How to convert all tables from MyISAM into InnoDB?

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If you omit the ENGINE option, the default storage engine is used. Normally, this is MyISAM, but you can change it by using the --default-storage-engine server startup option, or by setting the default-storage-engine option in the my.cnf configuration file.

You may also want to change the default storage engine just for the current session. You can do this by setting the storage_engine variable:

SET storage_engine=INNODB;

PHP Code to change the database engine

<?php
    // connect your database here first 
    // 

    // Actual code starts here 

    $sql = "SELECT TABLE_NAME FROM INFORMATION_SCHEMA.TABLES
        WHERE TABLE_SCHEMA = 'your_database_name' 
        AND ENGINE <> 'InnoDB'";

    $rs = mysql_query($sql);

    while($row = mysql_fetch_array($rs))
    {
        $tbl = $row[0];
        $sql = "ALTER TABLE $tbl ENGINE=INNODB";
        mysql_query($sql);
    }
?>
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