Conexion con hibernate

Al hacer un deploy en glassfish, todo funciona bien, pero luego de un tiempo me envia este error

Thu Jun 13 10:02:59 CST 2013
org.hibernate.exception.JDBCConnectionException: could not extract ResultSet
at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:132)
at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125)
at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:110)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:61)
at org.hibernate.loader.Loader.getResultSet(Loader.java:2036)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1836)
at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1815)
at org.hibernate.loader.Loader.doQuery(Loader.java:899)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:341)
at org.hibernate.loader.Loader.doList(Loader.java:2522)
at org.hibernate.loader.Loader.doList(Loader.java:2508)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2338)
at org.hibernate.loader.Loader.list(Loader.java:2333)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:490)
at org.hibernate.hql.internal.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:355)
at org.hibernate.engine.query.spi.HQLQueryPlan.performList(HQLQueryPlan.java:195)
at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1269)
at org.hibernate.internal.QueryImpl.list(QueryImpl.java:101)
at cr.co.prime.nomina.data.dao.EmpresaDAO.getEmpresaAll(EmpresaDAO.java:21)
at cr.co.prime.nomina.vNomina.datosEmpresa(vNomina.java:406)
at cr.co.prime.nomina.vNomina.initLogin(vNomina.java:111)
at cr.co.prime.nomina.vNomina.attach(vNomina.java:96)
at com.vaadin.ui.UI.setSession(UI.java:355)
at com.vaadin.server.AbstractCommunicationManager.getBrowserDetailsUI(AbstractCommunicationManager.java:2462)
at com.vaadin.server.AbstractCommunicationManager.handleBrowserDetailsRequest(AbstractCommunicationManager.java:2362)
at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:325)
at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:201)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:281)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:331)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
at com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
at java.lang.Thread.run(Thread.java:722)
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 55,811,709 milliseconds ago. The last packet sent successfully to the server was 55,811,709 milliseconds ago. is longer than the server configured value of ‘wait_timeout’. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property ‘autoReconnect=true’ to avoid this problem.
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:525)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2815)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2155)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2322)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:56)
… 48 more
Caused by: java.net.SocketException: Tubería rota
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:109)
at java.net.SocketOutputStream.write(SocketOutputStream.java:153)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3919)
… 55 more

podrian ayudarme. Gracias

El problema está en:
“Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 55,811,709 milliseconds ago. The last packet sent successfully to the server was 55,811,709 milliseconds ago. is longer than the server configured value of ‘wait_timeout’. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property ‘autoReconnect=true’ to avoid this problem.”
No recuerdo el valor por defecto de wait_timeout en mysql pero la idea es que si se agota el tiempo sin interactuar con la base de datos se cierran las conexiones.
Lo que debes hacer es aumentar el valor de wait_timeout. Si usas hibernate lo puedes configurar utilizando C3P0: http://www.mkyong.com/hibernate/how-to-configure-the-c3p0-connection-pool-in-hibernate/

this is problem of a attribute collection, in your query hibernate isnt call lazy load, its a problem of lazy load.