 6:16] Lars Tangvald
You probably need to run that as sudo as well
[22 Jun 2016 8:37] Stéphane Lambert
I upgraded the whole system a few days ago. Then I made a reboot. The mysql server died that day.

Sorry, I couldn't wait more, so I purged mysql and reinstalled everything. 

Thanks for your help anyway. I hope this will not happen to too many people.

Cheers :)
[22 Jun 2016 8:46] Lars Tangvald
No problem. Sorry we couldn't be of more help.