Communication Link Faulure (no replies)

we are getting the following problem While executing any query on the database.
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

The last packet successfully received from the server was 6 milliseconds ago. The last packet sent successfully to the server was 6 milliseconds ago.
at sun.reflect.GeneratedConstructorAccessor51.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:39)
at java.lang.reflect.Constructor.newInstance(Constructor.java:515)


This problem is happening while connecting the database from the webapplication and from Database client tool(remotely).

The server is running on unix. both web application and database are in same server.

Server version: 5.5.14 MySQL Community Server (GPL)

OS: linux

how to resolve this issue?