How to understand what is the problem on the server when there is a sharp excess of disk usage?

Question

linux

The bottom line is this: Periodically, at the time of saving files via ssh, the load on the disk and CPU increases sharply, as a result of which the server ceases to be available until you close all programs through which you are currently connected (browsers, ide, console, everything that is open). hosting support supplied atop.
I see just such a picture



They tell me that the problem is in SQL and the scripts that cause them, but sql gives only 20%.
In addition, according to my observations, it is at the moment of downloading or uploading a file via ssh that a problematic situation occurs. Yes, at this moment someone may be on the site, so it is not surprising that there is a load on the database, but it is not 100%

Answer 1

iotop -oka during the peak and see what eats

Answer 2

As already said, it looks like a memory problem.
Show the output
of free -m