tomcat程序连接服务器mysql数据库报错

tomcat程序连接服务器mysql数据库，报
错误，后来用java程序直接连接数据库，发现可以连得上，可以操作数据库，
在网上查了设置数据库连接等待时间(wait_timeout)设置，也没用。
奇怪的一点是，尽管控制台报错，但是还可以实现本人写的那个查询功能，可以从数据库中查到数据显示到页面
org.apache.commons.dbcp.SQLNestedException: Cannot create PoolableConnectionFactory (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 org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:855)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:540)
at org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:81)
at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:72)
at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:1881)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1174)
at org.springframework.orm.hibernate3.LocalSessionFactoryBean.newSessionFactory(LocalSessionFactoryBean.java:805)
at org.springframework.orm.hibernate3.LocalSessionFactoryBean.buildSessionFactory(LocalSessionFactoryBean.java:745)
at org.springframework.orm.hibernate3.AbstractSessionFactoryBean.afterPropertiesSet(AbstractSessionFactoryBean.java:134)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1175)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1145)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:427)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:144)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:261)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:109)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1073)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:835)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:423)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:144)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:279)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:360)
at org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:241)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:184)
at com.base.common.spring.SpringContextLoaderServlet.init(SpringContextLoaderServlet.java:23)
at javax.servlet.GenericServlet.init(GenericServlet.java:158)
at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1284)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1197)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:1087)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:5262)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5550)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:649)
at org.apache.catalina.startup.HostConfig.deployDirectory(HostConfig.java:1245)
at org.apache.catalina.startup.HostConfig$DeployDirectory.run(HostConfig.java:1895)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: com.mysql.jdbc.exceptions.jdbc4.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 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:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1118)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:343)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2308)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2122)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:774)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:49)
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:526)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:409)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:375)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:289)
at org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:37)
at org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:290)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:877)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:851)
… 46 more
Caused by: java.net.ConnectException: Connection refused: connect
at java.net.DualStackPlainSocketImpl.connect0(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(DualStackPlainSocketImpl.java:79)
at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:339)
at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:200)
at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:182)
at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:172)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
at java.net.Socket.connect(Socket.java:579)
at java.net.Socket.connect(Socket.java:528)
at java.net.Socket.<init>(Socket.java:425)
at java.net.Socket.<init>(Socket.java:241)
at com.mysql.jdbc.StandardSocketFactory.connect(StandardSocketFactory.java:256)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:292)
… 61 more