Fixing broken YUM on CentOS

Server power outages could cause several problems and one of them is braking YUM manager. When the server is going down while YUM processing (even in background) repo task you will probably face a problem (a very messy situation with yum failure).

Requesting YUM / RPM:

[[email protected] ~]# rpm -qa

You are usually see:

error: rpmdb: BDB0113 Thread/process 11074/47686246043008 failed: BDB1507 Thread died in Berkeley DB library
error: db5 error(-30973) from dbenv->failchk: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages index using db5 -  (-30973)
error: cannot open Packages database in /var/lib/rpm
error: rpmdb: BDB0113 Thread/process 11074/47686246043008 failed: BDB1507 Thread died in Berkeley DB library
error: db5 error(-30973) from dbenv->failchk: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: cannot open Packages database in /var/lib/rpm

The problem is a corrupted rpm database, mostly coming into existence because of an aborted update process.

How this YUM braking could be fixed?

You may fix this by cleaning out entire RPM database and then rebuilding the entire database again. To minimize risk, we should make a backup of files in /var/lib/rpm/

YUM step-by-step fixing

1. We will create a backup directory in which we need to copy the rpmdb backup using command:

[[email protected] ~]# mkdir /tmp/rpm_db_bak

2. Backing up the rpmdb files in the created backup directory in /tmp:

[[email protected] ~]# mv /var/lib/rpm/__db* /tmp/rpm_db_bak

3. Flushing all the yum cache by the following command:

[[email protected] ~]# yum clean all

4. Start building new rpmdb
We will do this by running the yum update command. It will rebuild the rpmdb and will fetch and apply the updates from the repositions:

[[email protected] ~]# yum update

Allow some time for this process:

[[email protected] ~]# yum update
Loaded plugins: fastestmirror
Determining fastest mirrors

[skipped]

(65/67): vim-filesystem-7.4.160-6.el7_6.x86_64.rpm                                                      |  10 kB  00:00:00     
(66/67): vim-minimal-7.4.160-6.el7_6.x86_64.rpm                                                         | 437 kB  00:00:00     
(67/67): kernel-3.10.0-957.27.2.el7.x86_64.rpm                                                          |  48 MB  00:00:10     
-------------------------------------------------------------------------------------------------------------------------------
Total                                                                                           11 MB/s | 157 MB  00:00:14     
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
  Updating   : 32:bind-license-9.9.4-74.el7_6.2.noarch                                                                   1/134 
  Updating   : selinux-policy-3.13.1-229.el7_6.15.noarch                                                                 2/134 

[skipped]

  nginx.x86_64 2:1.16.1-1.el7.ngx                                 proftpd.x86_64 0:1.3.5e-5.el7                               
  python.x86_64 0:2.7.5-80.el7_6                                  python-libs.x86_64 0:2.7.5-80.el7_6                         
  python-perf.x86_64 0:3.10.0-957.27.2.el7                        selinux-policy.noarch 0:3.13.1-229.el7_6.15                 
  selinux-policy-targeted.noarch 0:3.13.1-229.el7_6.15            systemd.x86_64 0:219-62.el7_6.9                             
  systemd-libs.x86_64 0:219-62.el7_6.9                            systemd-python.x86_64 0:219-62.el7_6.9                      
  systemd-sysv.x86_64 0:219-62.el7_6.9                            tuned.noarch 0:2.10.0-6.el7_6.4                             
  tzdata.noarch 0:2019b-1.el7                                     vim-common.x86_64 2:7.4.160-6.el7_6                         
  vim-enhanced.x86_64 2:7.4.160-6.el7_6                           vim-filesystem.x86_64 2:7.4.160-6.el7_6                     
  vim-minimal.x86_64 2:7.4.160-6.el7_6                           

Complete!

Great! You are now fine!

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