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:

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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.


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13 comment

  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.

    Reply

  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.

    Reply

  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!

    Reply

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