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XF 1.4 Speed Questions

#1
Hey, I'm having a few issues with speed and occasional lag on one of my sites. All sites are on the same high-end VPS, and it's only the larger site that's struggling. This is intermittent, but when it does happen it almost locks up for maybe 40 seconds. In this time, the admin CP functions absolutely fine with no lag at all, it's just the front end that really struggles. You can't load the index, new threads or post replies.

I do have occasional server errors, but they do not coincide with the timing of this lag. The server errors are:

Code:
Zend_Db_Statement_Mysqli_Exception: Mysqli statement execute error : Lock wait timeout exceeded; try restarting transaction - library/Zend/Db/Statement/Mysqli.php:214

#0 /home/youthdebates/public_html/forums/library/Zend/Db/Statement.php(297): Zend_Db_Statement_Mysqli->_execute(Array)
#1 /home/youthdebates/public_html/forums/library/Zend/Db/Adapter/Abstract.php(479): Zend_Db_Statement->execute(Array)
#2 /home/youthdebates/public_html/forums/library/XenForo/Model/Poll.php(322): Zend_Db_Adapter_Abstract->query('SELECT poll_id ...', 1245)
#3 /home/youthdebates/public_html/forums/library/XenForo/ControllerPublic/Thread.php(1585): XenForo_Model_Poll->voteOnPoll(1245, 4185)
#4 /home/youthdebates/public_html/forums/library/XenForo/FrontController.php(347): XenForo_ControllerPublic_Thread->actionPollVote()
#5 /home/youthdebates/public_html/forums/library/XenForo/FrontController.php(134): XenForo_FrontController->dispatch(Object(XenForo_RouteMatch))
#6 /home/youthdebates/public_html/forums/index.php(13): XenForo_FrontController->run()
#7 {main}

array(3) {
  ["url"] => string(93) "http://youthdebates.org/forums/threads/very-long-term-goal-with-no-guarantees.11174/poll/vote"
  ["_GET"] => array(0) {
  }
  ["_POST"] => array(5) {
    ["response"] => string(4) "4185"
    ["_xfToken"] => string(8) "********"
    ["_xfRequestUri"] => string(61) "/forums/threads/very-long-term-goal-with-no-guarantees.11174/"
    ["_xfNoRedirect"] => string(1) "1"
    ["_xfResponseType"] => string(4) "json"
  }
}
But as I said, these don't match the timing of the lag.

We have a few add-ons installed that I worry may not be helping. Our board is a decent size, with anywhere between 20 and 55 registered members online at any time, along with a couple of dozen guests. Is it fair to say most add-ons have a negative speed impact? A few I'm worrying about are Taigachat Pro, Tapatalk and Tab Alerts. I can test removing these, but it'll take hours and hours for me to tell if anything worked, so I figured I'd just ask for a bit of advice here as well.

We also have [bd] Cache and Defer JS installed, does anyone have anything negative to say about those? The performance increase when we're not lagging seems like it could be too good to be true?

Any advice welcome, thanks :)