CentOS: rpmdb: PANIC: fatal region error detected; run recovery error and solution

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I am using a CentOS Linux v6.5 on my home server and I am getting the following error when I execute yum command:


rpmdb: PANIC: fatal region error detected; run recovery
error: db3 error(-30974) from dbenv->open: DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db3 – (-30974)
error: cannot open Packages database in /var/lib/rpm
CRITICAL:yum.main:

Error: rpmdb open failed

How do I fix this problem on a CentOS / RHEL based system?

[donotprint][/donotprint]This is quite the messy situation. You may fix this by cleaning out rpm database. To minimize risk, make a backup of files in /var/lib/rpm/ using cp command:

mkdir /root/backups.rpm.mm_dd_yyyy/
cp -avr /var/lib/rpm/ /root/backups.rpm.mm_dd_yyyy/
To find list of __db* file, enter:
# ls -l /var/lib/rpm/_*
Sample outputs:

-rw-r--r-- 1 root root   24576 Jan 28 04:00 /var/lib/rpm/__db.001
-rw-r--r-- 1 root root  229376 Jan 28 04:00 /var/lib/rpm/__db.002
-rw-r--r-- 1 root root 1318912 Jan 28 04:00 /var/lib/rpm/__db.003
-rw-r--r-- 1 root root  753664 Jan 28 04:00 /var/lib/rpm/__db.004

To fix this problem, try:
# rm -f /var/lib/rpm/__db*
# db_verify /var/lib/rpm/Packages
# rpm --rebuilddb
# yum clean all
Verify that error has gone with the following yum command
# yum update
Sample outputs:

 

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Posted by: Vivek Gite

The author is the creator of nixCraft and a seasoned sysadmin, DevOps engineer, and a trainer for the Linux operating system/Unix shell scripting. Get the latest tutorials on SysAdmin, Linux/Unix and open source topics via RSS/XML feed or weekly email newsletter.

13 comment

  6. Awesome solution….i was stuck in this issue for past 3 days….the above steps resolved my issue….thanks man!!!

  7. Thank you! As someone who only has linux installed for one specific purpose and has nearly no understanding of it beyond that, this gave me exactly what I needed.

  9. Never written comments. However, in earnest I have learned a lot Linux and UNIX from cyberciti.biz, specifically your NixCraft site. With guys like Vivek Gite you can’t go wrong.

    Great and trusted work buddies – is all I can say.

    Wow.

  10. This solved my rpm database problem after a filesystem crash on a SLES machine, thank you very much!

    Under SLES, if you have zypper installed instead of yum, you need to run “zypper clean” instead of “yum clean all”.

    Thanks again!

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