Keep getting org.hibernate.exception.JDBCConnectionException: could not execute query

I've got a J2EE application which uses JSP pages as front end and Struts2 as controller. I also use Hibernate to map my objects into a MySql DB. when I deploy the application on the server It works fine but after an unpredictable period of time (like 1 or two days) wherever I've used hibernate queries I keep getting this error:

org.hibernate.exception.JDBCConnectionException: could not execute query

what makes it more interesting is the fact that when this situation happens, it's not like 100% of queries end up to this exception! sometimes some of them are executed properly.

an example piece of code in which the error occurs:

public synchronized static Player getPlayerByID(String playerID) throws NoSuchPlayer {

    Session session = HibernateUtil.getSessionFactory().getCurrentSession();
    session.beginTransaction();
    Player player = (Player) session.createQuery(
            "from Player as player where player.loginName = '" + playerID
                    + "'").uniqueResult();//THE ERROR HAPPENS HERE
    session.getTransaction().commit();

    if (player == null)
        throw new NoSuchPlayer();

    return player;
}

and this is the respective stacktrace:

    'org.hibernate.exception.JDBCConnectionException: could not execute query
        at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:99)
        at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
        at org.hibernate.loader.Loader.doList(Loader.java:2297)
        at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2172)
        at org.hibernate.loader.Loader.list(Loader.java:2167)
        at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:448)
        at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
        at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
        at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1258)
        at org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
        at org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:859)
        at com.hposg.domain.HPOSG.getPlayerByID(HPOSG.java:117)
        at com.hposg.login.UserSession.getPlayerById(UserSession.java:39)
        at com.hposg.controller.struts.BuyAction.execute(BuyAction.java:74)
        at sun.reflect.GeneratedMethodAccessor1098.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:441)
        at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:280)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:243)
        at com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doIntercept(DefaultWorkflowInterceptor.java:165)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(ValidationInterceptor.java:252)
        at org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:68)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:122)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:195)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:195)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:179)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.interceptor.MultiselectInterceptor.intercept(MultiselectInterceptor.java:75)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:94)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:235)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:89)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ScopedModelDrivenInterceptor.intercept(ScopedModelDrivenInterceptor.java:130)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(DebuggingInterceptor.java:267)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept(ChainingInterceptor.java:126)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:138)
        at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:165)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.interceptor.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:164)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInterceptor.java:179)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercept(ExceptionMappingInterceptor.java:176)
        at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
        at org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java:52)
        at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:488)
        at org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:395)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
        at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
        at java.lang.Thread.run(Thread.java:636)
    Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.Connection was implicitly closed due to underlying exception/error:


** BEGIN NESTED EXCEPTION ** 

com.mysql.jdbc.exceptions.jdbc4.CommunicationsException
MESSAGE: Communications link failure

Last packet sent to the server was 0 ms ago.

STACKTRACE:

com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure

Last packet sent to the server was 0 ms ago.
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:353)
    at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1074)
    at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2583)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2871)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1601)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1710)
    at com.mysql.jdbc.Connection.execSQL(Connection.java:2436)
    at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1402)
    at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1556)
    at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
    at org.hibernate.loader.Loader.getResultSet(Loader.java:1849)
    at org.hibernate.loader.Loader.doQuery(Loader.java:718)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
    at org.hibernate.loader.Loader.doList(Loader.java:2294)
    at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2172)
    at org.hibernate.loader.Loader.list(Loader.java:2167)
    at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:448)
    at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
    at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
    at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1258)
    at org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
    at com.hposg.domain.HPOSG.getGameList(HPOSG.java:222)
    at com.hposg.controller.struts.GamesLoadActionAjax.execute(GamesLoadActionAjax.java:23)
    at sun.reflect.GeneratedMethodAccessor1047.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:441)
    at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:280)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:243)
    at com.opensymphony.xwork2.interceptor.DefaultWorkflowInterceptor.doIntercept(DefaultWorkflowInterceptor.java:165)
    at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.validator.ValidationInterceptor.doIntercept(ValidationInterceptor.java:252)
    at org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:68)
    at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:122)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:195)
    at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:195)
    at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:179)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.interceptor.MultiselectInterceptor.intercept(MultiselectInterceptor.java:75)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:94)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:235)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:89)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ScopedModelDrivenInterceptor.intercept(ScopedModelDrivenInterceptor.java:130)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.interceptor.debugging.DebuggingInterceptor.intercept(DebuggingInterceptor.java:267)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept(ChainingInterceptor.java:126)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:138)
    at com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:87)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.I18nInterceptor.intercept(I18nInterceptor.java:165)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.intercepto开发者_JAVA技巧r.ServletConfigInterceptor.intercept(ServletConfigInterceptor.java:164)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.AliasInterceptor.intercept(AliasInterceptor.java:179)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at com.opensymphony.xwork2.interceptor.ExceptionMappingInterceptor.intercept(ExceptionMappingInterceptor.java:176)
    at com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:237)
    at org.apache.struts2.impl.StrutsActionProxy.execute(StrutsActionProxy.java:52)
    at org.apache.struts2.dispatcher.Dispatcher.serviceAction(Dispatcher.java:488)
    at org.apache.struts2.dispatcher.FilterDispatcher.doFilter(FilterDispatcher.java:395)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
    at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
    at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:588)
    at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
    at java.lang.Thread.run(Thread.java:636)
Caused by: java.io.EOFException
    at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1958)
    at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2372)
    ... 83 more


** END NESTED EXCEPTION **


    at sun.reflect.GeneratedConstructorAccessor139.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
    at com.mysql.jdbc.Util.handleNewInstance(Util.java:353)
    at com.mysql.jdbc.Util.getInstance(Util.java:336)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:985)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:957)
    at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
    at com.mysql.jdbc.Connection.checkClosed(Connection.java:1103)
    at com.mysql.jdbc.Connection.prepareStatement(Connection.java:3865)
    at com.mysql.jdbc.Connection.prepareStatement(Connection.java:3831)
    at org.hibernate.jdbc.AbstractBatcher.getPreparedStatement(AbstractBatcher.java:534)
    at org.hibernate.jdbc.AbstractBatcher.getPreparedStatement(AbstractBatcher.java:452)
    at org.hibernate.jdbc.AbstractBatcher.prepareQueryStatement(AbstractBatcher.java:161)
    at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1596)
    at org.hibernate.loader.Loader.doQuery(Loader.java:717)
    at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:270)
    at org.hibernate.loader.Loader.doList(Loader.java:2294)
    ... 74 more
'

and finally this is my hibernate config file:

<?xml version='1.0' encoding='utf-8'?>

    <!-- Database connection settings -->
    <property name="connection.driver_class">com.mysql.jdbc.Driver</property>
    <property name="hibernate.connection.url">
        jdbc:mysql://localhost/hposg?characterEncoding=UTF-8
    </property>
    <property name="connection.username">root</property>
    <property name="connection.password"></property>

    <!-- JDBC connection pool (use the built-in) -->
    <property name="connection.pool_size">1</property>

    <!-- Echo all executed SQL to stdout -->
    <property name="show_sql">true</property>

    <!-- SQL dialect -->
    <property name="dialect">org.hibernate.dialect.MySQLDialect</property>

    <!-- Enable Hibernate's automatic session context management -->
    <property name="current_session_context_class">thread</property>

    <!-- Disable the second-level cache -->
    <property name="cache.provider_class">org.hibernate.cache.NoCacheProvider</property>

    <!-- Drop and re-create the database schema on startup -->
    <property name="hbm2ddl.auto">update</property>

  <!-- Mapping files -->

  <mapping resource="com/hposg/hibernate/resources/Player.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Game.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Portfolio.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Purchase.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Sale.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Message.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Admin.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/News.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Invitation.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/CustomGameCreationRequest.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Alert.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/AlertLimits.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/StockIndex.hbm.xml"/>      
  <mapping resource="com/hposg/hibernate/resources/HPOSG.hbm.xml"/>  
  <mapping resource="com/hposg/hibernate/resources/Tradeable.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/GlobalGameConfig.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/Announcement.hbm.xml"/>  
  <mapping resource="com/hposg/hibernate/resources/AdviserMsg.hbm.xml"/>
  <mapping resource="com/hposg/hibernate/resources/SystemConfiguration.hbm.xml"/>  
</session-factory>

btw I'm not using c3p0 connection pool, I don't know if this is relevant or not. just felt to mention it.

Any ideas?

Hibernate uses a primitive connection pooling mechanism, which is not suitable for production purposes (it even says that in the log file!). You should always use a connection pooling mechanism, be it the one provided by your container, be it a mechanism bundled in your application (c3p0, for instance). The exception you are seeing is because MySQL closed an "old" connection which Hibernate is still using. You can try to add a JDBC URL option, like "autoReconnect", but that's really not a long-term solution.

Ideally, you should configure your container to supply the connections to your application through JNDI. This is easily done with a "-ds.xml" file in JBoss or with a context.xml for Tomcat.

Once I get a similary looking exception, when I used a connection pool and the connection was closed after some time, but the pool did not recognized it.

What helped me in this case was to add a validation query to my data source:

<bean id="dataSource"
    class="org.apache.commons.dbcp.BasicDataSource"
    destroy-method="close">
  ...
  <property name="validationQuery" value="select 1"/>
</bean>