Check /etc/mailips permissions:

Code:

# ls -lah /etc/mailips

It should show the following:

# ls -lah /etc/mailips
-rw-r----- 1 root mail 0 Mar 11 21:40 /etc/mailips

If it does not show root:mail for ownership, then fix that:

# chown root:mail /etc/mailips

If it doesn’t show 640 for file permissions, fix that:

# chmod 640 /etc/mailips

If it does have the right ownership and permissions, then next check the file isn’t set to be immutable:

# lsattr /etc/mailips

It might look like the following if it is okay:

# lsattr /etc/mailips
-------A----- /etc/mailips

Or below if it is unwritable

# lsattr /etc/mailips
----i--------e- /etc/mailips

An uppercase A is fine. If it has a lowercase i or a lowercase a, then it isn’t fine, and those need removed:

# chattr -ia /etc/mailips

Now it looks like

# lsattr /etc/mailips
-------------e- /etc/mailips

To enable WHM to automatically configure Exim to send mail from each domain’s dedicated IP address, perform the following steps:
You must have root user privileges on the server to configure Exim in this way.

If you manage the rDNS for your IP addresses, modify the rDNS for the IP address of each domain so that it points to that domain. If you do not manage the rDNS for your IP addresses, contact the owner of the IP addresses and request that they modify the rDNS for each IP address to point to each domain.

An incorrect rDNS configuration may cause mail servers to reject your server’s mail.

Enable the Send mail from account’s dedicated IP address option in WHM’s Exim Configuration Manager interface (Home >> Service Configuration >> Exim Configuration Manager).

If you select this option, cPanel & WHM uses the /usr/local/cpanel/scripts/updateuserdomains script to automatically configure Exim, and overrides any manual changes in the following files:

/etc/mailhelo
/etc/mailips
/etc/mail_reverse_dns  

How to manually configure Exim’s outgoing IP addresses

To use a custom Exim configuration, enable the following options in WHM’s Exim Configuration Manager – Basic Editor interface (Home >> Service Configuration >> Exim Configuration Manager):

Reference /etc/mailhelo for outgoing SMTP HELO
Reference /etc/mailips for outgoing SMTP connections
The /etc/mailhelo file

The /etc/mailhelo file contains Exim’s configuration for the HELO command. Exim uses the HELO command to initiate dialog between a mail server and a client. This file governs which domain should send the HELO command.
To create the /etc/mailhelo file, use a text editor such as nano, vi, or vim.
The following is example content of a /etc/mailhelo file:

example.com: example.com
sub.example.com: example.com
example.net: example.net
addon.example.net: example.net
*: hostname.example.com 

The /etc/mailips file
This file controls the IP address from which each domain should send mail. Your file should be similar to the following example:

example.com: 192.168.0.2
sub.example.com: 192.168.0.2
example.net: 192.168.0.3
addon.example.net: 192.168.0.3
*: 192.168.0.1

In the example above, the system will use the asterisk (*) entry to direct outbound mail for domains without entries within this file. In this case, this is your server’s main shared IP address. You can set it to another IP address if you ensure that the asterisk entry in the /etc/mailhelo file has the appropriate domain name.

Be sure to use only valid IP addresses that are publicly accessible via the Internet.

The /etc/mail_reverse_dns file
This file controls the domains that are associated with the IP addresses from which mail should send. Your file should be similar to the following example:

192.168.0.2: example.com
192.168.0.2: sub.example.com
192.168.0.3: example.net
192.168.0.3: addon.example.net

Logging in with an ssh user and then trying to su – as root results in a password incorrect error. Also, updates with yum update are not finding the servers.

Solution:

Check for mod_ruid2

https://documentation.cpanel.net/display/EA/Apache+Module:+ModRuid2

I’ve got customer nameservers added through WHM setup and the nameservers registered  ith wour registrar, but they don’t show up in the WHM NS record report at whm -> dns functions -> ns record report

Resolution:

You can force the report to load again in ssh with this command –

# /usr/local/cpanel/scripts/updatenameserverips

Go to cpanel > cron jobs > standard.
At the top is an email field
Change to an alternate email

Or

FThe way to change the email account WHMCS sends the daily cron reports to…

1. Log in to WHMCS.
2. Click on Configuration -> Administrators.
3. Click on the little edit-button for the full administrator.
4. Change the email address.

Alternatively, if you want to prevent these emails being sent out altogether, go to ..
1. Configuration -> Administrator Roles -> Full Administrator.
2. Uncheck the box right at the bottom that says ‘System Emails’.

Email accounts in addon domains

You can create email accounts for addon domains. To learn how to set up an email account for an addon domain, read our Email Accounts documentation.

When you remove the addon domain, is email accounts will no longer appear in the cPanel interface. However, the contents for this email account still exist in the home/username/mail directory.

If you add the domain back to the same account as the primary domain, an addon domain, or a parked domain, the email accounts will reappear in the cPanel interface.
If you move the domain to a different account, you must add the email accounts manually and move the contents of the email account manually. The email accounts must follow the same name and same domain format that they previously followed.
You can use the Email Accounts interface to add new accounts, or you can run the /scripts/addpop script to manually add new email accounts.
To move one email account under a domain, you can run the following command:

# mv /home/old_account/mail/domain_name/email_account /home/new_account/mail/domain_name/

After you run this command, the system creates the /home/new_account/mail/domain_name/ directory. To move all the email accounts under a domain, run the following command:

#mv /home/old_account/mail/domain_name /home/new_account/mail

After you move the files, run the following command to change the ownership of the new account:

# chown -R new_account:new_account /home/new_account/mail/domain_name

To move an addon domain from one cPanel to another:

1. Download the content of your addon domain to your local PC.
2. Backup any associated database(s).
3. Create a subfolder inside the new cPanel’s public_html folder.
4. Upload the content of your addon domain to this new folder.
5. Restore the database backup(s) into the new cPanel.
6. If the old cPanel and new cPanel are on the same server, go back to the old cPanel and remove the addon domain from under the Addon Domains icon. Note: The original content or original databases do not need to be deleted.
7. Go to the new cPanel.
8. Click the Addon Domains icon.
9. Enter the addon domain name where it says New Domain Name.
10. For the Document Root, you must enter /public_html/subfolder/ (replace ‘subfolder’ with the name you chose in step 3).
11. Fill out the remainder of the form and click the Add Domain button.
12. If the old cPanel and new cPanel are on different servers, then you will need to update your addon domain name’s nameservers or other DNS records.

For cPanel

Installing IonCube Loaders with cPanel & WHM can be done one of two ways:

1) Using EasyApache via WHM >> EasyApache, IonCube Loaders can be selected under the Exhaustive Options List prior to compiling.

2) As the user `root` via SSH, you can run the below command to install IonCube Loaders without having to recompile Apache:

# /scripts/phpextensionmgr install IonCubeLoader

For Non-Control panel Servers

Begin by downloading the latest loaders to your system. Linux 64 bit:

# cd /root
# wget http://downloads3.ioncube.com/loader_downloads/ioncube_loaders_lin_x86-64.tar.gz

Other loaders at:
http://www.ioncube.com/loaders.php

Extract the contents of the archived file

# tar -xvf ioncube_loaders_lin_x86-64.tar.gz

Put the Loader file for your php version in /usr/lib64/php/modules

Check php version:

# php -v
PHP 5.4.43 (cli) (built: Jul 13 2015 12:26:16) 
Copyright (c) 1997-2014 The PHP Group
Zend Engine v2.4.0, Copyright (c) 1998-2014 Zend Technologies

Put the Loader file for your php version in /usr/lib64/php/modules

# cp -r /root/ioncube/ /usr/lib64/php/modules/ioncube_loader_lin_5.4.so

Create a ioncube.ini file in your ini files directory, /etc/php.d

# cd /etc/php.d
# nano ioncube.ini

/pre>
# zend_extension = /usr/lib64/php/modules/ioncube_loader_lin_5.4.so
[/bash]

Restart the Apache server software.

service httpd restart

Check for ioncube

# php -m | grep ioncube
ionCube

See it the data is there

#echo  'select * from eximstats.sends limit 2;' | mysql
mailtime        msgid   email   processed       user    size    ip      auth    host    localsender     domain  spamscore
2014-12-09 21:38:11     1XyZyR-0004j1-5K        santa_2014@domain.com 0       -remote-        7134    37.48.84.200    localdelivery   domain.com    1               3.1
2014-12-03 05:19:07     1Xw9pe-0003aq-8b        mobileco@domain2.com    0       mobileco        3256    127.0.0.1       localuser       localhost       1     domain2.com  2.1

If data does exist (you can also check the other tables: defers, failures, smtp in the same way). If you get no data than for some reason data is not making it from exim into the database.

Check if an upgrade has failed.