Debugging MySql Gone away errors, randomly geting multiple sleeping threads - php

Question

To start with the issue itself: My server randomly has issues where pages stop loading for a few minutes (often reaching a 300sec timeout), or load extremely slowly. It does not necessarily correlate with an increase in traffic, but is more likely to happen when it increases. Sometimes I can just be messing around, things gets slow for a couple minutes, then everything is back to normal, same files acessed. The system itself is very simple: It does nothing beyong basic data insertion and reading, no table has more than a couple thousand rows. Google Analytics show peak concurrent access at around 300 per hour on peak times.
This is an old project that came to our company recently. The PHP code is very old, and I spent a lot of time refactoring queries to use a centralized PDO connection over using mysql_connect before every time. However, in the old server, these issues did not happen, just on the new.
Now, for the catch. Our hosting service said that this was actually an issue on their server, and I couldn't find a code reason for that either. After a couple months, we decided to change to a new, dedicated server on a different host...and the issue remains. So there has to be something wrong with the code, somewhere, or a configuration I need to change.
Thing is, there's no specific file or script causing it. Since now I have WHM control, I can see there's no issues with memory or CPU usage. Slow log query is empty, set at 20 seconds to log. What happens is that everything just runs very slowly, then just as easily returns to normal.
Errors that I can see on the log are MySql Gone away, or others like
AH01071: Got error 'Primary script unknown
or
(70007)The timeout specified has expired: [client IP] AH01075: Error dispatching request to : (polling) (Timeout is set at 300 seconds, nothing should take more than a couple to run).
I turned the general log on and noticed one interesting thing: When it happens, some threads take more than a minute to close. Query goes like this on the log
SELECT *,
COUNT(DISTINCT(command_type)) as conta,
MIN(event_time) as inicio,
MAX(event_time) as fim,
timediff(MAX(event_time),MIN(event_time)) as diferenca
FROM `general_log`
WHERE user_host LIKE '%hostname%'
GROUP BY thread_id HAVING diferenca > "00:01:00"
And it shows a couple results, one of which I know for a fact lines up to a perceived slowness. More interestingly, the last command before slowdown is this select
SELECT * FROM publicidade WHERE secao = 1 ORDER BY posicao ASC, data_insercao DESC LIMIT 2
Thing is, this select always runs fast, on a table with 29 rows, returning 1 result. Makes no sense for this to screw things up, but it always is the last query command shown, even found 2 situations where the thread never got to QUIT.
So at this point I'm at wits end. Problems keep happening, it's intermitent, comes and go for no discernible reason, and I cannot find out why. slow_queries log is empty, so it's not like there's a query hanging on, it just goes sleeping after this query until it timeouts, no further PHP errors, nothing. And then minutes later the same scripts just run fine as if nothing happened. I could even see situations where www / non www have different results (one is fine, other is not), as well as direct access via IP.
How can I debug what's going on? What could be a likely reason?
By the way persistent connections are off.

Answer 1

Unfortunately, it is simply not enough information to recommend anything useful.
Have you checked server I/O?
You should check if there is no reverse lookup issues if you mysql user permission checked 'per domain' (you can try to switch to 'per IP')
You can try MySQLTuner-perl, it might give you some hints you missed.
You can try to use webyog tools (trial). It might also give you some clues.