This is mostly due to any of the below two reasons
- Server timed out and closed the connection.
fix: try increasing the wait_timeout variable in your mysqld’s my.cnf/my.ini configuration file.
- Server dropped an incorrect or too large packet.
fix : increase the maximal packet size limit by increasing the value of max_allowed_packet in my.cnf/my.ini file.
Please change above value and do restart your mysql server.
Then do reindex and check it.
Still issue there then your module does not support flat catalog, so disable flat catalog and check it.