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Thread: Can't update MySQL/MariaDB with Custombuild on Debian 9, can't connect through socket

  1. #1
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    Question Can't update MySQL/MariaDB with Custombuild on Debian 9, can't connect through socket

    Code:
    ~# /usr/local/directadmin/custombuild/build mysql
    mv: 'mariadb-5.5.58-linux-x86_64.tar.gz' and '/usr/local/mariadb-5.5.58-linux-x86_64.tar.gz' are the same file
    Stopping mysqld ...
    Synchronizing state of mysqld.service with SysV service script with /lib/systemd/systemd-sysv-install.
    Executing: /lib/systemd/systemd-sysv-install enable mysqld
    update-rc.d: error: mysqld Default-Start contains no runlevels, aborting.
    Ensuring local-infile is disabled for security reasons in MySQL configuration file...
    Giving mysqld a few seconds to start up...
    /usr/local/mysql/bin/mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/usr/local/mysql/data/mysql.sock' (2) when trying to connect
    FATAL ERROR: Upgrade failed
    Restarting MySQL.
    I don't understand what's wrong with the socket. Every other application including mysqld has MySQL/MariaDB working perfectly with that same socket. It's only failing during upgrades like these.
    I've looked through past posts on this forum and tried suggestions, but haven't found a solution yet.

    Code:
    ~# ls -l /usr/local/mysql/data/mysql.sock
    srwxrwxrwx 1 mysql mysql 0 Jan 12 18:34 /usr/local/mysql/data/mysql.sock
    Code:
    ~# nano /etc/my.cnf
    [client]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqld]
    local-infile = 0
    interactive_timeout     = 60
    join_buffer_size        = 128K
    key_buffer_size         = 100M
    max_allowed_packet      = 16M
    max_connections         = 40
    max_heap_table_size     = 16M
    myisam_sort_buffer_size = 64M
    port                    = 3306
    query_cache_size        = 4M
    socket                  = /usr/local/mysql/data/mysql.sock
    table_open_cache        = 512
    thread_cache_size       = 8
    tmp_table_size          = 16M
    wait_timeout            = 30
    
    [mysqldump]
    max_allowed_packet      = 16M
    quick
    
    [mysql]
    no-auto-rehash
    
    [myisamchk]
    key_buffer_size         = 64M
    read_buffer             = 2M
    sort_buffer_size        = 64M
    write_buffer            = 2M
    
    [mysqlhotcopy]
    interactive-timeout
    Code:
    ~# /usr/local/directadmin/conf/mysql.conf
    user=da_admin
    passwd=**********
    socket=/usr/local/mysql/data/mysql.sock
    Code:
    ~# /usr/local/directadmin/conf/my.cnf
    [client]
    user=da_admin
    password=**********
    socket=/usr/local/mysql/data/mysql.sock
    Code:
    ~# mysql --help --verbose
    mysql  Ver 15.1 Distrib 5.5.58-MariaDB, for Linux (x86_64) using readline 5.1
    Copyright (c) 2000, 2017, Oracle, MariaDB Corporation Ab and others.
    
    Usage: mysql [OPTIONS] [database]
    
    Default options are read from the following files in the given order:
    /etc/my.cnf /etc/mysql/my.cnf ~/.my.cnf
    The following groups are read: mysql client client-server client-mariadb
    Code:
    ~# nano /home/mysql/**********.com.err
    180112 16:30:07 [Note] /usr/local/mysql/bin/mysqld: Normal shutdown
    
    180112 16:30:07 [Note] Event Scheduler: Purging the queue. 0 events
    180112 16:30:07  InnoDB: Starting shutdown...
    180112 16:30:09  InnoDB: Shutdown completed; log sequence number 234248205
    180112 16:30:10 [Note] /usr/local/mysql/bin/mysqld: Shutdown complete
    
    180112 16:30:10 mysqld_safe mysqld from pid file /usr/local/mysql/data/mysqld.pid ended
    180112 16:31:31 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
    180112 16:31:34 [Note] /usr/local/mysql/bin/mysqld (mysqld 5.5.58-MariaDB) starting as process 18726 ...
    180112 16:31:35 InnoDB: The InnoDB memory heap is disabled
    180112 16:31:35 InnoDB: Mutexes and rw_locks use GCC atomic builtins
    180112 16:31:35 InnoDB: Compressed tables use zlib 1.2.3
    180112 16:31:35 InnoDB: Using Linux native AIO
    180112 16:31:35 InnoDB: Initializing buffer pool, size = 128.0M
    180112 16:31:35 InnoDB: Completed initialization of buffer pool
    180112 16:31:35 InnoDB: highest supported file format is Barracuda.
    180112 16:31:42  InnoDB: Waiting for the background threads to start
    180112 16:31:43 Percona XtraDB (http://www.percona.com) 5.5.55-MariaDB-38.9 started; log sequence number 234248205
    180112 16:31:43 [Note] Server socket created on IP: '0.0.0.0'.
    180112 16:31:43 [Note] /usr/local/mysql/bin/mysqld: Normal shutdown
    
    180112 16:31:43 [Note] Event Scheduler: Loaded 0 events
    180112 16:31:43 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
    Version: '5.5.58-MariaDB'  socket: '/usr/local/mysql/data/mysql.sock'  port: 3306  Source distribution
    180112 16:31:43 [Note] Event Scheduler: Purging the queue. 0 events
    180112 16:31:43  InnoDB: Starting shutdown...
    180112 16:31:52  InnoDB: Shutdown completed; log sequence number 234248205
    180112 16:31:52 [Note] /usr/local/mysql/bin/mysqld: Shutdown complete
    
    180112 16:31:53 mysqld_safe mysqld from pid file /usr/local/mysql/data/mysqld.pid ended
    180112 16:31:53 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
    180112 16:31:53 [Note] /usr/local/mysql/bin/mysqld (mysqld 5.5.58-MariaDB) starting as process 19716 ...
    180112 16:31:53 InnoDB: The InnoDB memory heap is disabled
    180112 16:31:53 InnoDB: Mutexes and rw_locks use GCC atomic builtins
    180112 16:31:53 InnoDB: Compressed tables use zlib 1.2.3
    180112 16:31:53 InnoDB: Using Linux native AIO
    180112 16:31:53 InnoDB: Initializing buffer pool, size = 128.0M
    180112 16:31:53 InnoDB: Completed initialization of buffer pool
    180112 16:31:53 InnoDB: highest supported file format is Barracuda.
    180112 16:31:53  InnoDB: Waiting for the background threads to start
    180112 16:31:54 Percona XtraDB (http://www.percona.com) 5.5.55-MariaDB-38.9 started; log sequence number 234248205
    180112 16:31:54 [Note] Server socket created on IP: '0.0.0.0'.
    180112 16:31:54 [Note] Event Scheduler: Loaded 0 events
    180112 16:31:54 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
    Version: '5.5.58-MariaDB'  socket: '/usr/local/mysql/data/mysql.sock'  port: 3306  Source distribution
    Last edited by HolyDiver; 01-12-2018 at 09:55 AM.

  2. #2
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    Hello,

    Try and put the socket definition under every section of my.cnf file:

    Code:
    socket                  = /usr/local/mysql/data/mysql.sock
    One of our servers with Debian has this:

    Code:
    [mysqld_safe]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysql_upgrade]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysqladmin]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysqlbinlog]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysqlcheck]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysqldump]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    
    
    [mysqlimport]
    port                           = 3306
    socket                         = /usr/local/mysql/data/mysql.sock
    since Mar 26 2017 without modifications.

  3. #3
    Join Date
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    I've added the socket to each section of my.cnf, but the same error keeps happening

    Code:
    ~# nano /etc/my.cnf
    [client]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [myisamchk]
    key_buffer_size         = 64M
    port                    = 3306
    read_buffer             = 2M
    socket                  = /usr/local/mysql/data/mysql.sock
    sort_buffer_size        = 64M
    write_buffer            = 2M
    
    [mysql]
    no-auto-rehash
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysql_upgrade]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqladmin]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqlbinlog]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqlcheck]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqld]
    interactive_timeout     = 60
    join_buffer_size        = 128K
    key_buffer_size         = 100M
    local-infile            = 0
    max_allowed_packet      = 16M
    max_connections         = 40
    max_heap_table_size     = 16M
    myisam_sort_buffer_size = 64M
    port                    = 3306
    query_cache_size        = 4M
    socket                  = /usr/local/mysql/data/mysql.sock
    table_open_cache        = 512
    thread_cache_size       = 8
    tmp_table_size          = 16M
    wait_timeout            = 30
    
    [mysqld_safe]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqldump]
    max_allowed_packet      = 16M
    port                    = 3306
    quick
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqlhotcopy]
    interactive-timeout
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    
    [mysqlimport]
    port                    = 3306
    socket                  = /usr/local/mysql/data/mysql.sock
    Code:
    ~# /usr/local/directadmin/custombuild/build mysql
    mv: 'mariadb-5.5.58-linux-x86_64.tar.gz' and '/usr/local/mariadb-5.5.58-linux-x86_64.tar.gz' are the same file
    Stopping mysqld ...
    Synchronizing state of mysqld.service with SysV service script with /lib/systemd/systemd-sysv-install.
    Executing: /lib/systemd/systemd-sysv-install enable mysqld
    update-rc.d: error: mysqld Default-Start contains no runlevels, aborting.
    mv: cannot stat '/etc/mysql/my.cnf': No such file or directory
    Ensuring local-infile is disabled for security reasons in MySQL configuration file...
    Giving mysqld a few seconds to start up...
    /usr/local/mysql/bin/mysqlcheck: Got error: 2002: Can't connect to local MySQL server through socket '/usr/local/mysql/data/mysql.sock' (2) when trying to connect
    FATAL ERROR: Upgrade failed
    Restarting MySQL.
    Code:
    ~# nano /home/mysql/********.com.err
    180112 22:46:09 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
    180112 22:46:11 [Note] /usr/local/mysql/bin/mysqld (mysqld 5.5.58-MariaDB) starting as process 3329 ...
    180112 22:46:12 InnoDB: The InnoDB memory heap is disabled
    180112 22:46:12 InnoDB: Mutexes and rw_locks use GCC atomic builtins
    180112 22:46:12 InnoDB: Compressed tables use zlib 1.2.3
    180112 22:46:12 InnoDB: Using Linux native AIO
    180112 22:46:12 InnoDB: Initializing buffer pool, size = 128.0M
    180112 22:46:13 InnoDB: Completed initialization of buffer pool
    180112 22:46:13 InnoDB: highest supported file format is Barracuda.
    180112 22:46:18  InnoDB: Waiting for the background threads to start
    180112 22:46:19 Percona XtraDB (http://www.percona.com) 5.5.55-MariaDB-38.9 started; log sequence number$
    180112 22:46:19 [Note] Server socket created on IP: '0.0.0.0'.
    180112 22:46:19 [Note] /usr/local/mysql/bin/mysqld: Normal shutdown
    
    180112 22:46:20 [Note] Event Scheduler: Loaded 0 events
    180112 22:46:20 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
    Version: '5.5.58-MariaDB'  socket: '/usr/local/mysql/data/mysql.sock'  port: 3306  Source distribution
    180112 22:46:20 [Note] Event Scheduler: Purging the queue. 0 events
    180112 22:46:20  InnoDB: Starting shutdown...
    180112 22:46:45  InnoDB: Shutdown completed; log sequence number 234248235
    180112 22:46:45 [Note] /usr/local/mysql/bin/mysqld: Shutdown complete
    
    180112 22:46:45 mysqld_safe mysqld from pid file /usr/local/mysql/data/mysqld.pid ended
    180112 22:46:45 mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
    180112 22:46:45 [Note] /usr/local/mysql/bin/mysqld (mysqld 5.5.58-MariaDB) starting as process 4459 ...
    180112 22:46:45 InnoDB: The InnoDB memory heap is disabled
    180112 22:46:45 InnoDB: Mutexes and rw_locks use GCC atomic builtins
    180112 22:46:45 InnoDB: Compressed tables use zlib 1.2.3
    180112 22:46:45 InnoDB: Using Linux native AIO
    180112 22:46:45 InnoDB: Initializing buffer pool, size = 128.0M
    180112 22:46:45 InnoDB: Completed initialization of buffer pool
    180112 22:46:45 InnoDB: highest supported file format is Barracuda.
    180112 22:46:45  InnoDB: Waiting for the background threads to start
    180112 22:46:46 Percona XtraDB (http://www.percona.com) 5.5.55-MariaDB-38.9 started; log sequence number$
    180112 22:46:46 [Note] Server socket created on IP: '0.0.0.0'.
    180112 22:46:46 [Note] Event Scheduler: Loaded 0 events
    180112 22:46:46 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
    Version: '5.5.58-MariaDB'  socket: '/usr/local/mysql/data/mysql.sock'  port: 3306  Source distribution

  4. #4
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    Apr 2005
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    Seems something is really wrong with your setup. First you had issues with PHP-FPM sockets, and now you have an issue with MySQL. Did you by any chance change recursively permissions on root and/or parent directories?

    Code:
    ls -la /usr/local/mysql/data/mysql.sock
    ls -lda /usr/local/mysql/data/
    ls -lda /usr/local/mysql/
    ls -lda /usr/local/
    ls -lda /usr/
    ls -lda /
    ?

    Try to simlink /etc/my.cnf to /etc/mysql/my.cnf

    Does OS in Directadmin license match the version you really run? I mean do you really have a directadmin license for Debian 9?

    Do you have a native kernel? Or hardened from a 3rd party?

    If nothing helps, you might need to contact a directadmin support for a free help (they might login to your server and check what is wrong)? Or feel free to hire me for this job.

  5. #5
    Join Date
    Aug 2015
    Posts
    311
    What are you running at the moment? MySQL or MariaDB.
    Are you still on custombuild 1?
    Kind regards, Fred

    Alentejo Webdesign
    Webdesign with Passion is what we do
    Web development, Hosting, Speed Optimizing & More......

  6. #6
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    Quote Originally Posted by zEitEr View Post
    Seems something is really wrong with your setup. First you had issues with PHP-FPM sockets, and now you have an issue with MySQL. Did you by any chance change recursively permissions on root and/or parent directories?
    I think I have this issue with MySQL/MariaDB since I upgraded to Debian 8 last year, I used to think the upgrade sworked because the version number gets increased even with failed upgrades. I haven't touched the permission of those directories.
    Code:
    ~# ls -lda /usr/local/mysql/data/mysql.sock
    srwxrwxrwx 1 mysql mysql 0 Jan 12 22:46 /usr/local/mysql/data/mysql.sock
    
    ~# ls -lda /usr/local/mysql/data/
    drwx--x--x 11 mysql mysql 4096 Jan 12 22:56 /usr/local/mysql/data/
    
    ~# ls -lda /usr/local/mysql/
    drwxr-sr-x 12 mysql mysql 4096 Jan 12 22:46 /usr/local/mysql/
    
    ~# ls -lda /usr/local/
    drwxrwsr-x 20 root staff 4096 Jan 12 22:46 /usr/local/
    
    ~# ls -lda /usr/
    drwxr-xr-x 19 root root 4096 Jan  1 03:16 /usr/
    
    ~# ls -lda /
    drwxr-xr-x 24 root root 4096 Jan  2 21:36 /
    Quote Originally Posted by zEitEr View Post
    Try to simlink /etc/my.cnf to /etc/mysql/my.cnf
    I've tried this, but the result is the same.

    Quote Originally Posted by zEitEr View Post
    Does OS in Directadmin license match the version you really run? I mean do you really have a directadmin license for Debian 9?
    Yes, the license is set on Debian 9 64-bit. I even recompiled DirectAdmin to be sure it matches.

    Quote Originally Posted by zEitEr View Post
    Do you have a native kernel? Or hardened from a 3rd party?
    It runs on the latest native kernel provided by apt-get.
    Code:
    ~# uname -rv
    4.9.0-5-amd64 #1 SMP Debian 4.9.65-3+deb9u2 (2018-01-04)
    Quote Originally Posted by zEitEr View Post
    If nothing helps, you might need to contact a directadmin support for a free help (they might login to your server and check what is wrong)? Or feel free to hire me for this job.
    Good to know, though I hope to learn from this

    Quote Originally Posted by Awd View Post
    What are you running at the moment? MySQL or MariaDB.
    Are you still on custombuild 1?
    I'm running MariaDB 5.5 on Custombuild2.
    Last edited by HolyDiver; 01-13-2018 at 04:15 AM.

  7. #7
    Join Date
    Aug 2015
    Posts
    311
    Then to update you need to use this:

    Code:
    cd /usr/local/directadmin/custombuild
    ./build set mariadb 5.5
    ./build set mysql_inst mariadb
    ./build set mysql_backup yes
    ./build update
    ./build mariadb
    Kind regards, Fred

    Alentejo Webdesign
    Webdesign with Passion is what we do
    Web development, Hosting, Speed Optimizing & More......

  8. #8
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    Well permissions look more or less the same as I have here. The difference is only here:

    Code:
    drwxr-xr-x 81 mysql mysql 4096 Dec 27 05:08 /usr/local/mysql/data/
    MySQL logs do not show errors.

    If upgrade fails, I'd try and do a completely new installation of MariaDB on the server. Check https://help.directadmin.com/ for the instructions on how to re-install MySQL/MariaDB.

  9. #9
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    Location
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    I tried Awd's suggestion to try ./build mariadb instead (I thought it'd just run ./build mysql in the background) and the actual first time it didn't gave the socket error, instead it said to use --force to force an upgrade (which should be the default setting according to the DA documentation). Every other attempt after that, including trying /usr/local/mysql/bin/mysql_upgrade --force --defaults-extra-file=/usr/local/directadmin/conf/my.cnf, gave the socket error again.

    Changing the permissions of /usr/local/mysql/data/ to 755 had no effect either.

    I'll be trying a new installation of MariaDB later today

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