ERROR 2002 (HY000): Can't connect to local MySQL server after my.cnf update

Question

I'm trying to modify my my.cnf file in Ubuntu 12.04 to fine tune mysql. I copy pasted a file created with this tool https://tools.percona.com/wizard

This does speed up mysql but when I try to access mysql via CLI, I get the following errors:

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (13)

After I replaced my old my.cnf file everything works again. Here is my original file:

        #
        # 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
        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/

And here is my new file, anyone able to help me out here and see why I get this error after the file update? Thanks

    # Generated by Percona Configuration Wizard (http://tools.percona.com/) version REL5-20120208

    [mysql]

    # CLIENT #
    port                           = 3306
    socket                         = /var/lib/mysql/mysql.sock

    [mysqld]

    # GENERAL #
    user                           = mysql
    default-storage-engine         = InnoDB
    socket                         = /var/lib/mysql/mysql.sock
    pid-file                       = /var/lib/mysql/mysql.pid

    # MyISAM #
    key-buffer-size                = 32M
    myisam-recover                 = FORCE,BACKUP

    # SAFETY #
    max-allowed-packet             = 16M
    max-connect-errors             = 1000000

    # DATA STORAGE #
    datadir                        = /var/lib/mysql/

    # BINARY LOGGING #
    log-bin                        = /var/lib/mysql/mysql-bin
    expire-logs-days               = 14
    sync-binlog                    = 1

    # CACHES AND LIMITS #
    tmp-table-size                 = 32M
    max-heap-table-size            = 32M
    query-cache-type               = 0
    query-cache-size               = 0
    max-connections                = 500
    thread-cache-size              = 50
    open-files-limit               = 65535
    table-definition-cache         = 1024
    table-open-cache               = 2048

    # INNODB #
    innodb-flush-method            = O_DIRECT
    innodb-log-files-in-group      = 2
    innodb-log-file-size           = 256M
    innodb-flush-log-at-trx-commit = 1
    innodb-file-per-table          = 1
    innodb-buffer-pool-size        = 6G

    # LOGGING #
    log-error                      = /var/lib/mysql/mysql-error.log
    log-queries-not-using-indexes  = 1
    slow-query-log                 = 1
    slow-query-log-file            = /var/lib/mysql/mysql-slow.log

Answer 1

The simplest approach is to reset all reference to the altered path /var/lib/mysql/mysql.sock to its original value, that is /var/run/mysqld/mysqld.sock . The same goes for replacing /var/lib/mysql/mysql.pid by /var/run/mysqld/mysqld.pid . Then change references to /var/lib/mysql/error.log by /var/log/mysql/error.log , and /var/lib/mysql/mysql-slow.log to /var/log/mysql/mysql-slow.log

Alternative

Alternatively, you might add back the section "client" into your new configuration file, then update its value to match the one defined in the "mysqld" section of your new configuration file (that is /var/lib/mysql/mysqld.sock ).

[client]
    socket      = /var/lib/mysql/mysql.sock

You will then have to make sure that this directory exists, and is writable by user mysql .

Answer 2

Here is a complete replacement file.

[client]
port  = 3306
socket= /var/run/mysqld/mysqld.sock


[mysqld_safe]
socket= /var/run/mysqld/mysqld.sock
nice  = 0


[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
lc-messages-dir = /usr/share/mysql
skip-external-locking
bind-address  = 127.0.0.1
key_buffer= 16M
max_allowed_packet  = 16M
thread_stack  = 192K
thread_cache_size = 8
myisam-recover= BACKUP
query_cache_limit= 1M
query_cache_size  = 16M
log_error = /var/log/mysql/error.log
expire_logs_days = 10
max_binlog_size= 100M

###### Additions #######
default-storage-engine= InnoDB

key-buffer-size = 32M
myisam-recover  = FORCE,BACKUP

max-allowed-packet = 16M
max-connect-errors = 1000000


log-bin= /var/lib/mysql/mysql-bin
expire-logs-days= 14
sync-binlog  = 1

tmp-table-size  = 32M
max-heap-table-size= 32M
query-cache-type= 0
query-cache-size= 0
max-connections = 500
thread-cache-size  = 50
open-files-limit= 65535
table-definition-cache= 1024
table-open-cache= 2048

innodb-flush-method= O_DIRECT
innodb-log-files-in-group= 2
innodb-log-file-size  = 256M
innodb-flush-log-at-trx-commit = 1
innodb-file-per-table = 1
innodb-buffer-pool-size  = 6G

log-queries-not-using-indexes  = 1
slow-query-log  = 1
slow-query-log-file= /var/log/mysql/mysql-slow.log


[mysqldump]
quick
quote-names
max_allowed_packet  = 16M


[mysql]
port= 3306
socket = /var/run/mysqld/mysqld.sock

[isamchk]
key_buffer= 16M

!includedir /etc/mysql/conf.d/