We often run into the error while updating the yum on cPanel/WHM servers.
Error:
rpmdb: Thread/process 29586/140397819602848 failed: Thread died in Berkeley DB library error: db3 error(-30974) from dbenv->failchk: 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
It usually occurs when the RPM database is corrupted on the server
To fix this error, Login to your Server/VPS via SSH with root credentials.
Then we try to stash all the files used by the yum repository for the dependency resolution:
yum clean headers
Clean yum packages cache:
yum clean packages
Then we clean metadata:
yum clean metadata
Clean dbcache:
yum clean dbcache
Clean remaining:
yum clean all
Remove clean all RPM database files:
rm -f /var/lib/rpm/__db.*
Rebuilt RPM Database:
rpm -vv –rebuilddb
Finally, we run the update command:
yum update
To resolve this error, we can also try to rebuild the RPM database using the Rebuild RPM database tool in WHM:
“WHM Home » Software » Rebuild RPM Database”