Background
According to MySQL discussion forums, a max_allowed_packet value that is too low (such as 4M) can cause connection issues with MySQL, which can look like the following in Variphy Logs:
ERROR … com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception:
** BEGIN NESTED EXCEPTION **
java.net.SocketException
MESSAGE: socket closed
STACKTRACE:
java.net.SocketException: socket closed
Resolution
Within the [mysqld] section in my.cnf (my.ini on Windows):
max_allowed_packet=100M
innodb_lock_wait_timeout=120
In running config (via MySQL cmd line or workbench):
SET GLOBAL max_allowed_packet=104857600;
SET GLOBAL innodb_lock_wait_timeout = 120;