The problem looks like it is the MySQL side of the connection. You are getting an OS segmentation fault. Most likely this is then causing the the connection to terminate as the MySQL connector/listener dies. This results in the Java side error you see.
Check that MySQL works with the JDBC driver (test that you can connect) and that it executes whatever the SQL was that you were sending to it. Do this from a plain old Java program. However, judging by the exception, it is failing in establishing the connection.