Resolving RPM Database Corruption Before Package Upgrades
Issue: During system maintenance on the OCI Linux environment, we encountered an issue where the RPM database became corrupted, causing dnf upgrade to fail with the following error:
[root@omdmz ~]# dnf upgraade
error: rpmdb: BDB0113 Thread/process 590272/140176820012928 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: Error: rpmdb open failed
Step 1: Clean Up Stale RPM Database Files
To fix the issue, I first removed all temporary __db.* files: as this clears out incomplete or orphaned transactions that may have caused the corruption.
[root@omapps01 rpm]# rm -f __db.*
D: adding 1 entries to Installtid index.
D: adding 1 entries to Sigmd5 index.
D: adding "7ab75f337467cc17322ec627c0f5525bcd83a735" to Sha1header index.
D: read h# 2707
Header SHA256 digest: OK
Header SHA1 digest: OK
D: adding "flatpak" to Name index.
D: adding 129 entries to Basenames index.
D: adding "Unspecified" to Group index.
D: adding 78 entries to Requirename index.
D: adding 2 entries to Providename index.
D: adding 1 entries to Conflictname index.
D: adding 58 entries to Dirnames index.
D: adding 1 entries to Installtid index.
D: adding 1 entries to Sigmd5 index.
D: adding "453cd6fb88f9b42a07e8f9ab047f0e8e94e2fda8" to Sha1header index.
D: adding 2 entries to Recommendname index.
D: read h# 2201
Header SHA256 digest: OK
Header SHA1 digest: OK
D: adding "swtpm-tools" to Name index.
D: adding 34 entries to Basenames index.
D: adding "Unspecified" to Group index.
D: adding 36 entries to Requirename index.
D: adding 3 entries to Providename index.
D: adding 15 entries to Dirnames index.
D: adding 1 entries to Installtid index.
D: adding 1 entries to Sigmd5 index.
D: adding "53d49b3bac3d0da69c55add54e90f2c33c3c5c95" to Sha1header index.
D: read h# 667
Header SHA256 digest: OK
Header SHA1 digest: OK
D: adding "libXres" to Name index.
D: adding 8 entries to Basenames index.
D: adding "System Environment/Libraries" to Group index.
D: adding 11 entries to Requirename index.
D: adding 3 entries to Providename index.
D: adding 6 entries to Dirnames index.
D: adding 1 entries to Installtid index.
D: adding 1 entries to Sigmd5 index.
D: adding "6c7e1dc63b857095258408c570cc9ce6c15b8ec8" to Sha1header index.
D: closed db index /var/lib/rpm/Packages
D: closed db environment /var/lib/rpm
D: closed db index /var/lib/rpmrebuilddb.1125429/Packages
D: closed db index /var/lib/rpmrebuilddb.1125429/Enhancename
D: closed db index /var/lib/rpmrebuilddb.1125429/Supplementname
D: closed db index /var/lib/rpmrebuilddb.1125429/Suggestname
D: closed db index /var/lib/rpmrebuilddb.1125429/Recommendname
D: closed db index /var/lib/rpmrebuilddb.1125429/Transfiletriggername
D: closed db index /var/lib/rpmrebuilddb.1125429/Filetriggername
D: closed db index /var/lib/rpmrebuilddb.1125429/Sha1header
D: closed db index /var/lib/rpmrebuilddb.1125429/Sigmd5
D: closed db index /var/lib/rpmrebuilddb.1125429/Installtid
D: closed db index /var/lib/rpmrebuilddb.1125429/Dirnames
D: closed db index /var/lib/rpmrebuilddb.1125429/Triggername
D: closed db index /var/lib/rpmrebuilddb.1125429/Obsoletename
D: closed db index /var/lib/rpmrebuilddb.1125429/Conflictname
D: closed db index /var/lib/rpmrebuilddb.1125429/Providename
D: closed db index /var/lib/rpmrebuilddb.1125429/Requirename
D: closed db index /var/lib/rpmrebuilddb.1125429/Group
D: closed db index /var/lib/rpmrebuilddb.1125429/Basenames
D: closed db index /var/lib/rpmrebuilddb.1125429/Name
D: closed db environment /var/lib/rpmrebuilddb.1125429
==
Step 2: check the location of /var/lib/rpm
[root@omdmz ~]# cd /var/lib/rpm
[root@omdmz rpm]# ls
Basenames __db.001 __db.003 Enhancename Group Name Packages Recommendname Sha1header Suggestname Transfiletriggername
Conflictname __db.002 Dirnames Filetriggername Installtid Obsoletename Providename Requirename Sigmd5 Supplementname Triggername
[root@omdmz rpm]#
Step 3: Rebuild the RPM db
rpm -vv --rebuilddb
This command reindexes the RPM database and ensures all package metadata is intact. The verbose flag
-vv provides detailed output for troubleshooting, showing progress on database index handling.Result
After successfully rebuilding the database, the dnf upgrade worked without errors, and the package system went back to normal.
This is a common issue on systems where RPM operations are interrupted (e.g., forced reboots, crashes). If you notice package-related errors, it’s always good practice to rebuild the RPM database after such events.
