How to determine why a MySQL server has become slow and requests sometimes time out? I'm working on my first project that makes heavy use of a MySQL database and am struggling to understand performance issues I'm having.

Most of the time, responses are returned quickly from the server, but when I have certain scripts that make a lot of queries (both reading and writing data) running in the background, I'm finding that other requests are slow to receive responses, or are timing out entirely.

As an example, yesterday when a PHP script that makes a lot database queries was running, requests to the server for pages that made a number of queries before returning a response were timing out -- I couldn't even connect to the database with Navicat, as it timed out as well.

In the above example, I ran top/htop in an SSH console and found that there was very low CPU usage and memory usage was only at about 50%. Because of this, I think the problem lies with the database, but I'm having trouble understanding what is causing the issues, such as whether they might be due to:


Slow queries
Too many connections
Too many queries per second
Other potential issues I'm not aware of


I know about the slow query log, but none of my queries are very slow.

What methods or tools can I use to determine what is causing a MySQL database to become slow, sometimes with requests even timing out?
You need to tune your database. This is a complicated process with many variables and decision trees. Without specifics we can only really get you started here.
If you have a script that runs lots of SQL and slows down your DB, and your cpu and memory usage are fine while it's running, then you are probably running into I/O problems. i.e. You are hammering the disk. You need to look through the SQL used in the script and tune it. For example, it might be generating lots of full table scans or creating too many transaction logs that are slowing down the DB. To start with, check if any unneccessary full table scans are taking place, and see if you can add indexes to the relevant columns to reduce the I/O. then report back and we can go from there.
The above linked MySQLtuner script is excellent but understanding the results may be challenging for you if you are inexperienced with databases. Do read the disclaimers on the main page before you get started: https://github.com/major/MySQLTuner-perl