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]
| Tutorial details | |
|---|---|
| Difficulty level | Easy |
| Root privileges | Yes |
| Requirements | None |
| Est. reading time | 5m |
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:
Loaded plugins: downloadonly, fastestmirror, security Determining fastest mirrors * base: centos.mirrors.tds.net * extras: centos.corenetworks.net * updates: mirror.fdcservers.net base | 3.7 kB 00:00 base/primary_db | 4.4 MB 00:00 extras | 3.4 kB 00:00 extras/primary_db | 19 kB 00:00 updates | 3.4 kB 00:00 updates/primary_db | 2.0 MB 00:00 Setting up Update Process Resolving Dependencies --> Running transaction check ---> Package kernel.x86_64 0:2.6.32-431.5.1.el6 will be installed ---> Package kernel-firmware.noarch 0:2.6.32-431.3.1.el6 will be updated ---> Package kernel-firmware.noarch 0:2.6.32-431.5.1.el6 will be an update ---> Package mysql-libs.x86_64 0:5.1.71-1.el6 will be updated ---> Package mysql-libs.x86_64 0:5.1.73-3.el6_5 will be an update ---> Package nss.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package nss-sysinit.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss-sysinit.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package nss-tools.x86_64 0:3.15.3-3.el6_5 will be updated ---> Package nss-tools.x86_64 0:3.15.3-6.el6_5 will be an update ---> Package openldap.x86_64 0:2.4.23-32.el6_4.1 will be updated ---> Package openldap.x86_64 0:2.4.23-34.el6_5.1 will be an update ---> Package p11-kit.x86_64 0:0.18.5-2.el6 will be updated ---> Package p11-kit.x86_64 0:0.18.5-2.el6_5.2 will be an update ---> Package p11-kit-trust.x86_64 0:0.18.5-2.el6 will be updated ---> Package p11-kit-trust.x86_64 0:0.18.5-2.el6_5.2 will be an update ---> Package tzdata.noarch 0:2013i-1.el6 will be updated ---> Package tzdata.noarch 0:2013i-2.el6 will be an update ---> Package wget.x86_64 0:1.12-1.8.el6 will be updated ---> Package wget.x86_64 0:1.12-1.11.el6_5 will be an update ---> Package yum-plugin-downloadonly.noarch 0:1.1.30-14.el6 will be updated ---> Package yum-plugin-downloadonly.noarch 0:1.1.30-17.el6_5 will be an update ---> Package yum-plugin-fastestmirror.noarch 0:1.1.30-14.el6 will be updated ---> Package yum-plugin-fastestmirror.noarch 0:1.1.30-17.el6_5 will be an update ---> Package yum-plugin-security.noarch 0:1.1.30-14.el6 will be updated ---> Package yum-plugin-security.noarch 0:1.1.30-17.el6_5 will be an update ---> Package yum-utils.noarch 0:1.1.30-14.el6 will be updated ---> Package yum-utils.noarch 0:1.1.30-17.el6_5 will be an update --> Finished Dependency Resolution --> Running transaction check ---> Package kernel.x86_64 0:2.6.32-358.18.1.el6 will be erased --> Finished Dependency Resolution Dependencies Resolved ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: kernel x86_64 2.6.32-431.5.1.el6 updates 28 M Updating: kernel-firmware noarch 2.6.32-431.5.1.el6 updates 13 M mysql-libs x86_64 5.1.73-3.el6_5 updates 1.2 M nss x86_64 3.15.3-6.el6_5 updates 822 k nss-sysinit x86_64 3.15.3-6.el6_5 updates 40 k nss-tools x86_64 3.15.3-6.el6_5 updates 358 k openldap x86_64 2.4.23-34.el6_5.1 updates 265 k p11-kit x86_64 0.18.5-2.el6_5.2 updates 94 k p11-kit-trust x86_64 0.18.5-2.el6_5.2 updates 71 k tzdata noarch 2013i-2.el6 updates 448 k wget x86_64 1.12-1.11.el6_5 updates 483 k yum-plugin-downloadonly noarch 1.1.30-17.el6_5 updates 21 k yum-plugin-fastestmirror noarch 1.1.30-17.el6_5 updates 28 k yum-plugin-security noarch 1.1.30-17.el6_5 updates 38 k yum-utils noarch 1.1.30-17.el6_5 updates 102 k Removing: kernel x86_64 2.6.32-358.18.1.el6 @updates 116 M Transaction Summary ================================================================================ Install 1 Package(s) Upgrade 14 Package(s) Remove 1 Package(s) Total download size: 45 M Is this ok [y/N]: y Downloading Packages: (1/15): kernel-2.6.32-431.5.1.el6.x86_64.rpm | 28 MB 00:01 (2/15): kernel-firmware-2.6.32-431.5.1.el6.noarch.rpm | 13 MB 00:00 (3/15): mysql-libs-5.1.73-3.el6_5.x86_64.rpm | 1.2 MB 00:00 (4/15): nss-3.15.3-6.el6_5.x86_64.rpm | 822 kB 00:00 (5/15): nss-sysinit-3.15.3-6.el6_5.x86_64.rpm | 40 kB 00:00 (6/15): nss-tools-3.15.3-6.el6_5.x86_64.rpm | 358 kB 00:00 (7/15): openldap-2.4.23-34.el6_5.1.x86_64.rpm | 265 kB 00:00 (8/15): p11-kit-0.18.5-2.el6_5.2.x86_64.rpm | 94 kB 00:00 (9/15): p11-kit-trust-0.18.5-2.el6_5.2.x86_64.rpm | 71 kB 00:00 (10/15): tzdata-2013i-2.el6.noarch.rpm | 448 kB 00:00 (11/15): wget-1.12-1.11.el6_5.x86_64.rpm | 483 kB 00:00 (12/15): yum-plugin-downloadonly-1.1.30-17.el6_5.noarch. | 21 kB 00:00 (13/15): yum-plugin-fastestmirror-1.1.30-17.el6_5.noarch | 28 kB 00:00 (14/15): yum-plugin-security-1.1.30-17.el6_5.noarch.rpm | 38 kB 00:00 (15/15): yum-utils-1.1.30-17.el6_5.noarch.rpm | 102 kB 00:00 -------------------------------------------------------------------------------- Total 18 MB/s | 45 MB 00:02 Running rpm_check_debug Running Transaction Test Transaction Test Succeeded Running Transaction Warning: RPMDB altered outside of yum. ** Found 1 pre-existing rpmdb problem(s), 'yum check' output follows: 2:irqbalance-1.0.4-8.el6_5.x86_64 is a duplicate with 2:irqbalance-1.0.4-6.el6.x86_64 Updating : nss-sysinit-3.15.3-6.el6_5.x86_64 1/30 Updating : nss-3.15.3-6.el6_5.x86_64 2/30 Updating : nss-tools-3.15.3-6.el6_5.x86_64 3/30 Updating : p11-kit-0.18.5-2.el6_5.2.x86_64 4/30 Updating : kernel-firmware-2.6.32-431.5.1.el6.noarch 5/30 Installing : kernel-2.6.32-431.5.1.el6.x86_64 6/30 Updating : p11-kit-trust-0.18.5-2.el6_5.2.x86_64 7/30 Updating : openldap-2.4.23-34.el6_5.1.x86_64 8/30 Updating : wget-1.12-1.11.el6_5.x86_64 9/30 Updating : yum-plugin-fastestmirror-1.1.30-17.el6_5.noarch 10/30 Updating : mysql-libs-5.1.73-3.el6_5.x86_64 11/30 Updating : yum-plugin-downloadonly-1.1.30-17.el6_5.noarch 12/30 Updating : yum-utils-1.1.30-17.el6_5.noarch 13/30 Updating : yum-plugin-security-1.1.30-17.el6_5.noarch 14/30 Updating : tzdata-2013i-2.el6.noarch 15/30 Cleanup : kernel-2.6.32-358.18.1.el6.x86_64 16/30 Cleanup : kernel-firmware-2.6.32-431.3.1.el6.noarch 17/30 Cleanup : yum-plugin-fastestmirror-1.1.30-14.el6.noarch 18/30 Cleanup : yum-plugin-downloadonly-1.1.30-14.el6.noarch 19/30 Cleanup : yum-utils-1.1.30-14.el6.noarch 20/30 Cleanup : yum-plugin-security-1.1.30-14.el6.noarch 21/30 Cleanup : tzdata-2013i-1.el6.noarch 22/30 Cleanup : openldap-2.4.23-32.el6_4.1.x86_64 23/30 Cleanup : nss-tools-3.15.3-3.el6_5.x86_64 24/30 Cleanup : nss-sysinit-3.15.3-3.el6_5.x86_64 25/30 Cleanup : nss-3.15.3-3.el6_5.x86_64 26/30 Cleanup : p11-kit-trust-0.18.5-2.el6.x86_64 27/30 Cleanup : p11-kit-0.18.5-2.el6.x86_64 28/30 Cleanup : wget-1.12-1.8.el6.x86_64 29/30 Cleanup : mysql-libs-5.1.71-1.el6.x86_64 30/30 Removed: kernel.x86_64 0:2.6.32-358.18.1.el6 Installed: kernel.x86_64 0:2.6.32-431.5.1.el6 Updated: kernel-firmware.noarch 0:2.6.32-431.5.1.el6 mysql-libs.x86_64 0:5.1.73-3.el6_5 nss.x86_64 0:3.15.3-6.el6_5 nss-sysinit.x86_64 0:3.15.3-6.el6_5 nss-tools.x86_64 0:3.15.3-6.el6_5 openldap.x86_64 0:2.4.23-34.el6_5.1 p11-kit.x86_64 0:0.18.5-2.el6_5.2 p11-kit-trust.x86_64 0:0.18.5-2.el6_5.2 tzdata.noarch 0:2013i-2.el6 wget.x86_64 0:1.12-1.11.el6_5 yum-plugin-downloadonly.noarch 0:1.1.30-17.el6_5 yum-plugin-fastestmirror.noarch 0:1.1.30-17.el6_5 yum-plugin-security.noarch 0:1.1.30-17.el6_5 yum-utils.noarch 0:1.1.30-17.el6_5 Complete!
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Thanks alot for this information.Thanks again.
That was very helpful and made me solve the problem in minutes. Thanks!
Well written article and very helpful. Thank you – Resolved my problem.
Thanks for this. I had a power outage during an update that caused some corruption. Solved my issue.
Very helpful.
Thanks a lot
Awesome solution….i was stuck in this issue for past 3 days….the above steps resolved my issue….thanks man!!!
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.
Thank you for having consistently excellent and useful content!!
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.
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!
Thanks for sharing.
Helio Paixao
Thanks for that
Fixed my problem :)
Thanks alot. Its very helpful.