Hello,

In case that you are using Workbench, you can increase the timeout through there: Edit -> Preferences -> SQL Editor -> DBMS connection read time out (in seconds) -> Changed the value to 6000.

If this still does not work, you could try tweaking your MySQL configuration and increasing the max_allowed_packet and the innodb_buffer_pool_size.

For example, you could set them to:

max_allowed_packet=16M
innodb_buffer_pool_size=64M

Alternatively, I would recommend following the steps here on how to tweak MySQL/MariaDB Configuration for Increased Performance and Stability:

https://www.digitalocean.com/community/questions/how-to-tweak-mysql-mariadb-configuration-for-increased-performance-and-stability

Let me know how it goes!
Best,
Bobby