I encountered 2013 during mysqldump and when selecting from a specific table.
A good tip I found was to check Uptime after the query
Uptime: 7 min 4 sec
Which indicated the mysqld instance had restarted.
The best solution was for me was to check /var/log/mysql/mysql-error.log . It turned out advice from the log file saved the day:
InnoDB: It is also possible that your operating
InnoDB: system has corrupted its own file cache
InnoDB: and rebooting your computer removes the
After rebooting the OS the error was gone.
Other advice I found online was:
1. Check wait_timeout is long enough
mysql> show variables
The default is 28800 seconds (8 hours). This was set to the default and thus not the problem.
2. Set max_allowed_packet to something larger
I opted for one gigabyte
mysql> set max_allowed_packet=1000 * 1024 * 1024;
This also had no effect. It would have been better if I had checked the error log immediately which makes good sense after an unexpected restart.