May  5 07:21:22 pliersn-laptop mysqld_safe[7709]: started
May  5 07:21:22 pliersn-laptop kernel: [ 3430.063863] audit(1209946882.531:6): type=1503 operation="inode_create" requested_mask="w::" denied_mask="w::" name="/data/mysql/pliersn-laptop.lower-test" pid=7711 profile="/usr/sbin/mysqld" namespace="default"
May  5 07:21:22 pliersn-laptop mysqld[7713]: 080505  7:21:22 [Warning] Can't create test file /data/mysql/pliersn-laptop.lower-test
May  5 07:21:22 pliersn-laptop kernel: [ 3430.066267] audit(1209946882.531:7): type=1503 operation="inode_create" requested_mask="w::" denied_mask="w::" name="/data/mysql/pliersn-laptop.lower-test" pid=7711 profile="/usr/sbin/mysqld" namespace="default"
May  5 07:21:22 pliersn-laptop mysqld[7713]: 080505  7:21:22 [Warning] Can't create test file /data/mysql/pliersn-laptop.lower-test
May  5 07:21:22 pliersn-laptop kernel: [ 3430.094495] audit(1209946882.559:8): type=1503 operation="inode_create" requested_mask="w::" denied_mask="w::" name="/data/mysql/ibdata1" pid=7711 profile="/usr/sbin/mysqld" namespace="default"
May  5 07:21:22 pliersn-laptop mysqld[7713]: 080505  7:21:22  InnoDB: Operating system error number 13 in a file operation.
May  5 07:21:22 pliersn-laptop mysqld[7713]: InnoDB: The error means mysqld does not have the access rights to
May  5 07:21:22 pliersn-laptop mysqld[7713]: InnoDB: the directory.
May  5 07:21:22 pliersn-laptop mysqld[7713]: InnoDB: File name ./ibdata1
May  5 07:21:22 pliersn-laptop mysqld[7713]: InnoDB: File operation call: 'create'.
May  5 07:21:22 pliersn-laptop mysqld[7713]: InnoDB: Cannot continue operation.
May  5 07:21:22 pliersn-laptop mysqld_safe[7720]: ended

#
# 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
pid-file	= /var/run/mysqld/mysqld.pid
socket		= /var/run/mysqld/mysqld.sock
port		= 3306
basedir		= /usr
datadir		= /var/lib/mysql
tmpdir		= /tmp
language	= /usr/share/mysql/english
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		= 128K
thread_cache_size	= 8
#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.
#log		= /var/log/mysql/mysql.log
#
# Error logging goes to syslog. This is a Debian improvement :)
#
# 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
#
# * BerkeleyDB
#
# Using BerkeleyDB is now discouraged as its support will cease in 5.1.12.
skip-bdb
#
# * 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!
# You might want to disable InnoDB to shrink the mysqld process by circa 100MB.
#skip-innodb
#
# * 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

#
# * NDB Cluster
#
# See /usr/share/doc/mysql-server-*/README.Debian for more information.
#
# The following configuration is read by the NDB Data Nodes (ndbd processes)
# not from the NDB Management Nodes (ndb_mgmd processes).
#
# [MYSQL_CLUSTER]
# ndb-connectstring=127.0.0.1


#
# * 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/

$ls /data -l|grep mysql
drwxr-xr-x  3 mysql   mysql       4096 2008-05-04 22:16 mysql
$ls /data/mysql -l
total 4
drwxr-xr-x 2 mysql mysql 4096 2008-05-04 22:16 get
$ls /data/mysql/get -l
total 6736
-rwxr-xr-x 1 mysql mysql    8712 2008-05-04 22:16 xxx.frm
-rwxr-xr-x 1 mysql mysql 1433384 2008-05-04 22:16 xxx.MYD
-rwxr-xr-x 1 mysql mysql 1248256 2008-05-04 22:16 xxx.MYI
-rwxr-xr-x 1 mysql mysql      61 2008-05-04 22:16 db.opt
-rwxr-xr-x 1 mysql mysql    9006 2008-05-04 22:16 xxx.frm
-rwxr-xr-x 1 mysql mysql 2818732 2008-05-04 22:16 xxx.MYD
-rwxr-xr-x 1 mysql mysql  354304 2008-05-04 22:16 xxx.MYI
-rwxr-xr-x 1 mysql mysql    8618 2008-05-04 22:16 xxx.frm
-rwxr-xr-x 1 mysql mysql     400 2008-05-04 22:16 xxx.MYD
-rwxr-xr-x 1 mysql mysql    2048 2008-05-04 22:16 xxx.MYI
-rwxr-xr-x 1 mysql mysql   13042 2008-05-04 22:16 xxx.frm
-rwxr-xr-x 1 mysql mysql    3180 2008-05-04 22:16 xxx.MYD
-rwxr-xr-x 1 mysql mysql    2048 2008-05-04 22:16 xxx.MYI
-rwxr-xr-x 1 mysql mysql    8678 2008-05-04 22:16 xxx.frm
-rwxr-xr-x 1 mysql mysql  679892 2008-05-04 22:16 xxx.MYD
-rwxr-xr-x 1 mysql mysql  244736 2008-05-04 22:16 xxx.MYI

[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
pid-file        = /var/run/mysqld/mysqld.pid
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /data/mysql
tmpdir          = /tmp
language        = /usr/share/mysql/english

$ls -la /data
drwxrwxrwx  3 mysql   mysql       4096 2008-05-04 22:16 mysql
drwx------  4 pliersn pliersn     4096 2008-04-26 17:37 .Trash-1000
drwx------  2 pliersn pliersn     8192 2008-04-12 16:27 .Trash-pliersn
drwx------  2 root    root        4096 2007-03-05 10:10 .Trash-root

$ ls /data/mysql -la
total 12
drwxrwxrwx  3 mysql mysql   4096 2008-05-04 22:16 .
drwxrwxr-x 20 root  pliersn 4096 2008-04-30 21:22 ..
drwxrwxrwx  2 mysql mysql   4096 2008-05-04 22:16 get
$ ls /data/mysql/get -la
total 6744
drwxrwxrwx 2 mysql mysql    4096 2008-05-04 22:16 .
drwxrwxrwx 3 mysql mysql    4096 2008-05-04 22:16 ..
-rwxrwxrwx 1 mysql mysql    8712 2008-05-04 22:16 xxx.frm
-rwxrwxrwx 1 mysql mysql 1433384 2008-05-04 22:16 xxx.MYD
-rwxrwxrwx 1 mysql mysql 1248256 2008-05-04 22:16 xxx.MYI
-rwxrwxrwx 1 mysql mysql      61 2008-05-04 22:16 db.opt
-rwxrwxrwx 1 mysql mysql    9006 2008-05-04 22:16 xxx.frm
-rwxrwxrwx 1 mysql mysql 2818732 2008-05-04 22:16 xxx.MYD
-rwxrwxrwx 1 mysql mysql  354304 2008-05-04 22:16 xxx.MYI
-rwxrwxrwx 1 mysql mysql    8618 2008-05-04 22:16 xxx.frm
-rwxrwxrwx 1 mysql mysql     400 2008-05-04 22:16 xxx.MYD
-rwxrwxrwx 1 mysql mysql    2048 2008-05-04 22:16 xxx.MYI
-rwxrwxrwx 1 mysql mysql   13042 2008-05-04 22:16 xxx.frm
-rwxrwxrwx 1 mysql mysql    3180 2008-05-04 22:16 xxx.MYD
-rwxrwxrwx 1 mysql mysql    2048 2008-05-04 22:16 xxx.MYI
-rwxrwxrwx 1 mysql mysql    8678 2008-05-04 22:16 xxx.frm
-rwxrwxrwx 1 mysql mysql  679892 2008-05-04 22:16 xxx.MYD
-rwxrwxrwx 1 mysql mysql  244736 2008-05-04 22:16 xxx.MYI

$sudo /etc/init.d/mysql start

#!/bin/bash
#
### BEGIN INIT INFO
# Provides:          mysql
# Required-Start:    $remote_fs $syslog mysql-ndb
# Required-Stop:     $remote_fs $syslog mysql-ndb
# Should-Start:      $network $named $time
# Should-Stop:       $network $named $time
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: Start and stop the mysql database server daemon
# Description:       Controls the main MySQL database server daemon "mysqld"
#                    and its wrapper script "mysqld_safe".
### END INIT INFO
#
set -e
set -u
${DEBIAN_SCRIPT_DEBUG:+ set -v -x}

test -x /usr/sbin/mysqld || exit 0

. /lib/lsb/init-functions

SELF=$(cd $(dirname $0); pwd -P)/$(basename $0)
CONF=/etc/mysql/my.cnf
MYADMIN="/usr/bin/mysqladmin --defaults-file=/etc/mysql/debian.cnf"

# priority can be overriden and "-s" adds output to stderr
ERR_LOGGER="logger -p daemon.err -t /etc/init.d/mysql -i"

# Safeguard (relative paths, core dumps..)
cd /
umask 077

# mysqladmin likes to read /root/.my.cnf. This is usually not what I want
# as many admins e.g. only store a password without a username there and
# so break my scripts.
export HOME=/etc/mysql/

## Fetch a particular option from mysql's invocation.
#
# Usage: void mysqld_get_param option
mysqld_get_param() {
	/usr/sbin/mysqld --print-defaults \
		| tr " " "\n" \
		| grep -- "--$1" \
		| tail -n 1 \
		| cut -d= -f2
}

## Do some sanity checks before even trying to start mysqld.
sanity_checks() {
  # check for config file
  if [ ! -r /etc/mysql/my.cnf ]; then
    log_warning_msg "$0: WARNING: /etc/mysql/my.cnf cannot be read. See README.Debian.gz"
    echo                "WARNING: /etc/mysql/my.cnf cannot be read. See README.Debian.gz" | $ERR_LOGGER
  fi

  # check for diskspace shortage
  datadir=`mysqld_get_param datadir`
  if LC_ALL=C BLOCKSIZE= df --portability $datadir/. | tail -n 1 | awk '{ exit ($4>4096) }'; then
    log_failure_msg "$0: ERROR: The partition with $datadir is too full!"
    echo                "ERROR: The partition with $datadir is too full!" | $ERR_LOGGER
    exit 1
  fi
}

## Checks if there is a server running and if so if it is accessible.
#
# check_alive insists on a pingable server
# check_dead also fails if there is a lost mysqld in the process list
#
# Usage: boolean mysqld_status [check_alive|check_dead] [warn|nowarn]
mysqld_status () {
    ping_output=`$MYADMIN ping 2>&1`; ping_alive=$(( ! $? ))

    ps_alive=0
    pidfile=`mysqld_get_param pid-file`
    if [ -f "$pidfile" ] && ps `cat $pidfile` >/dev/null 2>&1; then ps_alive=1; fi
    
    if [ "$1" = "check_alive"  -a  $ping_alive = 1 ] ||
       [ "$1" = "check_dead"   -a  $ping_alive = 0  -a  $ps_alive = 0 ]; then
	return 0 # EXIT_SUCCESS
    else
  	if [ "$2" = "warn" ]; then
  	    echo -e "$ps_alive processes alive and '$MYADMIN ping' resulted in\n$ping_output\n" | $ERR_LOGGER -p daemon.debug
	fi
  	return 1 # EXIT_FAILURE
    fi
}

#
# main()
#

case "${1:-''}" in
  'start')
	sanity_checks;
	# Start daemon
	log_daemon_msg "Starting MySQL database server" "mysqld"
	if mysqld_status check_alive nowarn; then
	   log_progress_msg "already running"
	   log_end_msg 0
	else
  	    /usr/bin/mysqld_safe > /dev/null 2>&1 &
	    # 6s was reported in #352070 to be too few when using ndbcluster
	    for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14; do
                sleep 1
	        if mysqld_status check_alive nowarn ; then break; fi
		log_progress_msg "."
	    done
	    if mysqld_status check_alive warn; then
                log_end_msg 0
	        # Now start mysqlcheck or whatever the admin wants.
	        output=$(/etc/mysql/debian-start)
		[ -n "$output" ] && log_action_msg "$output"
	    else
	        log_end_msg 1
		log_failure_msg "Please take a look at the syslog"
	    fi
	fi

	# Some warnings
        if $MYADMIN variables | egrep -q have_bdb.*YES; then
            echo "BerkeleyDB is obsolete, see /usr/share/doc/mysql-server-5.0/README.Debian.gz" | $ERR_LOGGER -p daemon.info
        fi
        if [ -f /etc/mysql/debian-log-rotate.conf ]; then
            echo "/etc/mysql/debian-log-rotate.conf is obsolete, see /usr/share/doc/mysql-server-5.0/NEWS.Debian.gz" | $ERR_LOGGER -p daemon.info
        fi
	;;

  'stop')
	# * As a passwordless mysqladmin (e.g. via ~/.my.cnf) must be possible
	# at least for cron, we can rely on it here, too. (although we have 
	# to specify it explicit as e.g. sudo environments points to the normal
	# users home and not /root)
	log_daemon_msg "Stopping MySQL database server" "mysqld"
	if ! mysqld_status check_dead nowarn; then
	  set +e
	  shutdown_out=`$MYADMIN shutdown 2>&1`; r=$?
	  set -e
	  if [ "$r" -ne 0 ]; then
	    log_end_msg 1
	    [ "$VERBOSE" != "no" ] && log_failure_msg "Error: $shutdown_out"
	    log_daemon_msg "Killing MySQL database server by signal" "mysqld"
	    killall -15 mysqld
            server_down=
	    for i in 1 2 3 4 5 6 7 8 9 10; do
              sleep 1
              if mysqld_status check_dead nowarn; then server_down=1; break; fi
            done
          if test -z "$server_down"; then killall -9 mysqld; fi
	  fi
        fi

        if ! mysqld_status check_dead warn; then
	  log_end_msg 1
	  log_failure_msg "Please stop MySQL manually and read /usr/share/doc/mysql-server-5.0/README.Debian.gz!"
	  exit -1
	else
	  log_end_msg 0
        fi
	;;

  'restart')
	set +e; $SELF stop; set -e
	$SELF start 
	;;

  'reload'|'force-reload')
  	log_daemon_msg "Reloading MySQL database server" "mysqld"
	$MYADMIN reload
	log_end_msg 0
	;;

  'status')
	if mysqld_status check_alive nowarn; then
	  log_action_msg "$($MYADMIN version)"
	else
	  log_action_msg "MySQL is stopped."
	  exit 3
	fi
  	;;

  *)
	echo "Usage: $SELF start|stop|restart|reload|force-reload|status"
	exit 1
	;;
esac

mysql                       mysqld                      mysqlimport                 mysqltestmanager
mysqlaccess                 mysqld_multi                mysql_install_db            mysqltestmanagerc
mysqladmin                  mysqld_safe                 mysqlmanager                mysqltestmanager-pwgen
mysqlbinlog                 mysqldump                   mysqlreport                 mysql_tzinfo_to_sql
mysqlbug                    mysqldumpslow               mysql_secure_installation   mysql_upgrade
mysqlcheck                  mysql_explain_log           mysql_setpermission         mysql_upgrade_shell
mysql_client_test           mysql_find_rows             mysqlshow                   mysql_waitpid
mysql_client_test_embedded  mysql_fix_extensions        mysql_tableinfo             mysql_zap
mysql_config                mysql_fix_privilege_tables  mysqltest                   
mysql_convert_table_format  mysqlhotcopy                mysqltest_embedded

$ sudo mysql_install_db --user=mysql
Installing MySQL system tables...
080505 13:39:59 [Warning] Can't create test file /data/mysql/pliersn-laptop.lower-test
080505 13:39:59 [Warning] Can't create test file /data/mysql/pliersn-laptop.lower-test
ERROR: 1005  Can't create table 'db' (errno: 13)
080505 13:39:59 [ERROR] Aborting

080505 13:39:59 [Note] /usr/sbin/mysqld: Shutdown complete

Installation of system tables failed!

Examine the logs in /data/mysql for more information.
You can try to start the mysqld daemon with:
/usr/sbin/mysqld --skip-grant &
and use the command line tool
/usr/bin/mysql to connect to the mysql
database and look at the grant tables:

shell> /usr/bin/mysql -u root mysql
mysql> show tables

Try 'mysqld --help' if you have problems with paths. Using --log
gives you a log in /data/mysql that may be helpful.

The latest information about MySQL is available on the web at
 http://www.mysql.com
Please consult the MySQL manual section: 'Problems running mysql_install_db',
and the manual section that describes problems on your OS.
Another information source is the MySQL email archive.
Please check all of the above before mailing us!
And if you do mail us, you MUST use the /usr/bin/mysqlbug script!

Filesystem            Size  Used Avail Use% Mounted on
/dev/sda9              25G  9.1G   15G  40% /
varrun                728M  116K  728M   1% /var/run
varlock               728M     0  728M   0% /var/lock
udev                  728M   68K  728M   1% /dev
devshm                728M   36K  728M   1% /dev/shm
lrm                   728M   38M  690M   6% /lib/modules/2.6.24-16-generic/volatile
/dev/sda5              99M   24M   71M  26% /boot
/dev/sda8             9.0G  7.1G  1.5G  83% /data