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Cannot open packages database after NGINX update froze

Discussion in 'Nginx, PHP-FPM & MariaDB MySQL' started by Jon Snow, Feb 6, 2019.

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  1. Feb 6, 2019 #1
    Jon Snow

    Jon Snow Active Member

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    Local Time:
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    Nginx 1.13.9
    MariaDB 10.1.31
    Was updating NGINX today but it froze up.

    When I try to update again, I get:
    Code (Text):
    error: rpmdb: BDB0113 Thread/process 22369/140007812810816 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 openPackages database  in /var/lib/rpm
error: rpmdb: BDB0113 Thread/process 22369/140007812810816 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

    Do I delete the rpm database (corrupted?) and rebuild like? :
    Code (Text):
    yum clean all
rm -f /var/lib/rpm/__db*
rpm --rebuilddb
yum update
     
  2. Feb 6, 2019 #2
    eva2000

    eva2000 Administrator Staff Member

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    Nginx 1.19.x
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    how much memory on server, low memory is a common reason for corrupting yum database i.e. CentOS 7 needs minimum 1GB memory.

    yes those commands will rebuild the database.
     
  3. Feb 6, 2019 #3
    Jon Snow

    Jon Snow Active Member

    614
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    43
    Jun 30, 2017
    Ratings:
    +166
    Local Time:
    1:23 AM
    Nginx 1.13.9
    MariaDB 10.1.31
    Linode. 1 GB RAM.
     
  4. Feb 6, 2019 #4
    eva2000

    eva2000 Administrator Staff Member

    46,488
    10,557
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +16,390
    Local Time:
    2:23 PM
    Nginx 1.19.x
    MariaDB 5.5/10.x
    could be running close to free memory availability depending on what was running. CentOS 7 min is 1GB and recommended is 2GB :)
     
  5. Feb 6, 2019 #5
    Jon Snow

    Jon Snow Active Member

    614
    108
    43
    Jun 30, 2017
    Ratings:
    +166
    Local Time:
    1:23 AM
    Nginx 1.13.9
    MariaDB 10.1.31
    I think it's stuck again:
    [​IMG]

    I think it froze around this part last time too. I clearly remember "incubator pagespeed".
     
  6. Feb 6, 2019 #6
    eva2000

    eva2000 Administrator Staff Member

    46,488
    10,557
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +16,390
    Local Time:
    2:23 PM
    Nginx 1.19.x
    MariaDB 5.5/10.x
    nginx pagespeed module seems to take longer to compile just wait it out or disable nginx pagespeed if you are not using it
     
  7. Feb 6, 2019 #7
    eva2000

    eva2000 Administrator Staff Member

    46,488
    10,557
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +16,390
    Local Time:
    2:23 PM
    Nginx 1.19.x
    MariaDB 5.5/10.x
    nginx pagespeed module seems to take longer to compile just wait it out or disable nginx pagespeed if you are not using it
     
  8. Feb 6, 2019 #8
    Jon Snow

    Jon Snow Active Member

    614
    108
    43
    Jun 30, 2017
    Ratings:
    +166
    Local Time:
    1:23 AM
    Nginx 1.13.9
    MariaDB 10.1.31
    @eva2000 How would I go about getting this updated? It was excluded when I was updating everything.

    Code (Text):
    Following Updates are available:
-------------------------------------------------------------
python2-pip.noarch                       8.1.2-7.el7                        epel


    Code (Text):
    yum update --disableplugin=priorities --enablerepo=remi
Loaded plugins: fastestmirror, versionlock
Loading mirror speeds from cached hostfile
 * base: mirrors.linode.com
 * epel: mirror.compevo.com
 * extras: mirrors.linode.com
 * remi: repo1.dal.innoscale.net
 * rpmforge: mirror.lstn.net
 * updates: mirrors.linode.com
Excluding 1 update due to versionlock (use "yum versionlock status" to show it)
No packages marked for update


    Code (Text):
    yum versionlock status
Loaded plugins: fastestmirror, priorities, versionlock
Loading mirror speeds from cached hostfile
 * base: mirrors.linode.com
 * epel: mirror.compevo.com
 * extras: mirrors.linode.com
 * rpmforge: mirror.lstn.net
 * updates: mirrors.linode.com
284 packages excluded due to repository priority protections
0:python2-pip-8.1.2-7.el7.*
versionlock status done
     
  9. Feb 6, 2019 #9
    eva2000

    eva2000 Administrator Staff Member

    46,488
    10,557
    113
    May 24, 2014
    Brisbane, Australia
    Ratings:
    +16,390
    Local Time:
    2:23 PM
    Nginx 1.19.x
    MariaDB 5.5/10.x
    123.09beta01 latest code no longer uses python2-pip so it's locked to prevent conflict with new method of updating pip which is automatically done when you run centmin.sh
     
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