Issue Mysql issues

Discussion in 'Plesk Onyx' started by Mike Hughes, Apr 19, 2017 at 7:48 AM.

  1. Mike Hughes

    Mike Hughes New Pleskian

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    Hello all,

    I need your help please.

    I updated our centos server 6.8 Final to the new version of mysql. Its not gone well.

    I followed over the How to upgrade MySQL 5.5 to 5.6 on Linux

    • I did take a copy of my DB files.
    • I know my webserver files are still intacted
    I have lost access to the Plesk GUI but still have ssh access.

    Mysql is nor started and I get the following

    service mysqld start

    MySQL Daemon failed to start.
    Starting mysqld: [FAILED]
    [xxx@name ~]#


    Some more info so you can maybe help

    [xxx@name~]# mysql
    ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (111)

    Can any of you help point how to fix please?
     
  2. Peter Debik

    Peter Debik Golden Pleskian Plesk Guru

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    The issue here is that MySQL does not start. You need to find out why it does not start and solve the underlying problem. The first step is to check the error log of MySQL and /var/log/messages for details. The MySQL error_log location is normally mentioned in /etc/my.cnf.
     
  3. Mike Hughes

    Mike Hughes New Pleskian

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    Peter, many thanks for your reply.

    I have mysql up and ruining now.

    But I now have a new issues, I have move the DB back to the correct location. But I still cant get access to the Plesk GUI and my websites are not up either

    I assume the mysql upgrade some how disjointed the db connection to the Plesk gui website and wordpress sites.

    Is there any help you can offer around this?

    Thanks

    From File: /var/log/mysqld.log

    Code:
      2017-04-19T10:18:25.710473Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation $
    2017-04-19T10:18:25.816993Z 0 [Note] InnoDB: PUNCH HOLE support available
    2017-04-19T10:18:25.817023Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
    2017-04-19T10:18:25.817037Z 0 [Note] InnoDB: Uses event mutexes
    2017-04-19T10:18:25.817051Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
    2017-04-19T10:18:25.817064Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
    2017-04-19T10:18:25.817071Z 0 [Note] InnoDB: Using Linux native AIO
    2017-04-19T10:18:25.817394Z 0 [Note] InnoDB: Number of pools: 1
    2017-04-19T10:18:25.817589Z 0 [Note] InnoDB: Not using CPU crc32 instructions
    2017-04-19T10:18:25.829226Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
    2017-04-19T10:18:25.842722Z 0 [Note] InnoDB: Completed initialization of buffer pool
    2017-04-19T10:18:25.846122Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
    2017-04-19T10:18:25.951998Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
    2017-04-19T10:18:26.067158Z 0 [Note] InnoDB: Creating tablespace and datafile system tables.
    2017-04-19T10:18:26.134551Z 0 [Note] InnoDB: Tablespace and datafile system tables created.
    2017-04-19T10:18:26.141749Z 0 [Warning] InnoDB: Upgrading redo log: 2*3072 pages, LSN=208594302
    2017-04-19T10:18:26.245456Z 0 [Warning] InnoDB: Starting to delete and rewrite log files.
    2017-04-19T10:18:26.273096Z 0 [Note] InnoDB: Setting log file ./ib_logfile101 size to 48 MB
    2017-04-19T10:18:26.934005Z 0 [Note] InnoDB: Setting log file ./ib_logfile1 size to 48 MB
    2017-04-19T10:18:27.844757Z 0 [Note] InnoDB: Renaming log file ./ib_logfile101 to ./ib_logfile0
    2017-04-19T10:18:27.844873Z 0 [Warning] InnoDB: New log files created, LSN=208594302
    2017-04-19T10:18:28.013811Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
    2017-04-19T10:18:28.014132Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
    2017-04-19T10:18:28.112465Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
    2017-04-19T10:18:28.331078Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
    2017-04-19T10:18:28.331131Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
    2017-04-19T10:18:28.388653Z 0 [Note] InnoDB: Creating sys_virtual system tables.
    2017-04-19T10:18:28.393858Z 0 [Note] InnoDB: sys_virtual table created
    2017-04-19T10:18:28.394056Z 0 [Note] InnoDB: Waiting for purge to start
    2017-04-19T10:18:28.444251Z 0 [Note] InnoDB: 5.7.18 started; log sequence number 0
    2017-04-19T10:18:28.444973Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
    2017-04-19T10:18:28.445041Z 0 [ERROR] InnoDB: Cannot open '/var/lib/mysql/ib_buffer_pool' for reading: No such file or directory
    2017-04-19T10:18:28.445421Z 0 [Note] Plugin 'FEDERATED' is disabled.
    2017-04-19T10:18:28.575320Z 0 [Warning] System table 'plugin' is expected to be transactional.
    2017-04-19T10:18:28.577319Z 0 [Note] Salting uuid generator variables, current_pid: 24659, server_start_time: 1492597105, bytes_sent: 0,
    2017-04-19T10:18:28.577677Z 0 [Note] Generated uuid: '8800175b-24e9-11e7-af69-5254001fa66c', server_start_time: 6940891452200688068, bytes_sent: 62369104
    2017-04-19T10:18:28.577702Z 0 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: 8$
    2017-04-19T10:18:28.600197Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
    2017-04-19T10:18:28.622294Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
    2017-04-19T10:18:28.622655Z 0 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
    2017-04-19T10:18:28.622900Z 0 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
    2017-04-19T10:18:28.623117Z 0 [Note] Server socket created on IP: '0.0.0.0'.
    2017-04-19T10:18:28.626168Z 0 [Warning] Failed to open optimizer cost constant tables
    
    2017-04-19T10:18:28.721812Z 0 [Warning] 'user' entry 'horde@localhost' ignored in --skip-name-resolve mode.
    2017-04-19T10:18:28.721865Z 0 [ERROR] Fatal error: mysql.user table is damaged. Please run mysql_upgrade.
    2017-04-19T10:18:28.722033Z 0 [ERROR] Aborting
    
    2017-04-19T10:18:28.727183Z 0 [Note] Binlog end
    2017-04-19T10:18:28.727360Z 0 [Note] Shutting down plugin 'ngram'
    

    Some more info so you can maybe help

    [xxx@xxxxx ~]# mysql
    ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/lib/mysql/mysql.sock' (111)
     
  4. Peter Debik

    Peter Debik Golden Pleskian Plesk Guru

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    Looks like a full scale disaster. Have you tried to run
    # mysql_upgrade
    as recommended? You might need to run
    # mysqld --skip-grant-tables
    first, then mysql_upgrade.
     
  5. Mike Hughes

    Mike Hughes New Pleskian

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    Peter, again thanks for coming back to me, yes you are not wrong. I have mysql running now, go me! But, I know that Ples is not working. I took advice from the vendor who hires me the server, they advise to /usr/local/psa/admin/sbin/autoinstaller. That's all well and good, but that forces the server to fresh install and that means I loose my backs up.

    Here is the thing, I know there is backup on the server, I can see this via /var/lib/psa/dumps/

    Do you know of a way to restore CentOS. I have read over "pleskrestore: Restoration from Backup" (pleskrestore: Restoration from Backup) But I don't quite understand how to do the restore from my back up point.

    The goal I need is, Plesk up and working, my websites back up and running and no to loose my backups.

    Failing this I am in a screwed and will have to do a full fresh CentOS/Plesk intsalls ( i have this option via 123-reg)

    Thanks
    Mike
     
  6. UFHH01

    UFHH01 Platinum Pleskian Plesk Guru

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    Hi Mike Hughes,

    did you know that Plesk comes with the Plesk Repair Utility? In most cases, it will fix plesk-related issues/errors/problems and you don't have to re-install your server at all. ;)


    Example usage ( logged in as user "root" over SSH ):
    Code:
    plesk repair installation -y -y

     
  7. Peter Debik

    Peter Debik Golden Pleskian Plesk Guru

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    In case the repair fails, going back to the question with the local backups: If your backups are only local you can probably (no guarantee)

    a) look into /etc/psa/psa.conf to find out the backup paths. They will probaby be
    DUMP_D /var/lib/psa/dumps
    DUMP_TMP_D /usr/local/psa/PMM/tmp
    b) Copy the complete path content to a location off your server, e.g. an FTP storage space.
    c) Then reinstall the Plesk system.
    d) Then check if the paths were replaced by the reinstallation and in case they were, restore their content from your FTP backup.

    It should be possible to restore Plesk then from the local backups (through GUI, no need for the cli utitility), because the Plesk backup manager will look into the backup paths, see the XML backup definitions and list the local backups. There are some caveats, though. For one, if you have password-protected these backups with the "built-in" Plesk signature password, they cannot be restored to a "fresh" installation, because the key won't match. And you probably need to edit /usr/local/psa/admin/conf/panel.ini and set the "allowRestoreModifiedDumps" to "on":
    allowRestoreModifiedDumps = on
     
  8. Mike Hughes

    Mike Hughes New Pleskian

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    Thanks both for help.

    I now have Plesk (Version 17.0.17 Update #23, last updated on April 19, 2017 08:09 AM) back up and running. I can see my wordpress site in Plesk

    I still have a few issues here.

    The websites are giving out a 502 Bad-gate way error

    I attempted to install a a new test sub domain and install Wordpress on it and I get

    Code:
    Internal error: ODBC error #01000: [unixODBC][Driver Manager]Can't open lib '/usr/lib64/libmyodbc5.so' : file not found
    
    Message    ODBC error #01000: [unixODBC][Driver Manager]Can't open lib '/usr/lib64/libmyodbc5.so' : file not found
    File    aps_php.php
    Line    12519
    Type    Exception
    Can you offer help here? Sorry to be a pest!
     
  9. UFHH01

    UFHH01 Platinum Pleskian Plesk Guru

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