Plesk is not accessible and MariaDB service cannot start: InnoDB: Error: space header page consists of zero bytes in data file ./ibdata1

Symptoms

• Plesk is not accessible:

  500 PleskExceptionDatabase
  DB query failed: SQLSTATE[HY000] [2002] Connection refused 
  0: /usr/local/psa/admin/externals/Zend/Db/Adapter/Pdo/Abstract.php:144

• MariaDB service cannot start with the following error in /var/log/mariadb/mariadb.log (or /var/log/mysqld.log):

  InnoDB: Error: space header page consists of zero bytes in data file ./ibdata1

Cause

File /var/lib/mysql/ibdata1 is corrupted.

Resolution

File ibdata1 is the system tablespace for the InnoDB infrastructure. It contains several classes for information vital for InnoDB.

When the file is corrupted, the only possible solution is to restore data from backups.

Note: if you don’t have root access to Plesk server via SSH, contact your hosting provider regarding the issue

1. Connect to the server via SSH.

2. Back up the /var/lib/mysql/ directory:

   2.1. Create a new directory for storing backup:

   # mkdir /root/mysql_backup

   2.2. Backup data from the /var/lib/mysql/ to the newly created directory:

   # cp -a /var/lib/mysql/* /root/mysql_backup/

3. Remove /var/lib/mysql/ibdata1, and /var/lib/mysql/ib_logfile* files by executing commands below:

   # rm /var/lib/mysql/ibdata1

   # rm /var/lib/mysql/ib_logfile*

4. Start mariadb service:

   # service mariadb start

5. Restore Plesk related databases from a daily dump:

   # zcat mysql.daily.dump.0.gz | plesk db

6. Restore user’s databases from its dumps using backup manager.