mysql_install_db fails on percona server 5.6.16 (yum install on centos 6.5)

Bug #1291247 reported by johan on 2014-03-12
20
This bug affects 3 people
Affects Status Importance Assigned to Milestone
Percona Server
Status tracked in 5.6
5.1
Undecided
Unassigned
5.5
High
Tomislav Plavcic
5.6
High
Tomislav Plavcic

Bug Description

yum -y install Percona-Server-server-56.x86_64 Percona-Server-client-56.x86_64 percona-xtrabackup percona-toolkit

/usr/bin/mysql_install_db --force --datadir=/var/lib/mysql --basedir=/usr/ --user=mysql
FATAL ERROR: Could not find /fill_help_tables.sql

If you compiled from source, you need to run 'make install' to
copy the software into the correct location ready for operation.

If you are using a binary release, you must either be at the top
level of the extracted archive, or pass the --basedir option
pointing to that location.

rpm -qa |grep -i percona

percona-release-0.0-1.x86_64
Percona-Server-client-56-5.6.16-rel64.0.el6.x86_64
percona-xtrabackup-2.1.8-733.rhel6.x86_64
Percona-Server-shared-56-5.6.16-rel64.0.el6.x86_64
Percona-Server-shared-51-5.1.73-rel14.11.603.rhel6.x86_64
percona-toolkit-2.2.7-1.noarch
Percona-Server-server-56-5.6.16-rel64.0.el6.x86_64

cat /etc/my.cnf

[MYSQLD]
sql_mode=NO_ENGINE_SUBSTITUTION
user=mysql
basedir=/usr/
datadir=/var/lib/mysql
pid-file=mysqld.pid
socket=/var/lib/mysql/mysql.sock
port=3306
default-storage-engine=innodb
log-error=/var/log/mysqld.log
log-warnings=2
#log
#log-slow-queries
#OTHER THINGS, BUFFERS ETC
key-buffer-size = 8M
max-allowed-packet = 16M
#thread_cache_size=1024
myisam-sort-buffer-size = 8M
skip-name-resolve
memlock=0
event_scheduler=1
### INNODB
innodb-buffer-pool-size=614M
innodb-flush-log-at-trx_commit=2
innodb-file-per-table=1
innodb_data_file_path = ibdata1:100M:autoextend
innodb_log_file_size=64M
innodb-log-files-in-group=2
#innodb-buffer-pool-instances=4
innodb-thread-concurrency=0
#innodb-file-format=barracuda
innodb-flush-method=O_DIRECT
innodb_locks_unsafe_for_binlog=1
sysdate-is-now=1
max-connections=512
thread-cache-size=128
query-cache-type = 1
query-cache-size = 32M
table-open_cache=512
lower-case-table-names=0
# 5.6 backwards compatibility
explicit_defaults_for_timestamp=1
[MYSQL]
socket=/var/lib/mysql/mysql.sock
[client]
socket=/var/lib/mysql/mysql.sock
[MYSQLD_SAFE]
pid-file=mysqld.pid
log-error=error.log
basedir=/usr/
datadir=/var/lib/mysql

Tags: pkg Edit Tag help

Related branches

lp:~percona-core/percona-server/release-5.5.36-34.1
Laurynas Biveinis: Approve on 2014-03-27
lp:~percona-core/percona-server/release-5.6.16-64.1
Laurynas Biveinis: Approve on 2014-03-26
Mark Willis (mark-willis) wrote :

Changing the basedir in the command:

/usr/bin/mysql_install_db --force --datadir=/var/lib/mysql --basedir=/usr/share/percona-server --user=mysql

OR

in the my.cnf doesn't change the outcome of this.

Jericho Rivera (jericho-rivera) wrote :

I am getting this from a fresh CentOS 6.4 installation. Upgrade from previous version worked.

Running Transaction
  Installing : Percona-Server-shared-56-5.6.16-rel64.0.el6.x86_64 1/3
  Installing : Percona-Server-client-56-5.6.16-rel64.0.el6.x86_64 2/3
  Installing : Percona-Server-server-56-5.6.16-rel64.0.el6.x86_64 3/3
FATAL ERROR: Could not find /fill_help_tables.sql

If you compiled from source, you need to run 'make install' to
copy the software into the correct location ready for operation.

If you are using a binary release, you must either be at the top
level of the extracted archive, or pass the --basedir option
pointing to that location.

chmod: cannot access `/var/lib/mysql/mysql': No such file or directory
Percona Server is distributed with several useful UDF (User Defined Function) from Maatkit.
Run the following commands to create these functions:
mysql -e "CREATE FUNCTION fnv1a_64 RETURNS INTEGER SONAME 'libfnv1a_udf.so'"
mysql -e "CREATE FUNCTION fnv_64 RETURNS INTEGER SONAME 'libfnv_udf.so'"
mysql -e "CREATE FUNCTION murmur_hash RETURNS INTEGER SONAME 'libmurmur_udf.so'"
See http://code.google.com/p/maatkit/source/browse/trunk/udf for more details
  Verifying : Percona-Server-server-56-5.6.16-rel64.0.el6.x86_64 1/3
  Verifying : Percona-Server-shared-56-5.6.16-rel64.0.el6.x86_64 2/3
  Verifying : Percona-Server-client-56-5.6.16-rel64.0.el6.x86_64 3/3

Installed:
  Percona-Server-client-56.x86_64 0:5.6.16-rel64.0.el6 Percona-Server-server-56.x86_64 0:5.6.16-rel64.0.el6

Dependency Installed:
  Percona-Server-shared-56.x86_64 0:5.6.16-rel64.0.el6

[mysqld]
user = mysql
socket = /var/lib/mysql/mysqld.sock
port = 3306
datadir = /var/lib/mysql
tmpdir = /tmp
basedir = /usr
innodb_file_per_table = 1

key_buffer_size = 16M
max_allowed_packet = 16M

log_error = /var/lib/mysql/mysqld.err

[client]
socket = /var/lib/mysql/mysqld.sock

Removing

> basedir = /usr

though would not give me the error

Jericho Rivera (jericho-rivera) wrote :
Download full text (5.3 KiB)

I get a different error on PS 5.5.36. Still on a fresh CentOS installation.

[root@localhost /]# yum install Percona-Server-server-55 Percona-Server-client-55
Loaded plugins: fastestmirror, security
Loading mirror speeds from cached hostfile
 * base: mirror.symnds.com
 * extras: centos.someimage.com
 * updates: mirror.ash.fastserv.com
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package Percona-Server-client-55.x86_64 0:5.5.36-rel34.0.el6 will be installed
--> Processing Dependency: Percona-Server-shared-55 for package: Percona-Server-client-55-5.5.36-rel34.0.el6.x86_64
---> Package Percona-Server-server-55.x86_64 0:5.5.36-rel34.0.el6 will be installed
--> Running transaction check
---> Package Percona-Server-shared-55.x86_64 0:5.5.36-rel34.0.el6 will be installed
--> Finished Dependency Resolution

Dependencies Resolved

========================================================================================================================================================================
 Package Arch Version Repository Size
========================================================================================================================================================================
Installing:
 Percona-Server-client-55 x86_64 5.5.36-rel34.0.el6 percona 6.1 M
 Percona-Server-server-55 x86_64 5.5.36-rel34.0.el6 percona 15 M
Installing for dependencies:
 Percona-Server-shared-55 x86_64 5.5.36-rel34.0.el6 percona 646 k

Transaction Summary
========================================================================================================================================================================
Install 3 Package(s)

Total download size: 22 M
Installed size: 97 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): Percona-Server-client-55-5.5.36-rel34.0.el6.x86_64.rpm | 6.1 MB 00:01
(2/3): Percona-Server-server-55-5.5.36-rel34.0.el6.x86_64.rpm | 15 MB 00:03
(3/3): Percona-Server-shared-55-5.5.36-rel34.0.el6.x86_64.rpm | 646 kB 00:00
------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 2.1 MB/s | 22 MB 00:10
Running rpm_check_debug
Running Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing : Percona-Server-shared-55-5.5.36-...

Read more...

Only workaround possible here, is ln -s /usr/share/percona-server /usr/share/mysql (make sure /usr/share/mysql doesn't exist and is empty etc.)

johan (johan-severalnines) wrote :

Will you release a fixed build for this?

BR
johan

tags: added: pkg
linzuxiong (linzuxiong1988) wrote :

[root@localhost download]# rpm -ivh Percona-Server-devel-56-5.6.16-rel64.0.el6.x86_64.rpm Percona-Server-shared-56-5.6.16-rel64.0.el6.x86_64.rpm Percona-Server-client-56-5.6.16-rel64.0.el6.x86_64.rpm
Preparing... ########################################### [100%]
   1:Percona-Server-shared-5########################################### [ 33%]
   2:Percona-Server-devel-56########################################### [ 67%]
   3:Percona-Server-client-5########################################### [100%]
[root@localhost download]# rpm -ivh Percona-Server-server-56-5.6.16-rel64.0.el6.x86_64.rpm
Preparing... ########################################### [100%]
ls: 无法访问/var/lib/mysql/*.err: 没有那个文件或目录
ls: 无法访问/var/lib/mysql/*.err: 没有那个文件或目录
   1:Percona-Server-server-5########################################### [100%]
FATAL ERROR: Could not find /fill_help_tables.sql

[root@localhost download]# rpm -qa|fgrep Percona
Percona-Server-client-56-5.6.16-rel64.0.el6.x86_64
Percona-Server-shared-56-5.6.16-rel64.0.el6.x86_64
Percona-Server-shared-51-5.1.73-rel14.11.603.rhel6.x86_64
Percona-Server-server-56-5.6.16-rel64.0.el6.x86_64
Percona-Server-devel-56-5.6.16-rel64.0.el6.x86_64

It's too terrible in Production Environment.

Why do not you test on Full coverage , then Release Percona-Server??????????????????????

linzuxiong (linzuxiong1988) wrote :

It is a waste of my time, about 8 hours.

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