VPS ill ? - update failures, high disk usage, constant yum compilations going on

[andymc]

Hi,

I've noticed over the past few days, a number of emails about my VPS like -

An automatic check on myvps.com found the RPM database to be corrupted. The database was automatically repaired. A backup of the original state of the RPM database directory can be found at /var/lib/rpm.rebuild.backup*

and

/usr/local/cpanel/scripts/upcp was detected to be running as pid '11962'. Because it has been running for longer than 6 hours, the process will be killed and a new upcp will be run in it's place.

I have done several graceful server reboots

But I still get these warning emails.

I also got a disk getting full email:

Drive Warning: /dev/vzfs (/) is 81% full

But I've not tracked down file problems - mysql is < 1GB and so are the cpanel accounts.

Anyway I keep noticing these processes, which I assume are cpanel/rpm updates:

/usr/bin/python /usr/bin/yum --excludekernel* -y install autoconf autoconf261 automake automake19 bind bind9 bind9-devel bind9-utils bind-devel bind-libs bind-tools bind-utils binutils bison bzip2 caching-nameserver compat-db coreutils cpio cpp crontabs curl curl-devel db1 db1-dev db1-devel db1-tools db4 db4-dev db4-devel e2fsprogs-devel expat expat-dev expat-devel expect fileutils flex freetype freetype-dev freetype-devel ftp gamin gamin-devel gcc gcc-c++ gcc-c++-dev gcc-c++-devel gcc-c++-runtime gd gd-dev gd-devel gd-progs gd-utils gdbm gdbm-devel gentoolkit gettext gettext-devel glibc-dev glibc-devel glibc-kernheaders glibc-static gmake gnupg gzip imap imap-dev imap-devel initscripts iptables kernel-headers krb5-dev krb5-devel less lexlibpng10 lib64openssl0.9.7-devel lib64openssl0.9.7-static-devel libfreetype6 libfreetype6-dev libgcc libgd1 libgd1-devel libidn libidn-devel libjpeg libjpeg62 libjpeg62-dev libjpeg-dev libjpeg-devel libltdl libltdl3-devel libltdl-devel libopenssl0 libopenssl0.9.7-devel libopenssl0.9.7-static-devel libopenssl0-dev libopenssl0-devel libpng libpng10-devel libpng-dev libpng-devel libssl-dev libstdc++ libstdc++-dev libstdc++-devel libtiff libtiff-dev libtiff-devel libtool libtool-libltdl-devel libtool-ltdl libtool-ltdl-devel libX11-devel libxml libxml2 libxml2-devel libxml-devel libXpm libXpm-dev libXpm-devel libz-devel linux-headers lsof lynx make mirrorselect nano ncftp ncurses ncurses3 ncurses4 ncurses-dev ncurses-devel openssh openssh-client openssh-clients openssh-server openssl openssl095a openssl096 openssl096b openssl-dev openssl-devel openssl-misc pam pam-dev pam-devel passwd patch perl-CPAN perl-dev perl-devel pico pine popt portage pwdb python python-dev python-devel python-docs python-modules python-tools quota quota-devel rcs rdate rsync sed shadow-utils sharutils ssh ssl-dev strace stunnel sysstat tar tcl tclx tcp_wrappers-devel tix tk tkinter traceroute ucd-snmp ucd-snmp-devel ucd-snmp-utils unzip urw-fonts util-linux util-linux-ng vixie-cron wget which xfree XFree86-devel XFree86-libs xorg-x11-dev xorg-x11-devel zip zlib zlib1-devel zlib1g zlib1g-dev zlib-devel

(Don't know why X is there at all on a vps!)

These pop back even after server reboots.

I've tried using WHM to do a system adn SW update, but it just hangs

Also service status hangs on cpanel.

Any ideas ?

The websites are nowhere near high volume, user data is < 1GB as is mysql. but the system reports 13/15GB used.

Cheers

Andy

[Stan]

Hello Andy,

The issue is being looked into. An update would be posted shortly.

Thanks.

[Sarina]

Hi,

I've noticed over the past few days, a number of emails about my VPS like -

An automatic check on myvps.com found the RPM database to be corrupted. The database was automatically repaired. A backup of the original state of the RPM database directory can be found at /var/lib/rpm.rebuild.backup*

and

/usr/local/cpanel/scripts/upcp was detected to be running as pid '11962'. Because it has been running for longer than 6 hours, the process will be killed and a new upcp will be run in it's place.

I have done several graceful server reboots

But I still get these warning emails.

I also got a disk getting full email:

Drive Warning: /dev/vzfs (/) is 81% full

But I've not tracked down file problems - mysql is < 1GB and so are the cpanel accounts.

Anyway I keep noticing these processes, which I assume are cpanel/rpm updates:

/usr/bin/python /usr/bin/yum --excludekernel* -y install autoconf autoconf261 automake automake19 bind bind9 bind9-devel bind9-utils bind-devel bind-libs bind-tools bind-utils binutils bison bzip2 caching-nameserver compat-db coreutils cpio cpp crontabs curl curl-devel db1 db1-dev db1-devel db1-tools db4 db4-dev db4-devel e2fsprogs-devel expat expat-dev expat-devel expect fileutils flex freetype freetype-dev freetype-devel ftp gamin gamin-devel gcc gcc-c++ gcc-c++-dev gcc-c++-devel gcc-c++-runtime gd gd-dev gd-devel gd-progs gd-utils gdbm gdbm-devel gentoolkit gettext gettext-devel glibc-dev glibc-devel glibc-kernheaders glibc-static gmake gnupg gzip imap imap-dev imap-devel initscripts iptables kernel-headers krb5-dev krb5-devel less lexlibpng10 lib64openssl0.9.7-devel lib64openssl0.9.7-static-devel libfreetype6 libfreetype6-dev libgcc libgd1 libgd1-devel libidn libidn-devel libjpeg libjpeg62 libjpeg62-dev libjpeg-dev libjpeg-devel libltdl libltdl3-devel libltdl-devel libopenssl0 libopenssl0.9.7-devel libopenssl0.9.7-static-devel libopenssl0-dev libopenssl0-devel libpng libpng10-devel libpng-dev libpng-devel libssl-dev libstdc++ libstdc++-dev libstdc++-devel libtiff libtiff-dev libtiff-devel libtool libtool-libltdl-devel libtool-ltdl libtool-ltdl-devel libX11-devel libxml libxml2 libxml2-devel libxml-devel libXpm libXpm-dev libXpm-devel libz-devel linux-headers lsof lynx make mirrorselect nano ncftp ncurses ncurses3 ncurses4 ncurses-dev ncurses-devel openssh openssh-client openssh-clients openssh-server openssl openssl095a openssl096 openssl096b openssl-dev openssl-devel openssl-misc pam pam-dev pam-devel passwd patch perl-CPAN perl-dev perl-devel pico pine popt portage pwdb python python-dev python-devel python-docs python-modules python-tools quota quota-devel rcs rdate rsync sed shadow-utils sharutils ssh ssl-dev strace stunnel sysstat tar tcl tclx tcp_wrappers-devel tix tk tkinter traceroute ucd-snmp ucd-snmp-devel ucd-snmp-utils unzip urw-fonts util-linux util-linux-ng vixie-cron wget which xfree XFree86-devel XFree86-libs xorg-x11-dev xorg-x11-devel zip zlib zlib1-devel zlib1g zlib1g-dev zlib-devel

(Don't know why X is there at all on a vps!)

These pop back even after server reboots.

I've tried using WHM to do a system adn SW update, but it just hangs

Also service status hangs on cpanel.

Any ideas ?

The websites are nowhere near high volume, user data is < 1GB as is mysql. but the system reports 13/15GB used.

Cheers

Andy

Hello Andy,

I have checked the VPS and following is the detailed usage for your disk usage on the server:

0 aquota.group
0 aquota.user
3.6G backup
5.1M bin
4.0K boot
4.0K dev
23M etc
3.3G home
30M lib
4.0K media
4.0K mnt
25M opt
0 proc
55M root
23M sbin
0 scripts
5.9M scripts.20110601.022213.9628
4.0K selinux
4.0K srv
0 sys
72M tmp
3.3G usr
2.0G var

It seems you have configured the backups on the server which are utilizing almost 3.6GB of disk space on the server.
You should download the backups from the /backup folder on your local computer and remove the files from /backup so the /backup folder frees up. Also if you want you can opt for our backup service , so the backups are performed on remote server instead of the VPS. Refer HERE for our backup plans.
Also the /usr and /var are consuming 3.3GB and 2.0G respectively. If you want we can remove the logs from the folders to free up some more space.
Also, I have done a successful cPanel update on the VPS and did not receive any errors.

[andymc]

Hi,

Thanks for the reply -

Yep, I know about my backups, just seemed to hit 13G quickly

Ill try an update later, and see if those corrupt rpm and stalled process warnings stop

thanks for the help

Cheers

Andy

[andymc]

Hi,

I'm still getting update failures - upcp processing running for more than 6 hours and the RPM DB being corrupted - raised a support ticket, will post a resolution here when support sort me out

Cheers

Andy

[Ambrose]

Hello Andy,

As per the Ticket ID GMY-161-66736 , your issue is resolved now.

If you face any issues further with the same then kindly update the ticket.

[eUK-Alan]

Hello Andrew,

I am able to update cPanel as well as other packages like exim by cPanel script on your server. Ambrose has rebuilt rpm database and that fixed this issue.

Please let us know if you are still experiencing any issues further.

[andymc]

Hi,

Thanks all.

Looks like setting cpanel updates from release to stable sort it Doohh :P

Thanks

Andy

[Stan]

Hi,

Thanks all.

Looks like setting cpanel updates from release to stable sort it Doohh :P

Thanks

Andy

Hello Andy,

Pleased to know that the issues have now been sorted and things are back in shape at par to your expectations.

Please let us know incase you need any assistance with the same issue, we'd be glad to sort it out for you.

Thank you.

Best Regards,
Stan