1. Создаем необходимые нам папки и устанавливаем в них пустую базу

mkdir -p /var/lib/mysql2/mysql
mkdir /var/lib/mysql2/mysql/data
mkdir /var/lib/mysql2/mysql/log
mkdir /var/lib/mysql2/mysql/run
mkdir /var/lib/mysql2/mysql/lock
chown -R mysql:mysql /var/lib/mysql2/mysql
mysql_install_db --datadir=/var/lib/mysql2/mysql/data --user=mysql

2. Создаем новый минимальный конфигурационный файл для нашего нового сервера /etc/my2.cnf

my2.cnf

[mysqld]
port=3307
datadir=/var/lib/mysql2/mysql/data
socket=/var/lib/mysql2/mysql/mysql.sock
user=mysql
log-bin = /var/lib/mysql2/mysql/log/mysql-bin.log
[mysqld_safe]
log-error=/var/lib/mysql2/mysql/log/mysqld.log
pid-file=/var/lib/mysql2/run/mysqld.pid
[isamchk]
[myisamchk]

3. Создаем новый init.d скрипт /etc/init.d/mysql2

mysql2

#!/bin/bash
#
# mysqld.server2 This shell script takes care of starting and stopping
#               the MySQL subsystem (mysqld).
#
# chkconfig: - 64 36
# description:  MySQL database server 2nd instance.
# processname: mysqld
# config: /etc/my2.cnf
# pidfile: /var/lib/mysql2/mysql/run/mysqld.pid
# Source function library.
. /etc/rc.d/init.d/functions
# Source networking configuration.
. /etc/sysconfig/network
prog="MySQL"
# extract value of a MySQL option from config files
# Usage: get_mysql_option SECTION VARNAME DEFAULT
# result is returned in $result
# We use my_print_defaults which prints all options from multiple files,
# with the more specific ones later; hence take the last match.
get_mysql_option(){
        result=`/usr/bin/my_print_defaults "$1" | sed -n "s/^--$2=//p" | tail -n 1`
        if [ -z "$result" ]; then
            # not found, use default
            result="$3"
        fi
}
get_mysql_option mysqld datadir "/var/lib/mysql2/mysql/data"
datadir="/var/lib/mysql2/mysql/data"
get_mysql_option mysqld socket "$datadir/mysql.sock"
socketfile="$datadir/mysql.sock"
get_mysql_option mysqld_safe log-error "/var/lib/mysql2/mysql/log/mysqld.log"
errlogfile="/var/lib/mysql2/mysql/log/mysqld.log"
get_mysql_option mysqld_safe pid-file "/var/lib/mysql2/mysql/run/mysqld.pid"
mypidfile="/var/lib/mysql2/mysql/run/mysqld.pid"
start(){
        touch "$errlogfile"
        chown mysql:mysql "$errlogfile"
        chmod 0640 "$errlogfile"
        [ -x /sbin/restorecon ] && /sbin/restorecon "$errlogfile"
        if [ ! -d "$datadir/mysql" ] ; then
            action $"Initializing MySQL database: " /usr/bin/mysql_install_db
            ret=$?
            chown -R mysql:mysql "$datadir"
            if [ $ret -ne 0 ] ; then
                return $ret
            fi
        fi
        chown mysql:mysql "$datadir"
        chmod 0755 "$datadir"
        # Pass all the options determined above, to ensure consistent behavior.
        # In many cases mysqld_safe would arrive at the same conclusions anyway
        # but we need to be sure.
        /usr/bin/mysqld_safe --defaults-file=/etc/my2.cnf --datadir="$datadir" --socket="$socketfile" \
                --log-error="$errlogfile" --pid-file="$mypidfile" \
                >/dev/null 2>&1 &
        ret=$?
        # Spin for a maximum of N seconds waiting for the server to come up.
        # Rather than assuming we know a valid username, accept an "access
        # denied" response as meaning the server is functioning.
        if [ $ret -eq 0 ]; then
            STARTTIMEOUT=30
            while [ $STARTTIMEOUT -gt 0 ]; do
                RESPONSE=`/usr/bin/mysqladmin -uUNKNOWN_MYSQL_USER ping 2>&1` && break
                echo "$RESPONSE" | grep -q "Access denied for user" && break
                sleep 1
                let STARTTIMEOUT=${STARTTIMEOUT}-1
            done
            if [ $STARTTIMEOUT -eq 0 ]; then
                    echo "Timeout error occurred trying to start MySQL Daemon."
                    action $"Starting $prog: " /bin/false
                    ret=1
            else
                    action $"Starting $prog: " /bin/true
            fi
        else
            action $"Starting $prog: " /bin/false
        fi
        [ $ret -eq 0 ] && touch /var/lib/mysql2/mysql/lock/mysqld
        return $ret
}
stop(){
        MYSQLPID=`cat "$mypidfile"  2>/dev/null `
        if [ -n "$MYSQLPID" ]; then
            /bin/kill "$MYSQLPID" >/dev/null 2>&1
            ret=$?
            if [ $ret -eq 0 ]; then
                STOPTIMEOUT=60
                while [ $STOPTIMEOUT -gt 0 ]; do
                    /bin/kill -0 "$MYSQLPID" >/dev/null 2>&1 || break
                    sleep 1
                    let STOPTIMEOUT=${STOPTIMEOUT}-1
                done
                if [ $STOPTIMEOUT -eq 0 ]; then
                    echo "Timeout error occurred trying to stop MySQL Daemon."
                    ret=1
                    action $"Stopping $prog: " /bin/false
                else
                    rm -f /var/lib/mysql2/mysql/lock/mysqld
                    rm -f "$socketfile"
                    action $"Stopping $prog: " /bin/true
                fi
            else
                action $"Stopping $prog: " /bin/false
            fi
        else
            ret=1
            action $"Stopping $prog: " /bin/false
        fi
        return $ret
}
restart(){
    stop
    start
}
condrestart(){
    [ -e /var/lib/mysql2/mysql/lock/mysqld ] && restart || :
}
# See how we were called.
case "$1" in
  start)
    start
    ;;
  stop)
    stop
    ;;
  status)
    status mysqld
    ;;
  restart)
    restart
    ;;
  condrestart)
    condrestart
    ;;
  *)
    echo $"Usage: $0 {start|stop|status|condrestart|restart}"
    exit 1
esac
exit $?

4. Включаем автозапуск и стартуем

chmod +x /etc/init.d/mysqld2
chkconfig mysqld2 on
service mysqld2 start

5. Меняем пароль

mysqladmin -P 3307 --protocol=tcp -u root password 'NEWPASSWORD'

6. Подключаемся и смотрим

# mysql -P 3307 --protocol=tcp -uroot -p
Enter password:
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 11
Server version: 5.5.19-log Source distribution
Type 'help;' or '\h' for help. Type '\c' to clear the buffer.
mysql> show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| test               |
+--------------------+
3 rows in set (0.00 sec)
mysql>

7. Проверяеем запущеные демоны

# ps -ax | grep mysql
Warning: bad syntax, perhaps a bogus '-'? See /usr/share/doc/procps-3.2.8/FAQ
 2996 pts/1    S+     0:00 grep --color=auto mysql
15491 ?        S      0:00 /bin/sh /usr/bin/mysqld_safe --datadir=/var/lib/mysql --socket=/var/lib/mysql/mysql.sock --pid-file=/var/run/mysqld/mysqld.pid --basedir=/usr --user=mysql --open-files-limit=65535
16096 ?        Sl   5422:02 /usr/libexec/mysqld --basedir=/usr --datadir=/var/lib/mysql --plugin-dir=/usr/lib64/mysql/plugin --user=mysql --log-error=/var/log/mysqld.log --open-files-limit=65535 --pid-file=/var/run/mysqld/mysqld.pid --socket=/var/lib/mysql/mysql.sock
19765 ?        S      0:00 /bin/sh /usr/bin/mysqld_safe --defaults-file=/etc/my2.cnf --datadir=/var/lib/mysql2/mysql/data --socket=/var/lib/mysql2/mysql/data/mysql.sock --log-error=/var/lib/mysql2/mysql/log/mysqld.log --pid-file=/var/lib/mysql2/mysql/run/mysqld.pid
20343 ?        Sl    15:04 /usr/libexec/mysqld --defaults-file=/etc/my2.cnf --basedir=/usr --datadir=/var/lib/mysql2/mysql/data --plugin-dir=/usr/lib64/mysql/plugin --user=mysql --log-error=/var/lib/mysql2/mysql/log/mysqld.log --pid-file=/var/lib/mysql2/mysql/run/mysqld.pid --socket=/var/lib/mysql2/mysql/data/mysql.sock --port=3307

8. По мотивам статьи http://unixmen.com/linux-tutorials/1863--multiple-mysql-instance-on-fedoracentosredhatscientific-linux