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HTTP Status 500 - JDBC rollback failed using hibernate

I have a java application using Hibernate and tomcat server.my app is working fine for hours.Then is stop working..showing the following error.I have no idea what is happening and i m really new to hibernate technology.I read something about c3p0 lib but i dont know exacly how is working..
HTTP Status 500 - JDBC rollback failed
type Exception report
message JDBC rollback failed
description The server encountered an internal error that prevented it from fulfilling this request.
exception
org.hibernate.TransactionException: JDBC rollback failed
org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:200)
com.javawebtutor.service.LoginService.getUserByUserId(LoginService.java:37)
com.javawebtutor.service.LoginService.authenticateUser(LoginService.java:17)
com.javawebtutor.controller.LoginServlet.doPost(LoginServlet.java:33)
javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
root cause
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:423)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.Util.getInstance(Util.java:386)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1013)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:987)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:982)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:927)
com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1251)
com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1243)
com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:4723)
org.hibernate.transaction.JDBCTransaction.rollbackAndResetAutoCommit(JDBCTransaction.java:213)
org.hibernate.transaction.JDBCTransaction.rollback(JDBCTransaction.java:192)
com.javawebtutor.service.LoginService.getUserByUserId(LoginService.java:37)
com.javawebtutor.service.LoginService.authenticateUser(LoginService.java:17)
com.javawebtutor.controller.LoginServlet.doPost(LoginServlet.java:33)
javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
root cause
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 33,669,634 milliseconds ago. The last packet sent successfully to the server was 6 milliseconds ago.
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:423)
com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1116)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3589)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3478)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4019)
com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2490)
com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2683)
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2144)
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2310)
org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
org.hibernate.loader.Loader.getResultSet(Loader.java:1953)
org.hibernate.loader.Loader.doQuery(Loader.java:802)
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
org.hibernate.loader.Loader.doList(Loader.java:2533)
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
org.hibernate.loader.Loader.list(Loader.java:2271)
org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452)
org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
org.hibernate.impl.SessionImpl.list(SessionImpl.java:1268)
org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:890)
com.javawebtutor.service.LoginService.getUserByUserId(LoginService.java:33)
com.javawebtutor.service.LoginService.authenticateUser(LoginService.java:17)
com.javawebtutor.controller.LoginServlet.doPost(LoginServlet.java:33)
javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
root cause
java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3039)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3489)
com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3478)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4019)
com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2490)
com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2651)
com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2683)
com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2144)
com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2310)
org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
org.hibernate.loader.Loader.getResultSet(Loader.java:1953)
org.hibernate.loader.Loader.doQuery(Loader.java:802)
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
org.hibernate.loader.Loader.doList(Loader.java:2533)
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
org.hibernate.loader.Loader.list(Loader.java:2271)
org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:452)
org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:363)
org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:196)
org.hibernate.impl.SessionImpl.list(SessionImpl.java:1268)
org.hibernate.impl.QueryImpl.list(QueryImpl.java:102)
org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:890)
com.javawebtutor.service.LoginService.getUserByUserId(LoginService.java:33)
com.javawebtutor.service.LoginService.authenticateUser(LoginService.java:17)
com.javawebtutor.controller.LoginServlet.doPost(LoginServlet.java:33)
javax.servlet.http.HttpServlet.service(HttpServlet.java:648)
javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
note The full stack trace of the root cause is available in the Apache Tomcat/8.0.50 logs.
Apache Tomcat/8.0.50
my hibernate.cfg.xml is
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD 3.0//EN"
"http://www.hibernate.org/dtd/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.url">
jdbc:mysql://localhost:3306/dbname?UseUnicode=true&characterEncoding=utf8
</property>
<property name="hibernate.connection.username">dbusername</property>
<property name="hibernate.connection.password">dbpass</property>
<property name="show_sql">true</property>
<property name="hbm2ddl.auto">update</property>
<mapping class="com.javawebtutor.model.User" />
<mapping class="com.javawebtutor.model.Questionaire" />
</session-factory>
</hibernate-configuration>
Please help..

Hibernate connection to remote server refused, but regular mysql connection works

I have JSF web application that uses Hibernate. I have MySql server on the same machine I'm developing. I was using localhost Glassfish server until now and everything worked fine. Then I decided to try and install Glassfish on RaspberryPi and use it as web server instead. So far so good, web application is deploying and I can access it in the browser. The problem happens when it tries to initialize Hibernate. It's throwing java.net.ConnectException: Connection refused. I also tried to connect with mysql command (from raspberry) using same parameters given in the hibernate.cfg.xml and it works fine (so parameters are good). I have no idea what's wrong...
Machine that has MySql and is used for development is using Windows 10, and raspberry is using Raspbian.
Here's the stack trace:
javax.faces.el.EvaluationException: java.lang.ExceptionInInitializerError
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:101)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
at javax.faces.component.UICommand.broadcast(UICommand.java:315)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:790)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1282)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:658)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:318)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:416)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:283)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:283)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:200)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:132)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:111)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:536)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:591)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:571)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ExceptionInInitializerError
at hibernate.util.HibernateUtil.<clinit>(HibernateUtil.java:39)
at controllers.Login.login(Login.java:27)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at javax.el.ELUtil.invokeMethod(ELUtil.java:332)
at javax.el.BeanELResolver.invoke(BeanELResolver.java:537)
at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
at com.sun.el.parser.AstValue.invoke(AstValue.java:283)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:304)
at org.jboss.weld.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105)
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:87)
... 36 more
Caused by: org.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.engine.jdbc.env.spi.JdbcEnvironment]
at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:271)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:233)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:210)
at org.hibernate.engine.jdbc.internal.JdbcServicesImpl.configure(JdbcServicesImpl.java:51)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:94)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:242)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:210)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.handleTypes(MetadataBuildingProcess.java:352)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.complete(MetadataBuildingProcess.java:111)
at org.hibernate.boot.model.process.spi.MetadataBuildingProcess.build(MetadataBuildingProcess.java:83)
at org.hibernate.boot.internal.MetadataBuilderImpl.build(MetadataBuilderImpl.java:418)
at org.hibernate.boot.internal.MetadataBuilderImpl.build(MetadataBuilderImpl.java:87)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:691)
at hibernate.util.HibernateUtil.<clinit>(HibernateUtil.java:34)
... 50 more
Caused by: org.hibernate.exception.JDBCConnectionException: Error calling Driver#connect
at org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:115)
at org.hibernate.engine.jdbc.connections.internal.BasicConnectionCreator$1$1.convert(BasicConnectionCreator.java:101)
at org.hibernate.engine.jdbc.connections.internal.BasicConnectionCreator.convertSqlException(BasicConnectionCreator.java:123)
at org.hibernate.engine.jdbc.connections.internal.DriverConnectionCreator.makeConnection(DriverConnectionCreator.java:41)
at org.hibernate.engine.jdbc.connections.internal.BasicConnectionCreator.createConnection(BasicConnectionCreator.java:58)
at org.hibernate.engine.jdbc.connections.internal.PooledConnections.addConnections(PooledConnections.java:123)
at org.hibernate.engine.jdbc.connections.internal.PooledConnections.<init>(PooledConnections.java:42)
at org.hibernate.engine.jdbc.connections.internal.PooledConnections.<init>(PooledConnections.java:20)
at org.hibernate.engine.jdbc.connections.internal.PooledConnections$Builder.build(PooledConnections.java:161)
at org.hibernate.engine.jdbc.connections.internal.DriverManagerConnectionProviderImpl.buildPool(DriverManagerConnectionProviderImpl.java:109)
at org.hibernate.engine.jdbc.connections.internal.DriverManagerConnectionProviderImpl.configure(DriverManagerConnectionProviderImpl.java:72)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.configureService(StandardServiceRegistryImpl.java:94)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:242)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:210)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.buildJdbcConnectionAccess(JdbcEnvironmentInitiator.java:145)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:66)
at org.hibernate.engine.jdbc.env.internal.JdbcEnvironmentInitiator.initiateService(JdbcEnvironmentInitiator.java:35)
at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.initiateService(StandardServiceRegistryImpl.java:88)
at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:259)
... 63 more
Caused by: com.mysql.cj.jdbc.exceptions.CommunicationsException: Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at com.mysql.cj.jdbc.exceptions.SQLError.createCommunicationsException(SQLError.java:590)
at com.mysql.cj.jdbc.exceptions.SQLExceptionsMapping.translateException(SQLExceptionsMapping.java:57)
at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:1606)
at com.mysql.cj.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:633)
at com.mysql.cj.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:347)
at com.mysql.cj.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:219)
at org.hibernate.engine.jdbc.connections.internal.DriverConnectionCreator.makeConnection(DriverConnectionCreator.java:38)
... 78 more
Caused by: com.mysql.cj.core.exceptions.CJCommunicationsException: Communications link failure
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at com.mysql.cj.core.exceptions.ExceptionFactory.createException(ExceptionFactory.java:54)
at com.mysql.cj.core.exceptions.ExceptionFactory.createException(ExceptionFactory.java:93)
at com.mysql.cj.core.exceptions.ExceptionFactory.createException(ExceptionFactory.java:133)
at com.mysql.cj.core.exceptions.ExceptionFactory.createCommunicationsException(ExceptionFactory.java:149)
at com.mysql.cj.mysqla.io.MysqlaSocketConnection.connect(MysqlaSocketConnection.java:83)
at com.mysql.cj.mysqla.MysqlaSession.connect(MysqlaSession.java:122)
at com.mysql.cj.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:1726)
at com.mysql.cj.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:1596)
... 82 more
Caused by: java.net.ConnectException: Connection refused
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:589)
at com.mysql.cj.core.io.StandardSocketFactory.connect(StandardSocketFactory.java:202)
at com.mysql.cj.mysqla.io.MysqlaSocketConnection.connect(MysqlaSocketConnection.java:57)
... 85 more
And cfg file:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE hibernate-mapping PUBLIC "-//Hibernate/Hibernate Mapping DTD//EN" "http://hibernate.org/dtd/hibernate-mapping.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.MySQL5Dialect</property>
<property name="hibernate.connection.driver_class">com.mysql.cj.jdbc.Driver</property>
<property name="hibernate.connection.url">jdbc:mysql://192.168.0.11:3306/festivals2017?zeroDateTimeBehavior=convertToNull</property>
<property name="hibernate.connection.username">...</property>
<property name="hibernate.connection.password">...</property>
<property name="hibernate.show_sql">true</property>
<property name="hibernate.current_session_context_class">thread</property>
<property name="hibernate.query.factory_class">org.hibernate.hql.internal.classic.ClassicQueryTranslatorFactory</property>
<property name="hbm2ddl.auto">update</property>
</session-factory>
</hibernate-configuration>
#Edit:
auto.cfg file of MySql
[auto]
server-uuid=ce19411c-2f4b-11e7-bd70-74d02b2c9d64
I'll also add that I used Wireshark to track traffic on 3306 port on machine that has MySql and there's nothing when I use hibernate (but there is when I use mysql from terminal). I guess that problem is not in the MySql server since no traffic is reaching machine.

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

I've developed an application and it worked just fine locally , and when I uploaded it to a remote server it gave me com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException. I've tried the solution mentioned in the topic in this link :
https://stackoverflow.com/questions/7565143/com-mysql-jdbc-exceptions-jdbc4-mysqlnontransientconnectionexception-no-operati#=
here is the code that has access to database:
protected Number getCount(Class clazz){
Session currentSession = HibernateUtil.getSessionFactory().getCurrentSession();
Transaction transaction = currentSession.beginTransaction();
return (Number) currentSession.createCriteria(clazz).setProjection(Projections.rowCount()).uniqueResult();
}
and here is my hibernate configuration:
<hibernate-configuration>
<session-factory>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.current_session_context_class">thread</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/lyrics_db</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.password">123456</property>
<property name="hibernate.hbm2ddl.auto">update</property>
<property name="hibernate.show_sql">true</property>
<property name="connection.provider_class">org.hibernate.connection.C3P0ConnectionProvider</property>
<property name="c3p0.acquire_increment">1</property>
<property name="c3p0.idle_test_period">100</property>
<!-- seconds -->
<property name="c3p0.max_size">100</property>
<property name="c3p0.max_statements">0</property>
<property name="c3p0.min_size">10</property>
<property name="c3p0.timeout">1800</property>
<!-- seconds -->
</session-factory>
</hibernate-configuration>
and it's not working and I'm getting the same exception , and here is my full stack trace:
Dec 3, 2013 8:02:44 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet ServletAdaptor threw exception
org.hibernate.exception.JDBCConnectionException: could not execute query
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
at org.hibernate.loader.Loader.doList(Loader.java:2223)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283)
at daos.UltimateDao.listWithLimitWithOrder(UltimateDao.java:47)
at daos.LyricDao.getTopHundred(LyricDao.java:73)
at com.xeeapps.service.Service.getTopHundred(Service.java:91)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185)
at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1480)
at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1411)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1360)
at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1350)
at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:538)
at com.sun.jersey.spi.container.servlet.ServletContainer.service(ServletContainer.java:716)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
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:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:662)
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at sun.reflect.GeneratedConstructorAccessor127.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.Util.getInstance(Util.java:386)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1014)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:988)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:974)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1290)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1282)
at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4468)
at com.mysql.jdbc.ConnectionImpl.prepareStatement(ConnectionImpl.java:4434)
at com.mchange.v2.c3p0.impl.NewProxyConnection.prepareStatement(NewProxyConnection.java:1076)
at org.hibernate.jdbc.AbstractBatcher.getPreparedStatement(AbstractBatcher.java:505)
at org.hibernate.jdbc.AbstractBatcher.getPreparedStatement(AbstractBatcher.java:423)
at org.hibernate.jdbc.AbstractBatcher.prepareQueryStatement(AbstractBatcher.java:139)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1547)
at org.hibernate.loader.Loader.doQuery(Loader.java:673)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2220)
... 40 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 38,056,253 milliseconds ago. The last packet sent successfully to the server was 38,056,857 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:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1117)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3871)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2484)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2664)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2794)
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:144)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1787)
at org.hibernate.loader.Loader.doQuery(Loader.java:674)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236)
at org.hibernate.loader.Loader.doList(Loader.java:2220)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104)
at org.hibernate.loader.Loader.list(Loader.java:2099)
at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283)
at org.hibernate.impl.CriteriaImpl.uniqueResult(CriteriaImpl.java:305)
at daos.UltimateDao.get(UltimateDao.java:24)
at daos.SongDao.getSong(SongDao.java:31)
at daos.LyricDao.getLyricForSong(LyricDao.java:24)
at com.xeeapps.service.Service.getLyricForASong(Service.java:82)
... 32 more
Caused by: java.net.SocketException: Broken pipe
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:92)
at java.net.SocketOutputStream.write(SocketOutputStream.java:136)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3852)
... 53 more
Dec 3, 2013 8:02:44 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet Faces Servlet threw exception
com.sun.jersey.api.client.UniformInterfaceException: GET http://localhost:8080/LyricsService/webresources/service/getTopHundred returned a response status of 500 Internal Server Error
at com.sun.jersey.api.client.WebResource.handle(WebResource.java:686)
at com.sun.jersey.api.client.WebResource.access$200(WebResource.java:74)
at com.sun.jersey.api.client.WebResource$Builder.get(WebResource.java:507)
at client.LyricsClient.getTopHundred(LyricsClient.java:71)
at controllers.TopHundredController.init(TopHundredController.java:32)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.el.parser.AstValue.invoke(AstValue.java:191)
at org.apache.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:276)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105)
at com.sun.faces.facelets.tag.jsf.core.DeclarativeSystemEventListener.processEvent(EventHandler.java:128)
at javax.faces.component.UIComponent$ComponentSystemEventListenerAdapter.processEvent(UIComponent.java:2563)
at javax.faces.event.SystemEvent.processListener(SystemEvent.java:108)
at javax.faces.event.ComponentSystemEvent.processListener(ComponentSystemEvent.java:118)
at com.sun.faces.application.ApplicationImpl.processListeners(ApplicationImpl.java:2187)
at com.sun.faces.application.ApplicationImpl.invokeComponentListenersFor(ApplicationImpl.java:2135)
at com.sun.faces.application.ApplicationImpl.publishEvent(ApplicationImpl.java:289)
at com.sun.faces.application.ApplicationImpl.publishEvent(ApplicationImpl.java:247)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:107)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:662)
Does anyone know why this exception keeps happening even I changed my configuration?

I guess the problem was that I didn't commit the transaction , so it made some sort of lock.I figured this out from this topic:
What happens if you don't commit transaction in a database (say SQL Server)

JPA connection closed with EntityManager

Please excuse the possible improper formatting of this post as I have never posted here before. I have a Spring MVC web service running that calls into several DAO's that use JPA/hibernate to interact with a SQL Server database. The connection to the database seems to get closed after the web service has been running for a while.
An example of one of the DAO classes is the following:
#Repository
public class OceanClientDaoImpl {
// Create entity manager objects that will talk to the database
private EntityManagerFactory entityManagerFactory;
/**
* Load all clients in the database. Return as ClientLight objects.
*
* #return List of ClientLight objects.
*/
public List<Client> loadClients()
{
EntityManager entityManager = entityManagerFactory.createEntityManager();
entityManager.getTransaction().begin();
List<?> clients =
entityManager.createNativeQuery("select id, clientname, industry, logo, slug from client",
Client.class).getResultList();
entityManager.getTransaction().commit();
entityManager.close();
return Client.getCheckedList(clients);
}
}
The entityManagerFactory is injected via spring in the following way:
<bean id="dataSource" class="org.apache.tomcat.jdbc.pool.DataSource">
<property name="driverClassName" value="com.microsoft.sqlserver.jdbc.SQLServerDriver" />
<property name="url" value="url" />
<property name="username" value="user" />
<property name="password" value="pw" />
</bean>
<bean
class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean"
id="entityManagerFactory">
<property name="dataSource" ref="dataSource" />
</bean>
<context:component-scan base-package="com.theocean.dao">
<context:include-filter type="annotation"
expression="org.springframework.stereotype.Repository" />
</context:component-scan>
<bean class="org.springframework.orm.jpa.JpaTransactionManager"
id="transactionManager">
<property name="entityManagerFactory" ref="entityManagerFactory" />
</bean>
<bean id="oceanClientDaoImpl" class="com.theocean.dao.OceanClientDaoImpl">
<property name="entityManagerFactory" ref="entityManagerFactory"/>
</bean>
This all works fine when I first bring up the application. The application server is Tomcat. But, after the application is running for a while, requests to the server start receiving this error:
> SEVERE: Servlet.service() for servlet [spring] in context with path [/OceanWebService] threw exception [Request processing failed; nested exception is javax.persistence.PersistenceException: org.hibernate.TransactionException: JDBC begin failed: ] with root cause
com.microsoft.sqlserver.jdbc.SQLServerException: SQL Server did not return a response. The connection has been closed.
at com.microsoft.sqlserver.jdbc.SQLServerConnection.terminate(SQLServerConnection.java:1667)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.terminate(SQLServerConnection.java:1654)
at com.microsoft.sqlserver.jdbc.TDSReader.readPacket(IOBuffer.java:4844)
at com.microsoft.sqlserver.jdbc.TDSCommand.startResponse(IOBuffer.java:6154)
at com.microsoft.sqlserver.jdbc.TDSCommand.startResponse(IOBuffer.java:6106)
at com.microsoft.sqlserver.jdbc.SQLServerConnection$1ConnectionCommand.doExecute(SQLServerConnection.java:1756)
at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:5696)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:1715)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.connectionCommand(SQLServerConnection.java:1761)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.setAutoCommit(SQLServerConnection.java:1901)
at sun.reflect.GeneratedMethodAccessor32.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.apache.tomcat.jdbc.pool.ProxyConnection.invoke(ProxyConnection.java:126)
at org.apache.tomcat.jdbc.pool.JdbcInterceptor.invoke(JdbcInterceptor.java:99)
at org.apache.tomcat.jdbc.pool.DisposableConnectionFacade.invoke(DisposableConnectionFacade.java:58)
at com.sun.proxy.$Proxy32.setAutoCommit(Unknown Source)
at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:87)
at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1473)
at org.hibernate.ejb.TransactionImpl.begin(TransactionImpl.java:60)
at com.theocean.dao.OceanClientDaoImpl.loadClients(OceanClientDaoImpl.java:52)
at com.theocean.service.ExperienceClientService.loadClientsLight(ExperienceClientService.java:30)
at com.theocean.web.ExperienceController.loadClientsLight(ExperienceController.java:30)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.web.bind.annotation.support.HandlerMethodInvoker.invokeHandlerMethod(HandlerMethodInvoker.java:176)
at org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.invokeHandlerMethod(AnnotationMethodHandlerAdapter.java:436)
at org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.handle(AnnotationMethodHandlerAdapter.java:424)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:790)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:719)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:669)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:574)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:947)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1009)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
SEVERE: Servlet.service() for servlet [spring] in context with path [/OceanWebService] threw exception [Request processing failed; nested exception is javax.persistence.PersistenceException: org.hibernate.TransactionException: JDBC begin failed: ] with root cause
com.microsoft.sqlserver.jdbc.SQLServerException: SQL Server did not return a response. The connection has been closed.
at com.microsoft.sqlserver.jdbc.SQLServerConnection.terminate(SQLServerConnection.java:1667)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.terminate(SQLServerConnection.java:1654)
at com.microsoft.sqlserver.jdbc.TDSReader.readPacket(IOBuffer.java:4844)
at com.microsoft.sqlserver.jdbc.TDSCommand.startResponse(IOBuffer.java:6154)
at com.microsoft.sqlserver.jdbc.TDSCommand.startResponse(IOBuffer.java:6106)
at com.microsoft.sqlserver.jdbc.SQLServerConnection$1ConnectionCommand.doExecute(SQLServerConnection.java:1756)
at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:5696)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:1715)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.connectionCommand(SQLServerConnection.java:1761)
at com.microsoft.sqlserver.jdbc.SQLServerConnection.setAutoCommit(SQLServerConnection.java:1901)
at sun.reflect.GeneratedMethodAccessor32.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.apache.tomcat.jdbc.pool.ProxyConnection.invoke(ProxyConnection.java:126)
at org.apache.tomcat.jdbc.pool.JdbcInterceptor.invoke(JdbcInterceptor.java:99)
at org.apache.tomcat.jdbc.pool.DisposableConnectionFacade.invoke(DisposableConnectionFacade.java:58)
at com.sun.proxy.$Proxy32.setAutoCommit(Unknown Source)
at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:87)
at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1473)
at org.hibernate.ejb.TransactionImpl.begin(TransactionImpl.java:60)
at com.theocean.dao.OceanClientDaoImpl.loadClients(OceanClientDaoImpl.java:52)
at com.theocean.service.ExperienceClientService.loadClientsLight(ExperienceClientService.java:30)
at com.theocean.web.ExperienceController.loadClientsLight(ExperienceController.java:30)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.web.bind.annotation.support.HandlerMethodInvoker.invokeHandlerMethod(HandlerMethodInvoker.java:176)
at org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.invokeHandlerMethod(AnnotationMethodHandlerAdapter.java:436)
at org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.handle(AnnotationMethodHandlerAdapter.java:424)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:790)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:719)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:669)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:574)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:947)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1009)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:310)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
So, the connection is being closed. Obviously something is wrong with the implementation whether it be the injection method or the method for handling errors, etc. So, the question is - What is the proper way to do this? How can I avoid the connection closed error? Thanks much in advance.

I think what could be happening is that some of the DAO's are leaving database transactions open when an error occurs.
The example DAO above is doing programmatic management of the database transaction, but does not handle the rollback scenario. This is an example of a DAO implementation that would do so:
MyService {
private EntityManagerFactory emf;
public void myMethod() {
EntityManager em = emf.createEntityManager();
EntityTransaction tx = em.getTransaction();
MyDaoA myDaoA = new MyDaoA(em);
MyDaoB myDaoB = new MyDaoB(em);
try {
tx.begin();
myDaoA.doSomething();
myDaoB.doSomething();
tx.commit();
} catch(Exception e) {
tx.rollback();
}
}
}
All DAOs that do programmatic transaction management should use this pattern, otherwise sooner or later a transaction will not be rolled back and this could cause problems.
A much more frequent and less error prone way of implementing DAOs is to inject directly only an entity manager:
MyService {
#PersistenceContext
private EntityManager em;
#Autowired
private MyDaoA myDaoA;
#Autowired
private MyDaoB myDaoB;
#Transactional
public void myMethod() {
myDaoA.doSomething();
myDaoB.doSomething();
}
}
Injecting the EntityManagerFactory and doing manual transaction management should be reserved for exceptional cases, and the use of #Transactional be used by default.

I would say problem is with Connection pooling , so you can use c3p0 connection pooling library for fixing your problem, but you should be very carefull with connection pool properties.
Actually lot of ways you can do, I am giving you same code for reference. It might help.
Step 1: persistence.xml
<!-- c3p0 properties -->
<!-- Determines how many connections at a time c3p0 will try to acquire when the pool is exhausted -->
<property name="hibernate.c3p0.acquire_increment" value="1"/>
<!-- If this is a number greater than 0,
c3p0 will test all idle, pooled but unchecked-out connections, every this number of seconds -->
<property name="hibernate.c3p0.idle_test_period" value="60"/>
<property name="hibernate.c3p0.max_size" value="20"/>
<property name="hibernate.c3p0.max_statements" value="50"/>
<property name="hibernate.c3p0.min_size" value="5"/>
<property name="hibernate.connection.provider_class" value="org.hibernate.connection.C3P0ConnectionProvider" />
Step 2: And then we create c3p0.properties under src/main/resources/META-INF with following properties
c3p0.testConnectionOnCheckout=true
c3p0.preferredTestQuery=SELECT 1;
Step 3: You need to configure data source
<bean id="myJdbcDataSource" class="com.mchange.v2.c3p0.ComboPooledDataSource"
destroy-method="close">
<!-- Connection properties -->
<property name="driverClass" value="$DS{database.class}" />
<property name="jdbcUrl" value="$DS{database.url}" />
<property name="user" value="$DS{database.username}" />
<property name="password" value="$DS{database.password}" />
<bean/>

com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Too many connections

My simple web-app sometimes crashes when navigating around the site, the error message I've gotten from the logs are found below. I have absolutely no idea of what is causing this and would be very thankful for any tips that'll lead me in the right direction.
HTTP Status 500 - org.hibernate.exception.JDBCConnectionException: Cannot open connection
type Exception report
message org.hibernate.exception.JDBCConnectionException: Cannot open connection
description The server encountered an internal error that prevented it from fulfilling this request.
exception
org.apache.jasper.JasperException: org.hibernate.exception.JDBCConnectionException: Cannot open connection
org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:549)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:470)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
root cause
org.hibernate.exception.JDBCConnectionException: Cannot open connection
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:97)
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:52)
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:449)
org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
org.hibernate.jdbc.AbstractBatcher.prepareQueryStatement(AbstractBatcher.java:161)
org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1573)
org.hibernate.loader.Loader.doQuery(Loader.java:696)
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:259)
org.hibernate.loader.Loader.doList(Loader.java:2228)
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2125)
org.hibernate.loader.Loader.list(Loader.java:2120)
org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:118)
org.hibernate.impl.SessionImpl.list(SessionImpl.java:1596)
org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:306)
com.html.XmlSetting.getListOfhtml_connect(XmlSetting.java:55)
com.html.XmlSetting.removeXml(XmlSetting.java:121)
com.html.MarginSetting.removeXml(MarginSetting.java:291)
org.apache.jsp.check_jsp._jspService(check_jsp.java:183)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:432)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
root cause
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Too many connections
sun.reflect.GeneratedConstructorAccessor153.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:532)
com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
com.mysql.jdbc.Util.getInstance(Util.java:381)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:985)
com.mysql.jdbc.SQLError.createSQLException(SQLError.java:957)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3376)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3308)
com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:894)
com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:3808)
com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1256)
com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2032)
com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:729)
com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
sun.reflect.GeneratedConstructorAccessor145.newInstance(Unknown Source)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
java.lang.reflect.Constructor.newInstance(Constructor.java:532)
com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:302)
com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:283)
java.sql.DriverManager.getConnection(DriverManager.java:620)
java.sql.DriverManager.getConnection(DriverManager.java:169)
org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:133)
org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:446)
org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:167)
org.hibernate.jdbc.AbstractBatcher.prepareQueryStatement(AbstractBatcher.java:161)
org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1573)
org.hibernate.loader.Loader.doQuery(Loader.java:696)
org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:259)
org.hibernate.loader.Loader.doList(Loader.java:2228)
org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2125)
org.hibernate.loader.Loader.list(Loader.java:2120)
org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:118)
org.hibernate.impl.SessionImpl.list(SessionImpl.java:1596)
org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:306)
com.html.XmlSetting.getListOfhtml_connect(XmlSetting.java:55)
com.html.XmlSetting.removeXml(XmlSetting.java:121)
com.html.MarginSetting.removeXml(MarginSetting.java:291)
org.apache.jsp.check_jsp._jspService(check_jsp.java:183)
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:432)
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:390)
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:334)
javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
I m using Apache Tomcat 7
hibernate.cfg.xml
<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD 3.0//EN"
"http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">
<hibernate-configuration>
<session-factory>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/htmlcleaner</property>
<property name="hibernate.connection.password">root</property>
<property name="hibernate.connection.username">root</property>
<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.dialect">org.hibernate.dialect.MySQLDialect</property>
<property name="hibernate.connection.zeroDateTimeBehavior">convertToNull</property>
<property name="connection.pool_size">1000</property>
<!-- <property name="show_sql">true</property> -->
<mapping class="com.model.html_connect"/>
</session-factory>
</hibernate-configuration>

It looks like you are leaking connections big time. Are you closing your hibernate sessions when you are done with them?
You could also try and fiddle about with hibernate.connection.release_mode , by default, this is set to auto and it will release the connection when you close the session. However, you also have the options here to use after_transaction or after_statement (its rather self explanatory when it will release the connections for each of the two :P).
With that said though, you do need to find out where you leaks are :)

The possible reason for this is that your web application is possibly leaking connections or the connection pool size is very small due to which all the open connections are currently being used and the new connection cannot be obtained.
I am not sure about Tomcat but in JBoss, we generally refer to datasource file and you can set the connection pool size as
<max-pool-size>80</max-pool-size>
You can even log into the administrative console of Tomcat and check how many connections are actually in use whenever you get this exception. The administrative console will give you the maximum connection objects ever created and a variety of other information related to connection pool.

Its clearly seen hibernate is not able to create or open connection with database there could be many reason some them are
Your not closing session in your program after using session
Connection pool is small and too many threads are accessing the pool.
Kindly paste your configuration and exception point program
Add
<property name="hibernate.connection.release_mode">on_close</property>
property and call session.close(); at the end of your method