yum update on AlmalLinux WHM server fails with thread died, dbenv->failchk

On a perfectly stable AlmaLinux server you suddenly get the following error:

# yum update
error: rpmdb: BDB0113 Thread/process 3960860/140378867591040 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



You’ll get the original out and then something like this:

(exit code 1)
find_and_fix_rpm_issues: rpm issues have been found
find_and_fix_rpm_issues: Performing rpm rebuild

Thereafter yum update worked. The interesting thing was all it wanted to do was update the Kernel from 3.10 to 4.18.


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