Problem

You are not able to create an XML site backup, specifically when using MySQL as your database with Confluence. 

The following appears in the atlassian-confluence.log

Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
WARN [http-nio-8090-exec-58] [v2.c3p0.impl.NewPooledConnection] log [c3p0] Another error has occurred [ com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed. ] which will not be reported to listeners!

Cause

MySQL closes the database connection that Confluence is using while creating the XML backup, which is a long-running process.

Workaround

Increase the interactive_timeout and wait_timeout in MySQL.

interactive_timeout: The number of seconds the server waits for activity on an interactive connection before closing it. 

wait_timeout: The number of seconds the server waits for activity on a non-interactive connection before closing it.

• Find out your current timeout values by running the following in MySQL with a privileged account:

  SHOW VARIABLES LIKE '%timeout%';

• Edit the my.cnf file and increase the interactive_timeout and wait_timeout to be higher than the current value. You can do this by adding the respective variable and value under the [mysqld] section.

   

  Default Values

  [mysqld]
  wait_timeout = 28800
  interactive_timeout = 28800

• Restart MySQL to apply the changes