I have a java application that has long running processes and interact with db. It keeps getting the following:
The last packet successfully received from the server was 3,601,168 milliseconds ago. The last packet sent successfully to the server was 3,601,166 milliseconds ago.
The remote server has a wait_timeout 354600 which is in seconds. What could be wrong?
There could be a number of problems, but I don't believe wait_timeout is the culprit if your last packet was sent/received about 3600s ago and wait_timeout is 354600s. You could have lost the connection to the server or any other of a number of things. You need to post more about what your code is doing and more about what you expect to happen and what is actually happening.
As for Cassio's comment under the question... wait_timeout is in seconds. MySQL Docs - wait_timeout