First thing's first, check the size of the Apache logs. Chances are these aren't being rotated and may need removing:
Also check the size of the cPanel logs (if any):
Cpanel now provides the ability to rotate both the Apache and Cpanel logs, so I'd suggest enabling this option from within WHM if you haven't already. It's not perfect, but it may save you frustration in the future.
1. Restart the httpd service. This might free a little space some times.
2. Check for apache logs like error_log, access_log , suexec_log in /usr/local/apache/logs . These can either be cleared off or if you need the logs then you can take a zipped copy and keep it aside.
3. Same can be done for the files in cPanel logs (/usr/local/cpanel/logs) as well .
4. Domlogs – Get into the /usr/local/apache/domlogs/ directory. Run the following command :-
# ls -al -SR | head -10 —> It will list 10 files in the decreasing order according to their size
If the domlog file is too large for a domain then it is possible that awstats is not running . Check whether cpanellogd is running on the server using pstree . If not, restart it .
Else, it is possible that awstats for only that particular domain is not updating. Get into the directory /usr/local/cpanel/base and check if any file as ‘awstats.domainname.com.conf’ exists. If yes , delete that file.
Now, run /scripts/runweblogs for that user. It will update the awstats and automatically clear the domlogs file thereafter. Do not delete the domlogs file itself.
5. Remove old and unwanted backups of ‘apache’ that might have been taken long ago. Also, check for any other duplicate folders that can be removed safely.
6. Remove core files, if any . Normally, some core files (like core.1234) might be present in /usr/local/cpanel/whostmgr/docroot . Check for these and remove them.
I'm having a similar problem as above on Disk /dev/hda3 (/usr) 62 %
Since Nov last year, it's jumped to about 30%+ more via my logwatch mails. I've checked apache and cpanel logs and clr them but not change to /usr partition. All logs on rotation since about 2 months ago.
I do reboot httpd about every month to 35 days along with mysql but haven't seen much reduction either. In 12 hours it's jumped 2%.