Connecting to a MySQL database from time to time even after setting c3p0.testConnectionOnCheckout = true

I have an application using hibernate (v3.6.4), with the connection pool provided by C3P0 (v0.9.1.2).

The problem is that I get a JDBC link failure if I make a DB request if the application process (and therefore the C3P0 pool) is running longer than the MySQL wait_timeout value. I set the wait_timeout value in /etc/mysql/my.cnf to 600 seconds to check for this problem:

2013-01-27 20:08:00,088 ERROR [Thread-0] (JDBCExceptionReporter.java:234) - Communications link failure

The last packet successfully received from the server was 665,943 milliseconds ago.  The last packet sent successfully to the server was 6 milliseconds ago.
org.hibernate.exception.JDBCConnectionException: could not execute query
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:99)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at org.hibernate.loader.Loader.doList(Loader.java:2536)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
at org.hibernate.loader.Loader.list(Loader.java:2271)
at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:119)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1716)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:347) 
.....
Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
The last packet successfully received from the server was 665,943 milliseconds ago.  The last packet sent successfully to the server was 6 milliseconds ago.
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1116)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3102)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2991)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3532)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2002)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
at  com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1953)
at org.hibernate.loader.Loader.doQuery(Loader.java:802)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
at org.hibernate.loader.Loader.doList(Loader.java:2533)
... 9 more
Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost.
at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:2552)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3002)
... 22 more

2013-01-27 20:19:00,179  WARN [Thread-0] (NewPooledConnection.java:487) - [c3p0] Another error has occurred [ com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 1,326,037 milliseconds ago.  The last packet sent successfully to the server was 660,100 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. ] which will not be reported to listeners!
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 1,326,037 milliseconds ago.  The last packet sent successfully to the server was 660,100 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(Unknown Source)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1116)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3364)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1983)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2163)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2624)
at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2127)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2293)
at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:76)
at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:208)
at org.hibernate.loader.Loader.getResultSet(Loader.java:1953)
at org.hibernate.loader.Loader.doQuery(Loader.java:802)
at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:274)
at org.hibernate.loader.Loader.doList(Loader.java:2533)
at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2276)
at org.hibernate.loader.Loader.list(Loader.java:2271)
at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:119)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1716)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:347)
....
Caused by: java.net.SocketException: Broken pipe
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(Unknown Source)
at java.net.SocketOutputStream.write(Unknown Source)
at java.io.BufferedOutputStream.flushBuffer(Unknown Source)
at java.io.BufferedOutputStream.flush(Unknown Source)
at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3345)
... 20 more

This looked like a normal problem, so to solve this problem, I tried to set these hibernate / c3p0 properties after checking the hibernate / c3p0 documentation and answering questions already asked about stack overflow:

Relevant sleep mode properties:

<property name="hibernate.connection.driver_class">com.mysql.jdbc.Driver</property>
<property name="hibernate.connection.url">jdbc:mysql://localhost:3306/gsui?useUnicode=true&amp;characterEncoding=UTF-8&amp;autoReconnect=true</property>

<property name="hibernate.connection.autoReconnect">true</property>

<!-- C3p0 Performance Improvements -->
<property name="hibernate.c3p0.acquire_increment">1</property>
<property name="hibernate.c3p0.idle_test_period">300</property>
<property name="hibernate.c3p0.maxConnectionAge">3600</property>
<property name="hibernate.c3p0.timeout">120</property>
<property name="hibernate.c3p0.max_size">300</property>
<property name="hibernate.c3p0.min_size">1</property>
<property name="hibernate.c3p0.max_statements">100</property>
<property name="hibernate.c3p0.preferredTestQuery">select 1;</property>

<property name="hibernate.connection.useUnicode">
    true
</property>
<property name="hibernate.connection.characterEncoding">
    UTF-8
</property>
<property name="hibernate.connection.charSet">
    UTF-8
</property>

c3p0.testConnectionOnCheckout true c3p0, :

c3p0.testConnectionOnCheckout=true

C3P0 :

2013-01-27 19:45:04,607  INFO [main] (ConnectionProviderFactory.java:173) - Initializing connection provider: org.hibernate.connection.C3P0ConnectionProvider
2013-01-27 19:45:04,609  INFO [main] (C3P0ConnectionProvider.java:103) - C3P0 using driver: com.mysql.jdbc.Driver at URL: jdbc:mysql://localhost:3306/gsui?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true
2013-01-27 19:45:04,610  INFO [main] (C3P0ConnectionProvider.java:104) - Connection properties: {useUnicode=true, autoReconnect=true, user=root, password=****, shutdown=true, characterEncoding=UTF-8, charSet=UTF-8}
2013-01-27 19:45:04,610  INFO [main] (C3P0ConnectionProvider.java:107) - autocommit mode: false
2013-01-27 19:45:04,629  INFO [main] (MLog.java:80) - MLog clients using log4j logging.
2013-01-27 19:45:04,757  INFO [main] (C3P0Registry.java:204) - Initializing c3p0-0.9.1.2 [built 21-May-2007 15:04:56; debug? true; trace: 10]
2013-01-27 19:45:04,842  INFO [main] (C3P0ConnectionProvider.java:194) - JDBC isolation level: READ_COMMITTED
2013-01-27 19:45:04,871  INFO [main] (AbstractPoolBackedDataSource.java:462) - Initializing c3p0 pool... com.mchange.v2.c3p0.PoolBackedDataSource@9f4a7137 [ connectionPoolDataSource -> com.mchange.v2.c3p0.WrapperConnectionPoolDataSource@71b9e1e9 [ acquireIncrement -> 1, acquireRetryAttempts -> 30, acquireRetryDelay -> 1000, autoCommitOnClose -> false, automaticTestTable -> null, breakAfterAcquireFailure -> false, checkoutTimeout -> 0, connectionCustomizerClassName -> null, connectionTesterClassName -> com.mchange.v2.c3p0.impl.DefaultConnectionTester, debugUnreturnedConnectionStackTraces -> false, factoryClassLocation -> null, forceIgnoreUnresolvedTransactions -> false, identityToken -> z8kfsx8sz4pted1s4b69w|51f726b9, idleConnectionTestPeriod -> 300, initialPoolSize -> 1, maxAdministrativeTaskTime -> 0, maxConnectionAge -> 3600, maxIdleTime -> 120, maxIdleTimeExcessConnections -> 0, maxPoolSize -> 300, maxStatements -> 100, maxStatementsPerConnection -> 0, minPoolSize -> 1, nestedDataSource -> com.mchange.v2.c3p0.DriverManagerDataSource@58f45048 [ description -> null, driverClass -> null, factoryClassLocation -> null, identityToken -> z8kfsx8sz4pted1s4b69w|454b7177, jdbcUrl -> jdbc:mysql://localhost:3306/gsui?useUnicode=true&characterEncoding=UTF-8&autoReconnect=true, properties -> {useUnicode=true, autoReconnect=true, user=******, password=******, shutdown=true, characterEncoding=UTF-8, charSet=UTF-8} ], preferredTestQuery -> select 1;, propertyCycle -> 0, testConnectionOnCheckin -> false, testConnectionOnCheckout -> true, unreturnedConnectionTimeout -> 0, usesTraditionalReflectiveProxies -> false; userOverrides: {} ], dataSourceName -> null, factoryClassLocation -> null, identityToken -> z8kfsx8sz4pted1s4b69w|71ffd9f1, numHelperThreads -> 3 ]

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<property name="hibernate.connection.release_mode" value="after_transaction" />

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<property name="connection.provider_class">
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</property>
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