产生这种问题的原因是：
连接数超过了 MySQL 设置的值，与 max_connections 和 wait_timeout 都有关系。wait_timeout 的值越大，连接的空闲等待就越长，这样就会造成当前连接数越大。
解决方法：
修改MySQL配置文件/etc/my.cnf,设置成max_connections=1000,wait_timeout=5。如果没有此项设置可以自行添加，修改后重启MySQL服务即可。要不经常性报此错误，则要对服务器作整体性能优化
补充:
在工作中，大家或许常常遇到Too many connections这个错误，这时作为DBA想进数据库管理都进不去，是非常尴尬的一件事情。当然有同学说可以修改配置文件，但是修改配置文件是需要重启mysqld的，这在业务繁忙的数据库服务器上是不允许的。所以紧急情况下可以采用如下的方法，比如下面的测试。
[root@mysql-server-01 msb_5_6_19]# ./use
ERROR 1040 (HY000): Too many connections
[root@mysql-server-01 msb_5_6_19]#
我上面是采用MySQL沙箱环境，关于沙箱环境的简单安装及使用请参看我前面的文章。MySQL Sandbox安装使用
可以看见我上面已经报了错误，提示也非常明显，就是我们配置的连接数太小，现在已经用完了，这时我们刚想进数据库做些操作，那么采用如下方法：
[root@mysql-server-01 ~]# gdb -p $(cat /root/sandboxes/msb_5_6_19/data/mysql_sandbox5619.pid) -ex "set max_connections=500" -batch
[New LWP 27541]
[New LWP 27540]
[New LWP 27539]
[Thread debugging using libthread_db enabled]
0x00000031152df343 in poll () from /lib64/libc.so.6
[root@mysql-server-01 ~]#
下面再次登录数据库看看，并查看最大连接数是否已经修改
[root@mysql-server-01 msb_5_6_19]# ./use
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 22
Server version: 5.6.19-log MySQL Community Server (GPL)
Copyright (c) 2000, 2014, Oracle and/or its affiliates. All rights reserved.
Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql [localhost] {msandbox} ((none)) > show variables like 'max_connections';
+-----------------+-------+
| Variable_name | Value |
+-----------------+-------+
| max_connections | 500 |
+-----------------+-------+
1 row in set (0.00 sec)
mysql [localhost] {msandbox} ((none)) >
在Percona5.5的thread_pool里面提供了2个参数extra_port和extra_max_connections预留额外的连接，预防连接满了以后我们无法进入数据库进行相应的管理。
root@localhost : (none) 23:18:00> show variables like '%extra%';
+-----------------------+-------+
| Variable_name | Value |
+-----------------------+-------+
| extra_max_connections | 1 |
| extra_port | 10086 |
+-----------------------+-------+
2 rows in set (0.00 sec)
root@localhost : (none) 23:18:04>
[root@mysql-server-01 user_3307]# netstat -nltp | grep 10086
tcp 0 0 0.0.0.0:10086 0.0.0.0:* LISTEN 29655/mysqld
[root@mysql-server-01 user_3307]#
我这里使用了10086端口，以及最大连接数为1。有这么贴心的功能。必须给一个赞
总结：
通常控制最大连接数有两个参数控制max_connections（该实例允许最大的连接数 ），max_user_connections（该实例允许每个用户的最大连接数），通常情况下前期我们就需要规划好多少连接数合适。一般情况下建议不要超过300。因为MySQL在连接数上升的情况下性能下降非常厉害，如果需要大量连接，这时可以引入thread_pool。所以我们需要保持一个原则：系统创建的用户（给应用使用用户）数* max_user_connections < max_connections。这样就不会发生文章开始说的问题。
java提示Too many connections错误的解决办法
MySQL的错误,待解决[已解决]Data source rejected establishment of connection message from server: "Too many connections";
[15:22:53,461] [CustomExceptionHandler,44] - Handle Exception:hibernate operation: Cannot open connection; uncategorized SQLException for SQL [???]; SQL state [08004]; error code [1040]; Data source rejected establishment of connection message from server: "Too many connections"; nested exception is Java.sql.SQLException: Data source rejected establishment of connection message from server: "Too many connections"
org.springframework.jdbc.UncategorizedSQLException: Hibernate operation: Cannot open connection; uncategorized SQLException for SQL [???]; SQL state [08004]; error code [1040]; Data source rejected establishment of connection message from server: "Too many connections"; nested exception is java.sql.SQLException: Data source rejected establishment of connection message from server: "Too many connections"
java.sql.SQLException: Data source rejected establishment of connection message from server: "Too many connections"
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1997)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1906)
at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:2535)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:817)
at com.mysql.jdbc.Connection.createNewIO(Connection.java:1782)
at com.mysql.jdbc.Connection.<init>(Connection.java:450)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:411)
at java.sql.DriverManager.getConnection(DriverManager.java:525)
at java.sql.DriverManager.getConnection(DriverManager.java:140)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriverManager(DriverManagerDataSource.java:291)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriverManager(DriverManagerDataSource.java:277)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriverManager(DriverManagerDataSource.java:259)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnection(DriverManagerDataSource.java:241)
at org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:80)
at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:315)
at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:109)
at org.hibernate.jdbc.AbstractBatcher.prepareQueryStatement(AbstractBatcher.java:105)
at org.hibernate.loader.Loader.prepareQueryStatement(Loader.java:1561)
at org.hibernate.loader.Loader.doQuery(Loader.java:661)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
at org.hibernate.loader.Loader.doList(Loader.java:2150)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029)
at org.hibernate.loader.Loader.list(Loader.java:2024)
at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:369)
at org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:300)
at org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:146)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1093)
at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
at com.easou.framework.dao.hibernate.BaseDAOHibernate.pageListQuery(BaseDAOHibernate.java:164)
at com.vitamin.cn.manager.news.dao.hibernate.NewsDAOHibernate.searchNews(NewsDAOHibernate.java:38)
at com.vitamin.cn.manager.news.bl.impl.NewsManagerImpl.searchNews(NewsManagerImpl.java:24)
at com.vitamin.cn.manager.news.action.NewsAction.listNews(NewsAction.java:88)
at com.vitamin.cn.manager.news.action.NewsAction.execute(NewsAction.java:35)
at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:419)
at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1196)
at org.apache.struts.action.ActionServlet.doGet(ActionServlet.java:414)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at com.easou.framework.util.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:88)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:202)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:524)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:199)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:282)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:767)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:697)
at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:889)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684)
at java.lang.Thread.run(Thread.java:595)
1.可能是mysql的max connections设置的问题
2.可能是多次insert,update操作没有关闭session,需要在spring里配置transaction支持。
解决:
1.修改tomcat里的session 的time-out时间减少为20,(不是必改项)
2.对处理量大的对数据库insert或update的操作提供transaction支持.
=======================================
下面的是解决办法：
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: Data source rejected establishment of connection, message from server: "Too many connections"
原因：
因为你的mysql安装目录下的my.ini中设定的并发连接数太少或者系统繁忙导致连接数被占满
解决方式：
打开MYSQL安装目录打开MY.INI找到max_connections（在大约第93行）默认是100 一般设置到500～1000比较合适，重启mysql,这样1040错误就解决啦。
max_connections=1000
一定要重新启动MYSQL才能生效
CMD->
net stop mysql
net start mysql
关于改变innodb_log_file_size后无法启动mysql的问题
innodb_buffer_pool_size=768M
innodb_log_file_size=256M
innodb_log_buffer_size=8M
innodb_additional_mem_pool_size=4M
innodb_flush_log_at_trx_commit=0
innodb_thread_concurrency=20
以上是对innodb引擎的初步优化, 发现是更新innodb_log_file_size=256M时候出现了问题，只要加上这个就无法启动,
后来才知道原来要STOP服务先，然后再删除原来的文件………
打开/MySQL Server 5.5/data
删除ib_logfile0, ib_logfile1........ib_logfilen
再开启选项，成功启动。
一,修改配置文件文件
修改/etc/my.cnf这个文件，在[mysqld]中新增max_connections=N，如果你没有这个文件请从编译源码中的support-files文件夹中复制你所需要的*.cnf文件为到/etc/my.cnf。我使用的是my-medium.cnf,中型服务器配置。例如我的[mysqld]的内容如下
[mysqld]
port = 3306
socket = /tmp/mysql.sock
skip-locking
key_buffer = 160M
max_allowed_packet = 1M
table_cache = 64
sort_buffer_size = 512K
net_buffer_length = 8K
read_buffer_size = 256K
read_rnd_buffer_size = 512K
myisam_sort_buffer_size = 8M
max_connections=1000
由于对mysql还不是很熟悉，所以很多参数没有修改。哈哈。。
2、非使用mysqld脚本自动启动的用户。
修改$MYSQL_HOME/bin/mysqld_safe文件
例如：/usr/local/mysql/bin/mysqld_safe这个文件
grep -n 'max_connection' $MYSQL_HOME/bin/mysqld_safe
修改对应行号的max_connections参数值
以上方法为参考网上的做法写的
关于改变innodb_log_file_size后无法启动mysql的问题
innodb_buffer_pool_size=768M
innodb_log_file_size=256M
innodb_log_buffer_size=8M
innodb_additional_mem_pool_size=4M
innodb_flush_log_at_trx_commit=0
innodb_thread_concurrency=20
以上是对innodb引擎的初步优化, 发现是更新innodb_log_file_size=256M时候出现了问题，只要加上这个就无法启动,
后来才知道原来要STOP服务先，然后再删除原来的文件………
打开/MySQL Server 5.5/data
删除ib_logfile0, ib_logfile1........ib_logfilen
再开启选项，成功启动。