MySQL error log says "Got timeout reading communication packets"

Symptoms

In some MySQL configurations, you may find that connections to databases continuously timeout and correspond to the following entries in the MySQL error log:

[Warning] Aborted connection to db: 'username_site' user: 'username_site' host: 'localhost' (Got timeout reading communication packets)

Description 

Timeouts reading communication packets are often caused by low timeout values set in /etc/my.cnf.

wait_timeout=30
net_read_timeout=30
net_write_timeout=60

The wait_timeout setting controls the number of seconds the server waits for activity on a non-interactive connection before closing it. Changing this value first will often resolve most issues.

The net_read_timeout and net_write_timeout values may also contribute to timeouts if their values are set lower than wait_timeout. Setting these higher than wait_timeout may resolve any remaining issues.

Workaround

Refer to the following MySQL documentation to ensure these values are set to meet your server's needs:

MySQL Server System Variables documentation