Usually that happens when you exhaust one resource for the db session, such as memory, and mysql closes the connection.
Can you break the CSV file into smaller ones and process them? or do commit every 100 rows? The idea is that the transaction you're running shouldn't try to insert a large amount of data.
I forgot to add, this error is related to the configuration property max_allowed_packet, but I can't remember the details of what to change.
