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I'm in the process of upgrading from Drupal 6 to Drupal 7 and the upgrade process terminated due to disk usage error.

I found out that ibdata1 occupies 98% of /var. So I decided to empty this file so I can have the space again and re-run the update.php, but I got bunch of SQL PDO error.

PDOException: SQLSTATE[42000]: Syntax error or access violation: 1286 Unknown table engine 'InnoDB': SELECT name, value FROM {variable}; Array ( ) in variable_initialize() (line 943 of /var/www/vhosts/drupal/includes/bootstrap.inc).

    mysql> show engines;
    ERROR 2006 (HY000): MySQL server has gone away
    No connection. Trying to reconnect...
    Connection id:    177
    Current database: drupal_drupal

    +------------+---------+----------------------------------------------------------------+--------------+------+------------+
    | Engine     | Support | Comment                                                        | Transactions | XA   | Savepoints |
    +------------+---------+----------------------------------------------------------------+--------------+------+------------+
    | MyISAM     | DEFAULT | Default engine as of MySQL 3.23 with great performance         | NO           | NO   | NO         |
    | MRG_MYISAM | YES     | Collection of identical MyISAM tables                          | NO           | NO   | NO         |
    | BLACKHOLE  | YES     | /dev/null storage engine (anything you write to it disappears) | NO           | NO   | NO         |
    | CSV        | YES     | CSV storage engine                                             | NO           | NO   | NO         |
    | MEMORY     | YES     | Hash based, stored in memory, useful for temporary tables      | NO           | NO   | NO         |
    | FEDERATED  | NO      | Federated MySQL storage engine                                 | NULL         | NULL | NULL       |
    | ARCHIVE    | YES     | Archive storage engine                                         | NO           | NO   | NO         |
    +------------+---------+----------------------------------------------------------------+--------------+------+------------+
    7 rows in set (0.06 sec)

Do you have any idea?

  • Presumably you didn't just delete ibdata1 without taking a dump of all the databases on your server first (if you did you'll need to restore it from a backup). Have a look here for the proper steps to take to empty that file and have MySQL recreate it for you – Clive Jul 15 '12 at 12:58
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    That file is where MySQL stores it's data. You can't just delete it because it's big ;). As Clive said, you've hopefully made a backup that allows you to restore your data. – Berdir Jul 15 '12 at 13:09
  • Thanks Clive and Berdir...if you can add your answer so I can accept it as it is the steps I should take first before deleting anything owns by MySQL. Thanks for pointing me to the right direction man. Thanks also Berdir. – ninjascorner Jul 15 '12 at 13:36
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This solved my problem.

chmod 775 /var/lib/mysql

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