Steps that we had taken to correct the issue related to Hibernate MySql connection timeout problem are listed below

- Download Hibernate C3P0 and copy .jar files
- Set c3p0.properties
- Make changes to hibernate.cfg.xml
- Test MySQL connection timeout
- Hibernate, MySQL connection timeout related error messages

Download Hibernate C3P0 (JDBC Data sources/Resource pools)

Copy the following .jar files into WEB-INF/lib folder

- c3p0-0.9.2.jar
- mchange-commons-java-0.2.3.3.jar

Add c3p0.properties file under the folder identifiable by java CLASSPATH (WEB-INF/classes) and add the below line

c3p0.testConnectionOnCheckout=true

Open hibernate.cfg.xml and add the below set of lines

<property name=”c3p0.min_size”>5</property>
<property name=”c3p0.max_size”>20</property>
<property name=”c3p0.timeout”>1800</property>
<property name=”c3p0.max_statements”>50</property>
<property name=”connection.provider_class”>org.hibernate.connection.C3P0ConnectionProvider</property>

Restart tomcat instance.

To test MySQL connection timeout, open /etc/mysql/my.cnf (or my.ini file in windows) and under [mysqld] set (or modify) the wait_timeout value to say 120 seconds (2 minutes) to check how the application behaves after the above setting changes are made. You can reset it back once the testing is over.  Default timeout setting in MySQL is 8 hours.

[mysqld]
wait_timeout = 120

Some of the error messages associated with the hibernate mysql reconnect timeout issue are “org.hibernate.connection.C3P0ConnectionProvider cannot be found”, “org.hibernate.util.JDBCExceptionReporter: The last packet successfully received from the server was 73998 seconds ago”, “com.mysql.jdbc.CommunicationsException: Communications link failure due to underlying exception”

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* Search for PEAR_ENV.reg. Double click that file to register the PEAR settings as environment variable

* Go to the command prompt and type “pear list” to see what packages are installed and if PEAR is correctly installed. If PEAR cannot be accessed via the command line, it means the PATH setting is not set correctly. Environment PATH variable should include the path to where pear.bat is present

PHPSecLib installation is very simple.

PHPSecLib is a library of optional PHP extensions which comes in handy if the application were to be packaged as a solution for deployment to the end user.

Step 1: Register the channel

c:\> pear channel-discover phpseclib.sourceforge.net

Step 2: List the packages available

c:\> pear remote-list -c phpseclib

CHANNEL PHPSECLIB AVAILABLE PACKAGES:
=====================================
PACKAGE VERSION
Crypt_AES 0.3.1
Crypt_DES 0.3.1
Crypt_Hash 0.3.1
Crypt_RC4 0.3.1
Crypt_RSA 0.3.1
Crypt_Random 0.3.1
Crypt_Rijndael 0.3.1
Crypt_TripleDES 0.3.1
File_ANSI 0.3.1
File_ASN1 0.3.1
File_X509 0.3.1
Math_BigInteger 0.3.1
Net_SFTP 0.3.1
Net_SSH1 0.3.1
Net_SSH2 0.3.1

Step 3: Install the needed packages. For e.g. if you want Net_SFTP package

c:\> pear install phpseclib/Net_SFTP

For further instructions and notes go to PHP Secure Communications Library PEAR channel

If you have Php version 5.2.11, you may encounter issues installing phpseclib on it. For an easy install try a different version of php when you experiment with phseclib.

Sample program to test the functionality

<?php

set_include_path(get_include_path() . PATH_SEPARATOR . ‘/phpseclib’);

include(‘Net/SSH2.php’);
include(‘Net/SFTP.php’);

echo get_include_path();

$sftp = new Net_SFTP(‘greenland:22′);
if (!$sftp->login(‘root’, ‘evylouss’)) {
exit(‘Login Failed’);
}

?>

To remove the strange characters open the file in Vi editor and type

:%s/.$// 

This will search for the ^M pattern on the entire file and will remove all occurences.

Other option is to open the file with the strange characters and use the following search and replace pattern

:%s/^V^M//g

In the above command you need to press ctrl+v and ctrl+m in order for you to get the character ^M in the vi editor

$ df -T

Output from the command

Filesystem    Type   1K-blocks      Used Available Use% Mounted on
/dev/sda1     ext4    94088076   9090252  80218356  11% /
udev      devtmpfs     1023536         4   1023532   1% /dev

$ netstat -tln | grep mysql

If you cannot find the port number for mysql view my.cnf file to see if you can find the port number. If you see a line “skip-networking” try commenting out the line and then restart mysql daemon.

$ vi /etc/my.cnf

[mysqld]
set-variable=local-infile=0
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
# Default to using old password format for compatibility with mysql 3.x
# clients (those using the mysqlclient10 compatibility package).
old_passwords=1
skip-networking

[mysql.server]
user=mysql
basedir=/var/lib

[mysqld_safe]
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid

$ service mysqld restart

Download Apache Tomcat

$ wget http://apache.parentingamerica.com/tomcat/tomcat-6/v6.0.36/bin/apache-tomcat-6.0.36.tar.gz

Go to opt/ folder and extract Tomcat

$ cd /opt

$ tar -xzf apache-tomcat-6.0.36.tar.gz

Create a tomcat user

$ useradd -d /opt/apache-tomcat-6.0.36/ tomcatuser

Change user permission on tomcat folder

$ chown -R tomcatuser:tomcatuser apache-tomcat-6.0.36

$ vi /etc/init.d/tomcat

#!/bin/bash
#
# tomcat       Starts Tomcat Java server.
#
#
# chkconfig: 345 88 12
# description: Tomcat is the server for 
# Java servlet applications.
### BEGIN INIT INFO
# Provides: $tomcat
### END INIT INFO
 

JAVA_HOME=/usr/java/jdk1.6.0_37
export JAVA_HOME  
PATH=$JAVA_HOME/bin:$PATH  
export PATH  

TOMCAT_HOME=/opt/apache-tomcat-6.0.36/bin
START_TOMCAT=/opt/apache-tomcat-6.0.36/bin/startup.sh
STOP_TOMCAT=/opt/apache-tomcat-6.0.36/bin/shutdown.sh
 
# Source function library.
. /etc/init.d/functions
 
[ -f $START_TOMCAT ] || exit 0
[ -f $STOP_TOMCAT ] || exit 0
 
RETVAL=0
 
umask 077
 
start() {
        echo -n $"Starting Tomcat Java server: "
        daemon su -c $START_TOMCAT tomcatuser
        echo
        return $RETVAL
}
stop() {
        echo -n $"Shutting down Tomcat Java server: "
        daemon su -c $STOP_TOMCAT tomcatuser
        echo
        return $RETVAL
}
restart() {
        stop
        start
}
case "$1" in
  start)
        start
        ;;
  stop)
        stop
        ;;
  restart|reload)
        restart
        ;;
  *)
        echo $"Usage: $0 {start|stop|restart}"
        exit 1
esac
 
exit $?

Now save the file

Give executable rights for that script

$ chmod 755 /etc/init.d/tomcat

Add the script to CentOS services

$ chkconfig –add tomcat

Check the changes

$ chkconfig –level 234 tomcat on

$ chkconfig –list tomcat

tomcat 0:off 1:off 2:on 3:on 4:on 5:on 6:off

Test that the script is working and it gives no errors

$ service tomcat start
$ service tomcat restart
$ service tomcat stop

First set up a folder where you want to install java

$ cd /opt

$ wget http://download.oracle.com/otn-pub/java/jdk/6u37-b06/jdk-6u37-linux-x64-rpm.bin

$ chmod +x jdk-6u37-linux-x64-rpm.bin

$ ./jdk-6u37-linux-x64-rpm.bin

Check the current installation of java

$ rpm -qa | grep jre

$ rpm -qa | grep jdk

$ rpm -qa | grep openjdk

There may be scenarios where your OS might have multiple copies of java jre’s or jdk’s. To find which one is being used you can issue the following command in CentOs

$ alternatives –display java

To configure one of the distribution you can use

$ alternatives –config java

Following commands need to go in order to complete the proper setup of java (which is often forgotten)

$ alternatives –install /usr/bin/java java /usr/java/jdk1.6.0_37/jre/bin/java 20000
$ alternatives –install /usr/bin/javaws javaws /usr/java/jdk1.6.0_37/jre/bin/javaws 20000
$ alternatives –install /usr/bin/javac javac /usr/java/jdk1.6.0_37/bin/javac 20000
$ alternatives –install /usr/bin/jar jar /usr/java/jdk1.6.0_37/bin/jar 20000
$ alternatives –set java /usr/java/jdk1.6.0_37/jre/bin/java
$ alternatives –set javaws /usr/java/jdk1.6.0_37/jre/bin/javaws
$ alternatives –set javac /usr/java/jdk1.6.0_37/bin/javac
$ alternatives –set jar /usr/java/jdk1.6.0_37/bin/jar

To check the java version

$ java -version

java version “1.6.0_37″
Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)

$ rpm -qa | grep jre

$ rpm -qa | grep jdk

$ rpm -qa | grep openjdk

To remove the java installs

$ yum erase jre jdk openjdk

To install Fail2ban we need to download the application from the source. Login as the root user and go to /opt

$ cd /opt

$ wget http://downloads.sourceforge.net/project/fail2ban/fail2ban-stable/fail2ban-0.8.4/fail2ban-0.8.4.tar.bz2?use_mirror=transact

Next unzip the downloaded file

$ tar -xf fail2ban-0.8.4.tar.bz2

$ cd fail2ban-0.8.4

To install

$ python setup.py install

$ cp files/redhat-initd /etc/init.d/fail2ban

To add fail2ban to the service

$ chkconfig –add fail2ban

$ chkconfig fail2ban on

Next is to configure the jail.conf where the settings are given by default for the local host

$ vi /etc/fail2ban/jail.conf

Go to the line where “ignoreip” keyword is mentioned and add the list of IP’s or IP subnet from which you want to gain access to the service

Finally, start fail2ban application

$ service fail2ban start