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MySQLNonTransientConnectionException/CommunicationsException when validation is true in domain.xml?

Setup: Glassfish 3x, Java EE, EclipseLink.
jdbc connection pool config (from domain.xml):
<jdbc-connection-pool validation-table-name="dummy" pool-resize-quantity="5" max-pool-size="300" datasource-classname="com.mysql.jdbc.jdbc2.optional.MysqlXADataSource" wrap-jdbc-objects="false" res-type="javax.sql.XADataSource" steady-pool-size="25" name="mysql_bazaarify_rootPool" is-connection-validation-required="true" non-transactional-connections="true" validate-atmost-once-period-in-seconds="60">
<property name="URL" value="jdbc:mysql://demodb.mydb.com:3306/database?zeroDateTimeBehavior=convertToNull&useUnicode=yes"></property>
Getting CommunicationsException infrequently for different queries.
I have configured for connections to be validated before use with 60 seconds of validity.
wait_time on sql server is 8 hours.
Still I am seeing below error in my logs (~50 times a day)
Exception Trace:
Internal Exception:
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
Error Code: 0
....
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException:
The last packet successfully received from the server was 56,688,227 milliseconds ago.
The last packet sent successfully to the server was 56,688,227 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.
....
Caused by: java.net.SocketException: Connection timed out
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:113)
at java.net.SocketOutputStream.write(SocketOutputStream.java:159)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3832)
... 140 more
My question is, when I have set for connection to be validated (every 60 seconds), is it possible that I get a stale/broken connection from connection pool which says that the last communication with mysql was (>60seconds) ago?
Shouldn't the connection be validated until a healthy one is returned from the pool? Are these exceptions normal with the settings I have configured?
P.S.
I observed that in all such failures, the milliseconds ago value reported is always >8 hours. Does that help deduce anything?

How to overcome org.springframework.dao.RecoverableDataAccessException?

I keep receiving connectivity issues when connecting my Spring project to a MySQL server. I have tried various tricks that I have found online but to no avail. I need help in order to escape this quandary. I'm placing my Spring settings below and the stack trace as well.
Spring Settings
spring.datasource.tomcat.initialize=true
spring.dataSource.tomcat.url=jdbc:mysql://nope/canttellyou?
autoReconnect=true&useSSL=false&zeroDateTimeBehavior=convertToNull
spring.dataSource.tomcat.username=nope
spring.dataSource.tomcat.password=sorry
spring.dataSource.tomcat.driver-class-name=com.mysql.jdbc.Driver
spring.datasource.tomcat.test-on-borrow=true
spring.datasource.tomcat.validation-query=SELECT 1
spring.datasource.tomcat.log-validation-errors=true
StackTrace
stackTrace: org.springframework.dao.RecoverableDataAccessException:
PreparedStatementCallback; SQL [select catname from animals]; The last
packet successfully received from the server was 52,962,310
milliseconds ago. The last packet sent successfully to the server was
52,962,310 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.; nested
exception is com.mysql.jdbc.exceptions.jdbc4.CommunicationsException:
The last packet successfully received from the server was 52,962,310
milliseconds ago. The last packet sent successfully to the server was
52,962,310 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.

I've been having the same problem. I think the configuration setting we want to turn on is:
testWhileIdle
Here's the related tomcat connection pool docs
I won't know until tomorrow whether or not this worked for me.

Tomcat issue:The last packet successfully received from the server was 66,913,221 milliseconds ago.

I have installed tomcat on centos and deployed a java web application. I'm using mysql db. Everyday in the morning when I try to login as first user, it gieves me the following error:
Your login attempt was not successful, try again.
Reason: org.hibernate.exception.JDBCConnectionException: The last packet successfully received from the server was 66,913,221 milliseconds ago. The last packet sent successfully to the server was 66,913,221 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.
After this, When I try to relogin, it allows me to do so.
I have include the following in my context.xml
<Resource name="jdbc/CAR" auth="Container" type="javax.sql.DataSource"
maxActive="100" maxIdle="30" maxWait="30000"
username="root" password="" driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://130.1.18.2:3306/car" validationQuery="SELECT 1" testOnBorrow = true/>
Any help on this, I would appreciate. Thanks

Try to add autoReconnect=true parameter to the jdbc string to keep it alive when not receiving packets. In your case it would be
jdbc:mysql://130.1.18.2:3306/car?autoReconnect=true

or if you can, you can change to other database pool. I has the same problem before, and the autoReconnect not work for me. Now I am using HikariCP. this problem gone.

autoReconnect=true
is not working as per my knowledge, Mysql having its own connection closure timeout. ORM will mark it as stale connection if Mysql closes the connection.

Could not open JPA EntityManager for transaction; nested exception is javax.persistence.PersistenceException

when i run my code, i get this exception:
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:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
at com.mysql.jdbc.MysqlIO.<init>(MysqlIO.java:357)
at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2482)
at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2519)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2304)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:834)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:47)
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.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:416)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:346)
at java.sql.DriverManager.getConnection(DriverManager.java:664)
at java.sql.DriverManager.getConnection(DriverManager.java:208)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriverManager(DriverManagerDataSource.java:153)
at org.springframework.jdbc.datasource.DriverManagerDataSource.getConnectionFromDriver(DriverManagerDataSource.java:144)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnectionFromDriver(AbstractDriverBasedDataSource.java:155)
at org.springframework.jdbc.datasource.AbstractDriverBasedDataSource.getConnection(AbstractDriverBasedDataSource.java:120)
at org.hibernate.engine.jdbc.connections.internal.DatasourceConnectionProviderImpl.getConnection(DatasourceConnectionProviderImpl.java:139)
at org.hibernate.tool.hbm2ddl.SuppliedConnectionProviderConnectionHelper.prepare(SuppliedConnectionProviderConnectionHelper.java:51)
at org.hibernate.tool.hbm2ddl.DatabaseExporter.<init>(DatabaseExporter.java:52)
at org.hibernate.tool.hbm2ddl.SchemaExport.execute(SchemaExport.java:367)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:304)
at org.hibernate.tool.hbm2ddl.SchemaExport.create(SchemaExport.java:293)
at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:517)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1857)
The last packet sent successfully to the server was 0 milliseconds ago. The driver has not received any packets from the server.
Aug 25, 2015 8:23:45 PM com.sun.jersey.spi.container.ContainerResponse mapMappableContainerException
SCHWERWIEGEND: The RuntimeException could not be mapped to a response, re-throwing to the HTTP container
org.springframework.transaction.CannotCreateTransactionException: Could not open JPA EntityManager for transaction; nested exception is javax.persistence.PersistenceException: org.hibernate.exception.JDBCConnectionException: Could not open connection
at org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:431)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:457)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:276)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:207)
at com.sun.proxy.$Proxy76.create(Unknown Source)
I don't know where is the problem. But yesterday i worked fine.
my database.properties:
jdbc.driverClassName=com.mysql.jdbc.Driver
jdbc.url=jdbc:mysql://localhost:3306/streaming
jdbc.username=root
jdbc.password=password
hibernate.dialect=org.hibernate.dialect.MySQLDialect
hibernate.showsql=true
hibernate.hbm2ddl.auto=create
It is possible for me to run mysql directly from command line. Where is the problem? Was is wrong.
I use spring 4 and hibernate with mysql as database language.
Has someone any ideas?
Thank.

There is CommunicationsException: Communications link failure.
If you get a SQLException: Connection refused or Connection timed out or a MySQL specific
CommunicationsException: Communications link failure
then it means that the DB isn't reachable at all. This can have one or more of the following causes:
IP address or hostname in JDBC URL is wrong.
Hostname in JDBC URL is not recognized by local DNS server.
Port number is missing or wrong in JDBC URL.
DB server is down.
DB server doesn't accept TCP/IP connections.
DB server has run out of connections.
Something in between Java and DB is blocking connections, e.g. a firewall or proxy.
To solve the one or the other, follow the following advices:
Verify and test them with ping.
Refresh DNS or use IP address in JDBC URL instead.
Verify it based on my.cnf of MySQL DB.
Start the DB.
Verify if mysqld is started without the --skip-networking option.
Restart the DB and fix your code accordingly that it closes connections in finally.
Disable firewall and/or configure firewall/proxy to allow/forward the port.
Source: More Details

I see that #Amit Tamrakar have good answer but I want to add:
if you make a lot of requests to db, (I mean connections), may be that application (some app thread) just wait for use free connection from app db connection pool, but throws timeout exception.
.h.engine.jdbc.spi.SqlExceptionHelper : HikariPool-1 - Connection is not available, request timed out after 30005ms.
Could not open JPA EntityManager for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Unable to acquire JDBC Connection
You can try to increase db connection pool in application config file, for example:
spring.datasource.hikari.maximum-pool-size=20
You can set size which you need. This config in app by default is 8.
And we need remember that each db have own free db connection size which we don't need exceed.
I mean if db have 5 free connection and you want to use 10 connections in your app then we will receive so exceptions.

DB is down.
You must start the DB server and check connectivity with either telnet or mysql command line client first.

I was not unable to figure out the exact cause, but I realized that it was because of some thread pools since I was able to connect to the db using the terminal.
for checking the connectivity you can use the below command.
psql -h hostname -U username -d database
so restarting the server worked for me.

After some time MySql server goes off and I have to restart the server again and again

Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException:
The last packet successfully received from the server was 38,160,127
milliseconds ago. The last packet sent successfully to the server was
38,160,127 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.
1) As per the solutions given by TOMCAT I have increased the value of wait_timeout but, it is not working.
2) How to set autoReconnect=true in my URL I don't know. I tried with all the possibilities but it does not work.
URL:
<property
name="url"
value="jdbc:mysql://127.0.01:3306/PaxWeb3?zeroDateTimeBehavior" />
I have tried using:
value="jdbc:mysql://127.0.01:3306/PaxWeb3?zeroDateTimeBehavior&autoReconnect=true"
and
value="jdbc:mysql://127.0.01:3306/PaxWeb3?zeroDateTimeBehavior;&autoReconnect=true"
but they won't work either.