XF 1.2 MySQL Server has gone Away

[silence]

I get this error when rebuilding attachment thumbnails:

An exception occurred: Mysqli prepare error: MySQL server has gone away in /home/brogan/public_html/xenforo/library/Zend/Db/Statement/Mysqli.php on line 77

    Zend_Db_Statement_Mysqli->_prepare() in Zend/Db/Statement.php at line 115
    Zend_Db_Statement->__construct() in Zend/Db/Adapter/Mysqli.php at line 381
    Zend_Db_Adapter_Mysqli->prepare() in Zend/Db/Adapter/Abstract.php at line 478
    Zend_Db_Adapter_Abstract->query() in Zend/Db/Adapter/Abstract.php at line 825
    Zend_Db_Adapter_Abstract->fetchOne() in XenForo/Error.php at line 55
    XenForo_Error::unexpectedException() in XenForo/Application.php at line 363
    XenForo_Application::handleException()

I'm using Imagick, and I have 'wait_timeout' default and 'max_allowed_packet' set to 64M.

What can I do to fix this?

 

[Jeremy]

P: I get an error when attempting to load a page and it states "MySQL server has gone away".
S: This is an issue with your server and something your host will be the best to help you solve. If you attempt to reload the page/rerun the task you received the error on, it is a possibility that it will be successful. Here are some related links to this specific error:
http://dev.mysql.com/doc/refman/5.0/en/gone-away.html
http://xenforo.com/community/threads/unknown-error.56990/#post-607130

http://xenforo.com/community/threads/troubleshooting-faq-frequent-problems-solutions.62138/

 

[Mike]

You may want to try building significantly fewer per page.

 

[silence]

It's an unmanaged VPS and I'll retry building with less items per page.

 

[silence]

Ok I changed it to 10 per page and the error happens even faster now. What's weird is that php-fpm hogs all my ram during the process. I changed it from dynamic to static but it still happens.
This error is flooding my MySQL error log files:

131115  9:42:49 [Warning] Unsafe statement written to the binary log using statement format since BINLOG_FORMAT = STATEMENT. INSERT... ON DUPLICATE KEY UPDATE  on a table with more than one UNIQUE KEY is unsafe Statement: INSERT INTO xf_deferred

                                (execute_class, execute_data, unique_key, manual_execute, trigger_date)
                        VALUES
                                ('AttachmentThumb', 'a:2:{s:5:\"batch\";s:2:\"10\";s:8:\"position\";i:344;}', 'RebuildAttachmentThumb', '1', '1384526474')
                        ON DUPLICATE KEY UPDATE
                                execute_class = VALUES(execute_class),
                                execute_data = VALUES(execute_data),
                                manual_execute = VALUES(manual_execute),
                                trigger_date = VALUES(trigger_date)

 

[Mike]

Annoyingly, where you're getting the error is actually hiding the real error. We're supposed to be suppressing that second error but it doesn't seem to want to work.

If you submit a ticket with ACP and FTP details, I can have a look.

Regarding the other warning, that's either safe to ignore or you could change your binlog format (row vs statement logging).