--[ Ubuntu 14.04 hardening ]

    Assume that all these operations need to be performed as root, which you can either do with sudo or by logging in as root first. (I've noticed that Ubuntu users seem particularly averse to logging in as root, apparently preferring instead to issue an endless series of commands starting with sudo, but I'm afraid that kind of extra hassle is not for me, so I just log in as root first.)

    Harden SSH

    I generally regard it as a very sensible idea to disable any kind of root login over SSH, so in /etc/ssh/sshd_config changePermitRootLogin to no.
    If SSH on your servers is open to the world then I also advise running SSH on a non-standard port in order to avoid incoming SSH hacking attempts. To do that, in /etc/ssh/sshd_config change Port from 22 to another port of your choice, e.g. 1022. Note that you'll need to update your firewall or EC2 security rules accordingly.
    After making changes to SSH, reload the OpenSSH server:
    service ssh reload
    

    Limit su access to administrators only

    It generally seems like a sensible idea to make sure that only users in the sudo group are able to run the su command in order to act as (or become) root:
    dpkg-statoverride --update --add root sudo 4750 /bin/su
    

    Improve IP security

    Add the following lines to /etc/sysctl.d/10-network-security.conf to improve IP security:
    # Ignore ICMP broadcast requests
    net.ipv4.icmp_echo_ignore_broadcasts = 1
    
    # Disable source packet routing
    net.ipv4.conf.all.accept_source_route = 0
    net.ipv6.conf.all.accept_source_route = 0 
    net.ipv4.conf.default.accept_source_route = 0
    net.ipv6.conf.default.accept_source_route = 0
    
    # Ignore send redirects
    net.ipv4.conf.all.send_redirects = 0
    net.ipv4.conf.default.send_redirects = 0
    
    # Block SYN attacks
    net.ipv4.tcp_max_syn_backlog = 2048
    net.ipv4.tcp_synack_retries = 2
    net.ipv4.tcp_syn_retries = 5
    
    # Log Martians
    net.ipv4.conf.all.log_martians = 1
    net.ipv4.icmp_ignore_bogus_error_responses = 1
    
    # Ignore ICMP redirects
    net.ipv4.conf.all.accept_redirects = 0
    net.ipv6.conf.all.accept_redirects = 0
    net.ipv4.conf.default.accept_redirects = 0 
    net.ipv6.conf.default.accept_redirects = 0
    
    # Ignore Directed pings
    net.ipv4.icmp_echo_ignore_all = 1
    
    Load the new rules:
    service procps start
    

    PHP hardening

    If you're using PHP, these are changes worth making in /etc/php5/apache2/php.ini in order to improve the security of PHP:
    1. Add execsystemshell_exec, and passthru to disable_functions.
    2. Change expose_php to Off.
    3. Ensure that display_errorstrack_errors and html_errors are set to Off.

    Apache hardening

    If you're using Apache web server, it's worth making sure you have the following parameters set in /etc/apache2/conf-enabled/security.conf to make sure Apache is suitably hardened:
    ServerTokens Prod
    ServerSignature Off
    TraceEnable Off
    Header unset ETag
    FileETag None
    
    For these to take effect you'll need to enable mod_headers:
    ln -s /etc/apache2/mods-available/headers.load /etc/apache2/mods-enabled/headers.load
    
    Then restart Apache:
    service apache2 restart
    

    Install and configure ModSecurity

    If you're using Apache, the web application firewall ModSecurity is a great way to harden your web server so that it's much less vulnerable to probes and attacks. Firstly, install the necessary packages:
    apt-get install libapache2-mod-security2
    
    Prepare to enable the recommended configuration:
    mv /etc/modsecurity/modsecurity.conf-recommended /etc/modsecurity/modsecurity.conf
    
    Then edit /etc/modsecurity/modsecurity.conf:
    1. Set SecRuleEngine to On to activate the rules.
    2. Change SecRequestBodyLimit and SecRequestBodyInMemoryLimit to 16384000 (or higher as needed) to increase the file upload size limit to 16 MB.
    Next, install the Open Web Application Security Project Core Rule Set:
    cd /tmp
    wget https://github.com/SpiderLabs/owasp-modsecurity-crs/archive/master.zip
    apt-get install zip
    unzip master.zip
    cp -r owasp-modsecurity-crs-master/* /etc/modsecurity/
    mv /etc/modsecurity/modsecurity_crs_10_setup.conf.example /etc/modsecurity/modsecurity_crs_10_setup.conf
    ls /etc/modsecurity/base_rules | xargs -I {} ln -s /etc/modsecurity/base_rules/{} /etc/modsecurity/activated_rules/{}
    ls /etc/modsecurity/optional_rules | xargs -I {} ln -s /etc/modsecurity/optional_rules/{} /etc/modsecurity/activated_rules/{}
    
    To add the rules to Apache, edit /etc/apache2/mods-available/security2.conf and add the following line near the end, just before
:
Include "/etc/modsecurity/activated_rules/*.conf"
Restart Apache to active the new security rules:
service apache2 restart

Install and configure mod_evasive

If you're using Apache then it's a good idea to install mod_evasive to help protect against denial of service attacks. Firstly install the package:
apt-get install libapache2-mod-evasive
Next, set up the log directory:
mkdir /var/log/mod_evasive
chown www-data:www-data /var/log/mod_evasive
Configure it by editing /etc/apache2/mods-available/evasive.conf:
  1. Uncomment all the lines except DOSSystemCommand.
  2. Change DOSEmailNotify to your email address.
Link the configuration to make it active in Apache:
ln -s /etc/apache2/mods-available/evasive.conf /etc/apache2/mods-enabled/evasive.conf
Then activate it by restarting Apache:
service apache2 restart

Install and configure rootkit checkers

It's highly desirable to get alerted if any rootkits are found on your server, so let's install a couple of rootkit checkers:
apt-get install rkhunter chkrootkit
Next, let's make them do something useful:
  1. In /etc/chkrootkit.conf, change RUN_DAILY to "true" so that it runs regularly, and change "-q" to "" otherwise the output doesn't make much sense.
  2. In /etc/default/rkhunter, change CRON_DAILY_RUN and CRON_DB_UPDATE to "true" so it runs regularly.
Finally, let's run these checkers weekly instead of daily, because daily is too annoying:
mv /etc/cron.weekly/rkhunter /etc/cron.weekly/rkhunter_update
mv /etc/cron.daily/rkhunter /etc/cron.weekly/rkhunter_run
mv /etc/cron.daily/chkrootkit /etc/cron.weekly/

Install Logwatch

Logwatch is a great tool which provides regular reports nicely summarising what's been going on in the server logs. Install it like this:
apt-get install logwatch
Make it run weekly instead of daily, otherwise it gets too annoying:
mv /etc/cron.daily/00logwatch /etc/cron.weekly/
Make it show output from the last week by editing /etc/cron.weekly/00logwatch and adding --range 'between -7 days and -1 days' to the end of the /usr/sbin/logwatch command.

Enable automatic security updates

N.B. Be warned that enabling automatic updates can be potentially dangerous for a production server in a live environment. Only enable this for a server in such an environment if you really know what you are doing.
Run this command:
dpkg-reconfigure -plow unattended-upgrades
Then choose Yes.

Enable process accounting

Linux process accounting keeps track of all sorts of details about which commands have been run on the server, who ran them, when, etc. It's a very sensible thing to enable on a server where security is a priority, so let's install it:
apt-get install acct
touch /var/log/wtmp
To show users' connect times, run ac. To show information about commands previously run by users, run sa. To see the last commands run, run lastcomm. Those are a few commands to give you an idea of what's possible; just read the manpages to get more details if you need to.
Edit: I recently threw together a quick Bash script to send a weekly email with a summary of user activity, login information and commands run. To get the same report yourself, create a file called /etc/cron.weekly/pacct-report containing the following (don't forget to make this file executable) (you can grab this from GitHub if you prefer):
#!/bin/bash

echo "USERS' CONNECT TIMES"
echo ""

ac -d -p

echo ""
echo "COMMANDS BY USER"
echo ""

users=$(cat /etc/passwd | awk -F ':' '{print $1}' | sort)

for user in $users ; do
  comm=$(lastcomm --user $user | awk '{print $1}' | sort | uniq -c | sort -nr)
  if [ "$comm" ] ; then
    echo "$user:"
    echo "$comm"
  fi
done

echo ""
echo "COMMANDS BY FREQUENCY OF EXECUTION"
echo ""

sa | awk '{print $1, $6}' | sort -n | head -n -1 | sort -nr

Things I haven't covered

There are some additional issues you might want to consider which I haven't covered here for various reasons:
  1. This guide assumes your Ubuntu server is on a network behind a firewall of some kind, whether that's a hardware firewall of your own, EC2 security rules on Amazon Web Services, or whatever; and that the firewall is properly configured to only allow through the necessary traffic. However, if that's not the case then you'll need to install and configure a firewall on the Ubuntu server itself. The recommended software for this on Ubuntu is ufw.
  2. If you're running an SSH server then you're often told that you must install a tool such as fail2ban immediately if you don't want your server to be hacked to death within seconds. However, I've maintained servers with publicly-accessible SSH servers for many years, and I've found that simply moving SSH to a different port solves this problem far more elegantly. I monitor logs in order to identify incoming hacking attempts, and I haven't seen a single one in the many years I've been doing this. However, using this "security by obscurity" method doesn't mean that such an attack can't happen, and if you don't watch your logs regularly and respond quickly to them as I do, then you would be well advised to install fail2ban or similar as a precaution, in addition to moving your SSH server to another port as described above.
  3. Once you've hardened your server, you're advised to run some vulnerability scans and penetration tests against it in order to check that it's actually as invincible as you're now hoping it is. This is a topic which requires a post all of its own so I won't be covering it in any detail here, but a good starting point if you're not already familiar with it is the excellent Nmap security scanner.