Problem with connection pooling with Java and MySQL in Tomcat web application

Question

Hello

I recently wrote and deployed a Java web application to a server and I'm finding an unusual problem which didn't appear during development or testing.

When a user logs in after so long and goes to display data from the database, the page indicates that there are no records to see. But upon page refresh, the first x records are shown according to the pagination rules.

Checking the logs, I find:

ERROR|19 09 2009|09 28 54|http-8080-4|myDataSharer.database_access.Database_Metadata_DBA| - Error getting types of columns of tabular Dataset 12

com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception: 

** BEGIN NESTED EXCEPTION ** 

java.io.EOFException

STACKTRACE:

java.io.EOFException
    at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1956)
    at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2368)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2867)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1616)

And so on for several hundred lines.

The application is currently set for about 100 users but is not yet in full use. It uses connection pooling between the Apache Tomcat servlets / jsps and a MySQL database with the following code example forming the general arrangement of a database operation, of which there are typically several per page:

// Gets a Dataset.
public static Dataset getDataset(int DatasetNo) {
    ConnectionPool_DBA pool = ConnectionPool_DBA.getInstance();
    Connection connection = pool.getConnection();
    PreparedStatement ps = null;
    ResultSet rs = null;

    String query = ("SELECT * " +
                    "FROM Dataset " +
                    "WHERE DatasetNo = ?;");

    try {
        ps = connection.prepareStatement(query);
        ps.setInt(1, DatasetNo);
        rs = ps.executeQuery();
        if (rs.next()) {
            Dataset d = new Dataset();
            d.setDatasetNo(rs.getInt("DatasetNo"));
            d.setDatasetName(rs.getString("DatasetName"));
            ...

            }

            return d;
        }
        else {
            return null;
        }
    }
    catch(Exception ex) {
        logger.error("Error getting Dataset " + DatasetNo + "\n", ex);            
        return null;
    }
    finally {
        DatabaseUtils.closeResultSet(rs);
        DatabaseUtils.closePreparedStatement(ps);
        pool.freeConnection(connection);
    }
}

Is anyone able to advise a way of correcting this problem?

I believe it is due to MySQL leaving connection poll connections open for up to eight hours but am not certain.

Thanks

Martin O'Shea.

Answer 1

I'd wonder why you're using ConnectionPool_DBA in your code instead of letting Tomcat handle the pooling and simply looking up the connection using JNDI.

Why are you using an Oracle connection pool with MySQL? When I do JNDI lookups and connection pooling, I prefer the Apache DBCP library. I find that it works very well.

I'd also ask if your DatabaseUtils methods throw any exceptions, because if either of the calls prior to your call to pool.freeConnection() throw one you'll never free up that connection.

I don't like your code much because a class that performs SQL operations should have its Connection instance passed into it, and should not have the dual responsibility of acquiring and using the Connection. A persistence class can't know if it's being used in a larger transaction. Better to have a separate service layer that acquires the Connection, manages the transaction, marshals the persistence classes, and cleans up when it's complete.

UPDATE:

Google turned up the Oracle class with the same name as yours. Now I really don't like your code, because you wrote something of your own when a better alternative was easily available. I'd ditch yours right away and redo this using DBCP and JNDI.

Answer 2

There are a few pointers on avoiding this situation, obtained from other sources, especially from the connection pool implementations of other drivers and from other application servers. Some of the information is already available in the Tomcat documentation on JNDI Data Sources.

1. Establish a cleanup/reaper schedule that will close connections in the pool, if they are inactive beyond a certain period. It is not good practice to leave a connection to the database open for 8 hours (the MySQL default). On most application servers, the inactive connection timeout value is configurable and is usually less than 15 minutes (i.e. connections cannot be left in the pool for more than 15 minutes unless they are being reused time and again). In Tomcat, when using a JNDI DataSource, use the removeAbandoned and removeAbandonedTimeout settings to do the same.
2. When a new connection is return from the pool to the application, ensure that it is tested first. For instance, most application servers that I know, can be configured so that connection to an Oracle database are tested with an execute of "SELECT 1 FROM dual". In Tomcat, use the validationQuery property to set the appropriate query for MySQL - I believe this is "SELECT 1" (without quotes). The reason why setting the value of the validationQuery property helps, is because if the query fails to execute, the connection is dropped from the pool, and new one is created in its place.

As far are the behavior of your application is concerned, the user is probably seeing the result of the pool returning a stale connection to the application for the first time. The second time around, the pool probably returns a different connection that can service the application's queries.

Tomcat JNDI Data Sources are based on Commons DBCP, so the configuration properties applicable to DBCP will apply to Tomcat as well.

Answer 3

Just to clarify one point made about my method of connection pooling, it isn't Oracle that I'm using in my application but a class of my own as follows:

package myDataSharer.database_access;

import java.sql.*;
import javax.sql.DataSource;
import javax.naming.InitialContext;
import org.apache.log4j.Logger;

public class ConnectionPool_DBA {

    static Logger logger = Logger.getLogger(ConnectionPool_DBA.class.getName());

    private static ConnectionPool_DBA pool = null;
    private static DataSource dataSource = null;


    public synchronized static ConnectionPool_DBA getInstance() {
        if (pool == null) {
            pool = new ConnectionPool_DBA();
        }
        return pool;
    }

    private ConnectionPool_DBA() {
        try {
            InitialContext ic = new InitialContext();
            dataSource = (DataSource) ic.lookup("java:/comp/env/jdbc/myDataSharer");
        }
        catch(Exception ex) {
            logger.error("Error getting a connection pool's datasource\n", ex);
        }
    }

    public void freeConnection(Connection c) {
        try {
            c.close();
        }
        catch (Exception ex) {
            logger.error("Error terminating a connection pool connection\n", ex);           
        }
    }

    public Connection getConnection() {
        try {
            return dataSource.getConnection();
        }
        catch (Exception ex) {
            logger.error("Error getting a connection pool connection\n", ex);            
            return null;
        }
    }    
}

I think the mention of Oracle is due to me using a similar name.

Answer 4

Is there a router between the web server and the database that transparently closes idle TCP/IP connections?

If so, you must have your connection pool either discard unused-for-more-than-XX-minutes connections from the pool, or do some kind of ping every YY minutes on the connection to keep it active.

Answer 5

This error indicates server closes connection unexpectedly. This can occur in following 2 cases,

1. MySQL closes idle connection after certain time (default is 8 hours). When this occurs, no thread is responsible for closing the connection so it gets stale. This is most likely the cause if this error only happens after long idle.

2. If you don't completely read all the responses, the connection may get returned to the pool in busy state. Next time, a command is sent to MySQL and it closes connection for wrong state. If the error occurs quite frequent, this is probably the cause.

Meanwhile, setting up an eviction thread will help to alleviate the problem. Add something like this to the Data Source,

          ...
          removeAbandoned="true"
          removeAbandonedTimeout="120"
          logAbandoned="true"
          testOnBorrow="false"
          testOnReturn="false"
          timeBetweenEvictionRunsMillis="60000"
          numTestsPerEvictionRun="5"
          minEvictableIdleTimeMillis="30000"
          testWhileIdle="true"
          validationQuery="select now()"

Answer 6

On the off chance you haven't found your answer I've been dealing with this for the last day. I am essentially doing the same thing you are except that I'm basing my pooling off of apache.commons.pool. Same exact error you are seeing EOF. Check your mysqld error log file which is most likely in your data directory. Look for mysqld crashing. mysqld_safe will restart your mysqld quickly if it crashes so it won't be apparent that this is the case unless you look in its logfile. /var/log is not help for this scenario.

Connections that were created before the crash will EOF after the crash.