How to secure your WHM/cPanel server

After the initial setup of cPanel server the server is not very secure and there are many things that can be done to secure your server.
In this tutorial we will go over some steps that include few software installation and web server security settings modification.
The collection of these easy steps is a results of years of experience in maintenance and management of linux servers.
secure capnel whm

1) Updates & Installation

Update cPanel to the latest version from the WHM interface:
Navigate to: Home » cPanel » Upgrade to Latest Version
Next, install the Apache mod_security with EasyApache:
Navigate to: Home » Software » EasyApache (Apache Update)
On step 4 check the “Mod Security” option and click the “Save and Build” button.
Next, login to the cPanel server as root via SSH and run OS update, then install some softwares from ConfigServer:

yum update -y
wget http://www.configserver.com/free/csf.tgz
tar -xzf csf.tgz
cd csf/
sh install.sh
cd ..
rm -Rfv csf/ csf.tgz
wget http://configserver.com/free/cmc.tgz
tar -xzf cmc.tgz
cd cmc/
sh install.sh
cd ..
rm -Rfv cmc/ cmc.tgz

2) Use The Security Advisors

If your cPanel version is 11.42+ and CSF is installed on your server there is two Security Advisors on your server that will check the security level of your server and will suggest recommendations on how fix the security issues.
For cPanel Security Advisor navigate to:
Home » Security Center » Security Advisor
For ConfigServer Firewall Security Advisor navigate to:
Home » Plugins » ConfigServer Security & Firewall » Check Server Security
* Follow all the recommendations and make the necessary changes to fix your server security issues.
We recommend to run the Security Advisors at least once a month.

3) Web Server Security & Firewall (ModSecurity)

Our choice for Mod Security rules is the Comodo Web Application Firewall (CWAF) agent. The cPanel\WHM plugin automate the installation & configuration of CWAF on the server and the deployment of periodically published predefined firewall rules set updates.
1) To get access to Comodo Mod Security rules and CWAF free sign up is needed: https://waf.comodo.com
2) To download the comodo client agent login to the web administration console and click the “Download latest installer” link (top right of the screen) “cwaf_client_install.sh”.
3) Copy the agent setup file to a local directory in the server E.g. /root
4) Run the installation script as root via SSH:

bash /root/cwaf_client_install.sh

Follow the instructions in the setup wizard!
Next edit mod_security conf file and include the CWAF Rules.

vi /usr/local/apache/conf/modsec2.conf

And add this line:

Include "/var/cpanel/cwaf/etc/cwaf.conf"

The file should look like this:

LoadFile /opt/xml2/lib/libxml2.so 
# LoadFile /opt/lua/lib/liblua.so 
LoadModule security2_module  modules/mod_security2.so 
<IfModule mod_security2.c> 
SecRuleEngine On 
SecTmpDir /tmp 
SecDataDir /tmp 
SecRequestBodyAccess On 
SecAuditEngine RelevantOnly 
SecPcreMatchLimitRecursion 250000 
SecDebugLog logs/modsec_debug_log 
SecPcreMatchLimit 250000 
SecAuditLog logs/modsec_audit.log 
SecDebugLogLevel 0 
Include "/var/cpanel/cwaf/etc/cwaf.conf" 
</IfModule>

5) Now login to WHM as root and navigate to:
Home » Plugins » Comodo WAF
At the “Main” tab you can run updates if needed,
At the “Catalog” tab you can set or unset rules for all vhosts or for a singel domain.
6) Restart Apache

service httpd restart

7) Set new Apache configuration:
Home » Service Configuration » Apache Configuration » Global Configuration

Change to:
SSL Cipher Suite = (PCI recommended)
Trace Enable = Off
Server Signature = Off
Server Tokens = ProductOnly
File ETag = None
Then clicking on “Save”
8) Set new PHP configuration:
Home » Service Configuration » PHP Configuration Editor
Select the “Advanced Mode” and set the following settings:
allow_url_fopen = off
expose_php = Off
enable_dl= Off
register_globals = off
display_errors = off
disable_functions = show_source, system, shell_exec, passthru, exec, popen, proc_open, eval, symlink, link, readlink, dl, escapeshellarg, escapeshellcmd, ini_restore, apache_get_modules, ini_get_all, get_cfg_var
9) Restart Apache

service httpd restart

 10) Enable failure detection of repeated Apache mod_security rule triggers
Navigate to:
Home » Plugins » ConfigServer Security & Firewall » Firewall Configuration

And set the number of failures between 3 and 5 by changing the value:
LF_MODSEC = 3

4) Tweaks

1) Install and config “tmpwatch”

yum install tmpwatch

Edit the tmpwatch cron file:

vi /etc/cron.daily/tmpwatch

The file should look like this:

#! /bin/sh
flags=-umc
/usr/sbin/tmpwatch "$flags" -x /tmp/.X11-unix -x /tmp/.XIM-unix \
	-x /tmp/.font-unix -x /tmp/.ICE-unix -x /tmp/.Test-unix \
	-X '/tmp/hsperfdata_*' -m 24 /tmp
/usr/sbin/tmpwatch "$flags" -m 12 /var/tmp
for d in /var/{cache/man,catman}/{cat?,X11R6/cat?,local/cat?}; do
    if [ -d "$d" ]; then
	/usr/sbin/tmpwatch "$flags" -mf 12 "$d"
    fi
done

2) Disable Compilers for all accounts from:
Home » Security Center » Compiler Access
3) Disable Anonymous FTP & Logins with root
Home » Service Configuration » FTP Server Configuration

5) eXploit Scanner

The eXploit Scanner is the best tool out there for detecting malicious code on the server and for real time detection while files are uploaded to the server.
eXploit Scanner detecting malicious code uploaded real time and deny the upload and blocks the IP address from which the file is upload.
1) Install ClamAV:
Home » cPanel » Manage Plugins
Select “clamavconnector” and Seve.
2) The “eXploit Scanner” is not free, but worth every cent. Buy license at:
http://configserver.com/cp/cxs.html
3) Once you received the confirmation email of the activation of the license you can start the installation of the eXploit Scanner plugin:

wget http://www.configserver.com/free/cxsinstaller.tgz
tar -xzf cxsinstaller.tgz
perl cxsinstaller.pl
rm -fv cxsinstaller.*
mkdir -m 1777 /usr/suspicious_files
touch /var/log/cxs.log
chmod 0666 /var/log/cxs.log
cp /etc/cxs/cxs.defaults.example /etc/cxs/cxs.defaults
cp /etc/cxs/cxs.ignore.example /etc/cxs/cxs.ignore
cp /etc/cxs/cxs.xtra.example /etc/cxs/cxs.xtra
chmod 644 /etc/cxs/cxs.xtra /etc/cxs/cxs.defaults /etc/cxs/cxs.ignore
chmod 755 /etc/cxs/cxscgi.sh /etc/cxs/cxsftp.sh

4) Enable the pure-ftp upload script:

vi /etc/pure-ftpd.conf

And change the “CallUploadScript” value
From:
# CallUploadScript yes
To:
CallUploadScript yes
Next, restart the pure-uploadscript daemon:

/etc/init.d/pure-uploadscript restart

5) Edit the config files and comment any exiting line with # in this files:
Edit cxscgi.sh file:

vi /etc/cxs/cxscgi.sh

Add:

/usr/sbin/cxs -Z --cgi --block --smtp --mail root --delete --qoptions Mexv -I /etc/cxs/cxs.ignore --xtra /etc/cxs/cxs.xtra "$1"

Edit cxsftp.sh file:

vi /etc/cxs/cxsftp.sh

And set the line:

/usr/sbin/cxs -Z --ftp --block --smtp --mail root --delete --qoptions Mexv -I /etc/cxs/cxs.ignore --xtra /etc/cxs/cxs.xtra "$1"

Edit cxswatch.sh file:

vi /etc/cxs/cxswatch.sh

And set the line:

/usr/sbin/cxs --Wstart --allusers --www --block --smtp --mail root --quarantine /usr/suspicious_files --qoptions Mexv --xtra /etc/cxs/cxs.xtra --Wmaxchild 5 --Wloglevel 0 --Wsleep 3 --filemax 0 --Wrateignore 300

6) Create Cron jobs via the UI from:
Home » Plugins » ConfigServer eXploit Scanner
Click on “Edit Cron Jobs” and add the command:

/usr/sbin/cxs --mail root --exp --vir -I /etc/cxs/cxs.ignore -X /etc/cxs/cxs.xtra -Q /usr/suspicious_files --options mMOLfSGchexdnwWZDRPu --qoptions Mexv -Z --sum -S 1000000 -F 10000 -C /var/clamd -T 2 --MD5 -B --allusers

Add the auto update cron command:

/usr/sbin/cxs --upgrade --quiet

Create the cxs suspicious files folder:

mkdir /usr/suspicious_files

* Enable detection of repeated cxs and mod_security rules trigger. This option will block the user IP address if cxs or ModSecurity triger is detected.
Navigate to:
Home » Plugins » ConfigServer Security & Firewall » Firewall Configuration

And set: LF_CXS = 1
Finally we finished securing your server!

To set up firewall on your dedicated server click.