yum update fails and complains about duplicate pid

[monty solomon]

Error in PREIN scriptlet in rpm package Percona-Server-server-56-5.6.24-rel72.2.el6.x86_64
You have more than one PID file:
-rw-rw---- 1 mysql mysql 6 Mar 29 18:00 /opt/mysql/dbprod/monty-q0.pid
-rw-rw---- 1 mysql mysql 6 Mar 29 18:00 /opt/mysql/dbprod/monty-q0.pid
Please check which one (if any) corresponds to a running server
and delete all others before repeating the MySQL upgrade.

[monty solomon (monty+launchpad)]

Downloading Packages:
(1/4): Percona-Server-client-56-5.6.24-rel72.2.el6.x86_6 | 6.4 MB 00:00
(2/4): Percona-Server-devel-56-5.6.24-rel72.2.el6.x86_64 | 1.0 MB 00:00
(3/4): Percona-Server-server-56-5.6.24-rel72.2.el6.x86_6 | 20 MB 00:00
(4/4): Percona-Server-shared-56-5.6.24-rel72.2.el6.x86_6 | 724 kB 00:00
--------------------------------------------------------------------------------
Total 53 MB/s | 28 MB 00:00
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Updating : Percona-Server-shared-56-5.6.24-rel72.2.el6.x86_64 1/8
  Updating : Percona-Server-client-56-5.6.24-rel72.2.el6.x86_64 2/8
Error in PREIN scriptlet in rpm package Percona-Server-server-56-5.6.24-rel72.2.el6.x86_64
You have more than one PID file:
-rw-rw---- 1 mysql mysql 6 Mar 29 18:00 /opt/mysql/dbprod/monty-q0.pid
-rw-rw---- 1 mysql mysql 6 Mar 29 18:00 /opt/mysql/dbprod/monty-q0.pid
Please check which one (if any) corresponds to a running server
and delete all others before repeating the MySQL upgrade.
error: %pre(Percona-Server-server-56-5.6.24-rel72.2.el6.x86_64) scriptlet failed, exit status 1
error: install: %pre scriptlet failed (2), skipping Percona-Server-server-56-5.6.24-rel72.2.el6
  Updating : Percona-Server-devel-56-5.6.24-rel72.2.el6.x86_64 4/8
  Cleanup : Percona-Server-devel-56-5.6.23-rel72.1.el6.x86_64 5/8
  Cleanup : Percona-Server-client-56-5.6.23-rel72.1.el6.x86_64 6/8
  Cleanup : Percona-Server-shared-56-5.6.23-rel72.1.el6.x86_64 7/8
  Verifying : Percona-Server-client-56-5.6.24-rel72.2.el6.x86_64 1/8
  Verifying : Percona-Server-devel-56-5.6.24-rel72.2.el6.x86_64 2/8
  Verifying : Percona-Server-shared-56-5.6.24-rel72.2.el6.x86_64 3/8
Percona-Server-server-56-5.6.23-rel72.1.el6.x86_64 was supposed to be removed but is not!
  Verifying : Percona-Server-server-56-5.6.23-rel72.1.el6.x86_64 4/8
  Verifying : Percona-Server-devel-56-5.6.23-rel72.1.el6.x86_64 5/8
  Verifying : Percona-Server-client-56-5.6.23-rel72.1.el6.x86_64 6/8
  Verifying : Percona-Server-shared-56-5.6.23-rel72.1.el6.x86_64 7/8
  Verifying : Percona-Server-server-56-5.6.24-rel72.2.el6.x86_64 8/8

Updated:
  Percona-Server-client-56.x86_64 0:5.6.24-rel72.2.el6
  Percona-Server-devel-56.x86_64 0:5.6.24-rel72.2.el6
  Percona-Server-shared-56.x86_64 0:5.6.24-rel72.2.el6

Failed:
  Percona-Server-server-56.x86_64 0:5.6.23-rel72.1.el6
  Percona-Server-server-56.x86_64 0:5.6.24-rel72.2.el6

Complete!

[monty solomon (monty+launchpad)]

After the script fails a mix of versions is installed on the server.

[monty solomon (monty+launchpad)]

CentOS release 6.5 (Final)

Linux 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

[monty solomon (monty+launchpad)]

When mysql is shut down before the update the script displays a message about waiting for it to exit

Running Transaction
  Updating : Percona-Server-server-56-5.6.24-rel72.2.el6.x86_64 1/2
Giving mysqld 5 seconds to exit nicely

[monty solomon (monty+launchpad)]

I found the source of the problem -- the RPM script is not following the rule that when multiple instances of a given option are found, the last instance takes precedence. A similar issue caused bug 1201036.

Excerpt from the documentation
http://dev.mysql.com/doc/refman/5.6/en/option-files.html

If multiple instances of a given option are found, the last instance takes precedence.

My /etc/my.cnf file ends with an include directive

<!includedir /etc/mysql/conf.d/>

and the /etc/mysql/conf.d/001-basic-config.cnf file contains a duplicate pid entry

# tail -1 /etc/my.cnf
!includedir /etc/mysql/conf.d/

# grep -i pid /etc/my.cnf /etc/mysql/conf.d/001-basic-config.cnf
/etc/my.cnf:pid-file = /opt/mysql/dbprod/monty-q0.pid
/etc/mysql/conf.d/001-basic-config.cnf:pid-file = /opt/mysql/dbprod/monty-q0.pid

[Valerii Kravchuk (valerii-kravchuk)]

Yes, code in percona-server.spec looks like this:

  PID_FILE_PATT=`%{_bindir}/my_print_defaults server mysqld | grep '^--pid-file=' | sed -n 's/--pid-file=//p'`

So, we have to check what my_print_defaults outputs in case like yours:

[openxs@centos percona-server]$ my_print_defaults mysqld | grep pid
error: Found option without preceding group in config file: /tmp/pt.cnf at line: 1
--pid-file=/tmp/mysql.pid
--pid-file=/tmp/mysql.pid
[openxs@centos percona-server]$ my_print_defaults mysqld | grep buffer
error: Found option without preceding group in config file: /tmp/pt.cnf at line: 1
--innodb_buffer_pool_size=5M
--innodb_buffer_pool_size=100M

That is, my_print_defaults does not recognize the case of duplicated setting and just reports them all in order. .spec file should take this case into account for --pid-file it seems.

[Tomislav Plavcic (tplavcic)]

From what I see upstream handles this the same way. Anyway what I did is just put sort with removal of duplicates - should solve this case and have no effect on others.
PR's:
https://github.com/percona/percona-server/pull/198
https://github.com/percona/percona-server/pull/197

[monty solomon (monty+launchpad)]

The upstream package does not fail during the update. It stops and starts the server during the update process.

# yum -y update mysql-community*
Loaded plugins: downloadonly, fastestmirror, replace
Loading mirror speeds from cached hostfile
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package mysql-community-client.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-client.x86_64 0:5.6.27-2.el6 will be an update
---> Package mysql-community-common.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-common.x86_64 0:5.6.27-2.el6 will be an update
---> Package mysql-community-devel.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-devel.x86_64 0:5.6.27-2.el6 will be an update
---> Package mysql-community-libs.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-libs.x86_64 0:5.6.27-2.el6 will be an update
---> Package mysql-community-libs-compat.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-libs-compat.x86_64 0:5.6.27-2.el6 will be an update
---> Package mysql-community-server.x86_64 0:5.6.25-2.el6 will be updated
---> Package mysql-community-server.x86_64 0:5.6.27-2.el6 will be an update
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package Arch Version Repository Size
================================================================================
Updating:
 mysql-community-client x86_64 5.6.27-2.el6 mysql56-community 18 M
 mysql-community-common x86_64 5.6.27-2.el6 mysql56-community 307 k
 mysql-community-devel x86_64 5.6.27-2.el6 mysql56-community 3.3 M
 mysql-community-libs x86_64 5.6.27-2.el6 mysql56-community 1.9 M
 mysql-community-libs-compat x86_64 5.6.27-2.el6 mysql56-community 1.6 M
 mysql-community-server x86_64 5.6.27-2.el6 mysql56-community 53 M

Transaction Summary
================================================================================
Upgrade 6 Package(s)

Total download size: 78 M
Downloading Packages:
(1/6): mysql-community-client-5.6.27-2.el6.x86_64.rpm | 18 MB 00:00
(2/6): mysql-community-common-5.6.27-2.el6.x86_64.rpm | 307 kB 00:00
(3/6): mysql-community-devel-5.6.27-2.el6.x86_64.rpm | 3.3 MB 00:00
(4/6): mysql-community-libs-5.6.27-2.el6.x86_64.rpm | 1.9 MB 00:00
(5/6): mysql-community-libs-compat-5.6.27-2.el6.x86_64.r | 1.6 MB 00:00
(6/6): mysql-community-server-5.6.27-2.el6.x86_64.rpm | 53 MB 00:01
--------------------------------------------------------------------------------
Total 31 MB/s | 78 MB 00:02
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Updating : mysql-community-common-5.6.27-2.el6.x86_64 1/12
  Updating : mysql-community-libs-5.6.27-2.el6.x86_64 2/12
  Updating : mysql-community-client-5.6.27-2.el6.x86_64 3/12
  Updating : mys...

[monty solomon (monty+launchpad)]

The same is true during a downgrade.

# yum downgrade mysql-community*
Loaded plugins: downloadonly, fastestmirror, replace
Setting up Downgrade Process
Loading mirror speeds from cached hostfile
No Match for available package: mysql-community-bench-5.6.20-4.el6.x86_64
No Match for available package: mysql-community-embedded-5.6.15-1.el6.i686
No Match for available package: mysql-community-embedded-5.6.15-1.el6.x86_64
No Match for available package: mysql-community-embedded-devel-5.6.15-1.el6.i686
No Match for available package: mysql-community-embedded-devel-5.6.15-1.el6.x86_64
No Match for available package: mysql-community-test-5.6.15-1.el6.x86_64
Resolving Dependencies
--> Running transaction check
---> Package mysql-community-client.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-client.x86_64 0:5.6.27-2.el6 will be erased
---> Package mysql-community-common.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-common.x86_64 0:5.6.27-2.el6 will be erased
---> Package mysql-community-devel.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-devel.x86_64 0:5.6.27-2.el6 will be erased
---> Package mysql-community-libs.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-libs.x86_64 0:5.6.27-2.el6 will be erased
---> Package mysql-community-libs-compat.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-libs-compat.x86_64 0:5.6.27-2.el6 will be erased
---> Package mysql-community-release.noarch 0:el6-4 will be a downgrade
---> Package mysql-community-release.noarch 0:el6-5 will be erased
---> Package mysql-community-server.x86_64 0:5.6.26-2.el6 will be a downgrade
---> Package mysql-community-server.x86_64 0:5.6.27-2.el6 will be erased
--> Finished Dependency Resolution

Dependencies Resolved

================================================================================
 Package Arch Version Repository Size
================================================================================
Downgrading:
 mysql-community-client x86_64 5.6.26-2.el6 mysql56-community 18 M
 mysql-community-common x86_64 5.6.26-2.el6 mysql56-community 307 k
 mysql-community-devel x86_64 5.6.26-2.el6 mysql56-community 3.2 M
 mysql-community-libs x86_64 5.6.26-2.el6 mysql56-community 1.9 M
 mysql-community-libs-compat x86_64 5.6.26-2.el6 mysql56-community 1.6 M
 mysql-community-release noarch el6-4 mysql-tools-community 5.0 k
 mysql-community-server x86_64 5.6.26-2.el6 mysql56-community 53 M

Transaction Summary
================================================================================
Downgrade 7 Package(s)

Total download size: 78 M
Is this ok [y/N]: y
Downloading Packages:
(1/7): mysql-community-client-5.6.26-2.el6.x86_64.rpm | 18 MB 00:00
(2/7): mysql-community-common-5.6.26-2.el6.x86_64.rpm | 307 kB 00:00
(3/7): mysql-community-devel-5.6.26-2.el6.x86_64.rpm | 3.2 MB 00:00
(4/7): mysql-community-libs-5.6.26-2.el6.x86_64.rpm | 1.9 MB 00:00
(5/7): mysql-community-libs-compat-5.6.26-...

[Shahriyar Rzayev (rzayev-sehriyar)]

Percona now uses JIRA for bug reports so this bug report is migrated to: https://jira.percona.com/browse/PS-902