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Upgrade Errors after updating centminmod

Discussion in 'Install & Upgrades or Pre-Install Questions' started by redbird, Jun 29, 2021.

  1. redbird

    redbird Member

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    Hi,

    Just upgraded centmin on several servers from linode, vultr etc. But last one from Ramnode is throwing some errors after updating and re-running centmin.


    Any recommendations how to fix this?

    Code:
    [16:09][root@xxxxx.com ~]# centmin
    /usr/local/src/centminmod ~
    
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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 19470/140467489609536 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
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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 19470/140467489609536 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
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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
    CRITICAL:yum.main:
    
    Error: rpmdb open failed
    
    real    0m0.207s
    user    0m0.140s
    sys     0m0.048s
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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
    CRITICAL:yum.cli:Yum Error: Error: rpmdb open failed
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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 19470/140467489609536 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
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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
    CRITICAL:yum.main:
    
    Error: rpmdb open failed
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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
    CRITICAL:yum.main:
    
    Error: rpmdb open failed
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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 19470/140467489609536 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
    error: rpmdb: BDB0113 Thread/process 19470/140467489609536 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
    CRITICAL:yum.main:
    
    Error: rpmdb open failed
    --------------------------------------------------------
         Centmin Mod Menu 123.09beta01 centminmod.com
    --------------------------------------------------------
    1).  Centmin Install
    2).  Add Nginx vhost domain
    3).  NSD setup domain name DNS
    4).  Nginx Upgrade / Downgrade
    5).  PHP Upgrade / Downgrade
    6).  XCache Re-install
    7).  APC Cache Re-install
    8).  XCache Install
    9).  APC Cache Install
    10). Memcached Server Re-install
    11). MariaDB MySQL Upgrade & Management
    12). Zend OpCache Install/Re-install
    13). Install/Reinstall Redis PHP Extension
    14). SELinux disable
    15). Install/Reinstall ImagicK PHP Extension
    16). Change SSHD Port Number
    17). Multi-thread compression: zstd,pigz,pbzip2,lbzip2
    18). Suhosin PHP Extension install
    19). Install FFMPEG and FFMPEG PHP Extension
    20). NSD Install/Re-Install
    21). Data Transfer (TBA)
    22). Add Wordpress Nginx vhost + Cache Plugin
    23). Update Centmin Mod Code Base
    24). Exit
    --------------------------------------------------------
    Enter option [ 1 - 24 ] 24
    --------------------------------------------------------
    
    

    • CentOS Version: CentOS 7 64bit
    • Centmin Mod Version Installed: i.e. 123.08stable or 123.09beta01
    • Nginx Version Installed: 1.19.6
    • PHP Version Installed: 7.1.30
    • MariaDB MySQL Version Installed:
     
  2. eva2000

    eva2000 Administrator Staff Member

    47,501
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    Brisbane, Australia
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    Local Time:
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    Nginx 1.19.x
    MariaDB 5.5/10.x
    how much disk space/ram do these VPS have it could be low ram/disk space that corrupted your YUM RPM databases

    output for commands
    Code (Text):
    free -mlt
    df -hT
    


    see error: rpmdb: BDB0113 Thread/process failed: BDB1507 Thread died in Berkeley DB

    Code (Text):
    DT=$(date +"%d%m%y-%H%M%S")
    mkdir -p /home/backup_rpmdb_$DT
    cp -avr /var/lib/rpm/ /home/backup_rpmdb_$DT/
    rm -f /var/lib/rpm/__db*
    db_verify /var/lib/rpm/Packages
    rpm --rebuilddb
    yum clean all
    
     
  3. redbird

    redbird Member

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    Code:
                  total        used        free      shared  buff/cache   available
    Mem:           1024         356           0         300         667         367
    Low:           1024        1023           0
    High:             0           0           0
    Swap:           512         335         176
    Total:         1536         691         176
    
    Code:
    Filesystem        Type      Size  Used Avail Use% Mounted on
    /dev/ploop13629p1 ext4      211G   20G  180G  10% /
    none              tmpfs     512M     0  512M   0% /sys/fs/cgroup
    none              devtmpfs  512M     0  512M   0% /dev
    tmpfs             tmpfs     512M     0  512M   0% /dev/shm
    tmpfs             tmpfs     512M  447M   66M  88% /run
    tmpfs             tmpfs     103M     0  103M   0% /run/user/0
    tmpfs             tmpfs     103M     0  103M   0% /run/user/997
    tmpfs             tmpfs     103M     0  103M   0% /run/user/1000
    You have new mail in /var/spool/mail/root
    
    looks fine to me
     
  4. redbird

    redbird Member

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    Rebuilding DB seems to get rid of those errors.

    Thank you George as always )
     
  5. redbird

    redbird Member

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    However, on a second note, now after re-launching centmin I'm getting this message with different code at the end each time:

    Code:
    [10:11][root@xxx.com ~]# centmin
    /usr/local/src/centminmod ~
    
    BDB2053 Freeing read locks for locker 0xb7: 18176/140585354585920
    
     
  6. eva2000

    eva2000 Administrator Staff Member

    47,501
    10,779
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +16,752
    Local Time:
    5:20 PM
    Nginx 1.19.x
    MariaDB 5.5/10.x
    Probably corruption on the disk itself ? Probably best to move VPS servers but try re-running those commands again