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I'm troubleshooting a series of reoccurring errors: WordPress database error MySQL server has gone away for query ...

I think I've found a solution here but it's a few years old and I want to better understand the MySQL wait_timeout and it's relationship to Wordpress before I start monkeying with core files or reconfiguring my server. (I'm on a virtual dedicated server, so I have the option to change the wait_timeout on the server.)

I checked by running SHOW VARIABLES; from phpMyAdmin and wait_timeout is currently set to 35. That seems low to me, but I don't fully understand what it does. I'm considering changing it to 600.

My main question is whether this is a responsible thing to do or not. But I think that broader question can be divided into smaller parts: 1. Do I have the option to override this setting with PHP (Wordpress)? 2. What is the optimal setting is for medium-large Wordpress site? 3. Are there any Wordpress configuration options or filters that I could use to change the setting without modifying core files?

Thanks.

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wait_timeout is the time mysql will hold a non-interactive connection open for before closing it basically.

So increasing it to 600 seconds could solve your problem, however, if you set it to 600 seconds and you have lots of people running a slow page on your site at the same time you can get to a point where mysql starts refusing connections and then apache will start queueing requests until it subsequently refuses requests and your server takes a dive.

My suggestion would be to try and find out why a single request is taking over 35 seconds because to be honest, that seems a rather long load time on a single page from a blog to me.

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My understanding was that wait_timeout was also the amount of time to wait for subsequent queries. So this wouldn't necessarily indicate that a single script was taking longer then 35 seconds. Is that not correct?
I did some research and I understand better. The wait_timeout is the wait for a response. So it means a query is running for a really long time? 35 seconds seems like a VERY long time to wait.
It's the number of seconds of inactivity on a single connection mysql will wait for before terminating a connection. For instance you may make a connection 1 second into script execution then go away and do 40 seconds of work in php and when you go back to use your connection again, mysql has killed it.
I see. So the actual MySQL query doesn't necessarily have to run for that long. It could be PHP getting stuck somewhere in between calls. Am I following you correctly?
That's quite possible, yes. I've had this exact problem before with an offline script running overnight and to solve that I just changed the wait_timeout as a session variable (as described in your initial link) because I knew that this one connection needed to stay open. In an idea world I guess Wordpress would provide an option for you to auto-reconnect should a connection drop like this. Changing the wait_timeout for every page would seem potentially more dangerous to me though and is avoiding the problem instead of finding the code which is causing a page to take so long to load.
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