MySQL 5.5 Configuration – Cannot Configure or Start

configurationmysql-5.5

On a brand new Kubuntu 14.04 install, I ran sudo aptitude install mysql-server-core-5.6. The install could not complete due to dependencies of some KDE packages on mysql-server-core-5.5, which would have been replaced. Now when I run sudo aptitude install mysql-server-5.5 I get this error after specifying a password:

Configuring mysql-server-5.5
Unable to set password for the MySQL "root" user
An error occurred while setting the password for the MySQL administrative user. This may have happened
because the account already has a password, or because of a communication problem with the MySQL server.
You should check the account's password after the package installation.
Please read the /usr/share/doc/mysql-server-5.5/README.Debian file for more information.

I have in fact read /usr/share/doc/mysql-server-5.5/README.Debian but there was nothing relevant for my situation. The MySQL log helps:

$ tail /var/log/mysql/error.log 
140818 10:17:16 InnoDB: Completed initialization of buffer pool
140818 10:17:16 InnoDB: highest supported file format is Barracuda.
140818 10:17:16  InnoDB: Waiting for the background threads to start
140818 10:17:17 InnoDB: 5.5.38 started; log sequence number 1595675
140818 10:17:17 [ERROR] /usr/sbin/mysqld: unknown option '--explicit_defaults_for_timestamp'
140818 10:17:17 [ERROR] Aborting

140818 10:17:17  InnoDB: Starting shutdown...
140818 10:17:18  InnoDB: Shutdown completed; log sequence number 1595675
140818 10:17:18 [Note]

However I cannot find in which script the --explicit_defaults_for_timestamp option is set. I tried to start mysql without service to avoid the --explicit_defaults_for_timestamp option but it still won't start:

$ ps aux | grep mysql
dotanco+ 25458  0.0  0.0  11748   928 pts/4    S+   10:30   0:00 grep --color=auto mysql

$ sudo mysqld_safe --skip-grant-tables &
[1] 25470
140818 10:30:54 mysqld_safe Can't log to error log and syslog at the same time.  Remove all --log-error configuration options for --syslog to take effect.
140818 10:30:54 mysqld_safe Logging to '/var/log/mysql/error.log'.
140818 10:30:54 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
140818 10:30:57 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended

[1]+  Done                    sudo mysqld_safe --skip-grant-tables

$ ps aux | grep mysql
dotanco+ 25810  0.0  0.0  11748   932 pts/4    S+   10:31   0:00 grep --color=auto mysql

The error tells me to Remove all --log-error configuration options. I therefore edited /etc/mysql/my.cnf and commented out the following line:

log-error  = /var/log/mysql/error.log

Now I get no error but still cannot log in:

$ sudo mysqld_safe --skip-grant-tables &
[1] 26558
140818 10:34:37 mysqld_safe Logging to syslog.
140818 10:34:38 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
140818 10:34:40 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended

[1]+  Done                    sudo mysqld_safe --skip-grant-tables

$ mysql -uroot
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

What might be the issue? How should I proceed?

EDIT

I've now commented out the explicit-defaults-for-timestamp line in my.cnf. Here is the entire file, minus header comments:

$ cat /etc/mysql/my.cnf 

[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

[mysqld_safe]
pid-file        = /var/run/mysqld/mysqld.pid
socket          = /var/run/mysqld/mysqld.sock
nice            = 0

[mysqld]
user            = mysql
pid-file        = /var/run/mysqld/mysqld.pid
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /var/lib/mysql
tmpdir          = /tmp
lc-messages-dir = /usr/share/mysql
#explicit_defaults_for_timestamp

bind-address    = 127.0.0.1

#log-error      = /var/log/mysql/error.log

sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES

symbolic-links=0

!includedir /etc/mysql/conf.d/

This is what happens when I try to run MySQL:

$ sudo echo 1 >> /var/log/mysql/error.log

$ tail /var/log/mysql/error.log 
140818 10:31:49  InnoDB: Waiting for the background threads to start
140818 10:31:50 InnoDB: 5.5.38 started; log sequence number 1595675
140818 10:31:50 [ERROR] /usr/sbin/mysqld: unknown option '--explicit_defaults_for_timestamp'
140818 10:31:50 [ERROR] Aborting

140818 10:31:50  InnoDB: Starting shutdown...
140818 10:31:51  InnoDB: Shutdown completed; log sequence number 1595675
140818 10:31:51 [Note] 
140818 10:31:51 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
1

$ sudo service mysql start
start: Job failed to start

$ tail /var/log/mysql/error.log 
140818 10:31:49  InnoDB: Waiting for the background threads to start
140818 10:31:50 InnoDB: 5.5.38 started; log sequence number 1595675
140818 10:31:50 [ERROR] /usr/sbin/mysqld: unknown option '--explicit_defaults_for_timestamp'
140818 10:31:50 [ERROR] Aborting

140818 10:31:50  InnoDB: Starting shutdown...
140818 10:31:51  InnoDB: Shutdown completed; log sequence number 1595675
140818 10:31:51 [Note] 
140818 10:31:51 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
1

$ grep explicit_defaults_for_timestamp /etc/mysql/my.cnf /etc/init.d/mysql /etc/default/mysql
/etc/mysql/my.cnf:#explicit_defaults_for_timestamp
grep: /etc/default/mysql: No such file or directory

As can be seen, nothing new is written to the logs, and the explicit_defaults_for_timestamp option is not set anywhere.

I was able to reinstall mysql-server-core-5.5 but that did not resolve the issue:

$ sudo aptitude reinstall mysql-server-core-5.5
The following packages will be REINSTALLED:
  mysql-server-core-5.5 
0 packages upgraded, 0 newly installed, 1 reinstalled, 0 to remove and 0 not upgraded.
Need to get 3,213 kB of archives. After unpacking 0 B will be used.
Get: 1 http://il.archive.ubuntu.com/ubuntu/ trusty-updates/main mysql-server-core-5.5 amd64 5.5.38-0ubuntu0.14.04.1 [3,213 kB]
Fetched 3,213 kB in 1s (3,163 kB/s)                
(Reading database ... 217167 files and directories currently installed.)
Preparing to unpack .../mysql-server-core-5.5_5.5.38-0ubuntu0.14.04.1_amd64.deb ...
Unpacking mysql-server-core-5.5 (5.5.38-0ubuntu0.14.04.1) over (5.5.38-0ubuntu0.14.04.1) ...
Replaced by files in installed package mysql-common (5.6.20-1ubuntu14.04) ...
Processing triggers for man-db (2.6.7.1-1) ...
Setting up mysql-server-core-5.5 (5.5.38-0ubuntu0.14.04.1) ...

$ sudo service mysql status
mysql stop/waiting

$ sudo service mysql start
start: Job failed to start

$ tail /var/log/mysql/error.log 
140818 10:31:49  InnoDB: Waiting for the background threads to start
140818 10:31:50 InnoDB: 5.5.38 started; log sequence number 1595675
140818 10:31:50 [ERROR] /usr/sbin/mysqld: unknown option '--explicit_defaults_for_timestamp'
140818 10:31:50 [ERROR] Aborting

140818 10:31:50  InnoDB: Starting shutdown...
140818 10:31:51  InnoDB: Shutdown completed; log sequence number 1595675
140818 10:31:51 [Note] 
140818 10:31:51 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
1

That 1 on the last line of the log was added earlier with echo, and indicates that nothing new was added to the log.

Best Answer

You installed mysql-server-core-5.6, which partially failed or partially installed.

The -explicit_defaults_for_timestamp is only for MySQL 5.6. Its probable that the partial installation of mysql-server-core-5.6 added this option. I am going to suggest now that you remove any trace of mysql-server-core-5.6 and reinitialize the data directory.

kill any running mysqld processes:
```
ps aux | grep mysql
kill pid
```
Uninstall the mysql-server-core-5.6 packages:
```
apt-get remove mysql-server-core-5.6
```
A list of files is here
Reinitialize the database directory:

A. rm -Rf /var/lib/mysql/*

B. mysql_install_db /var/lib/mysql
Comment out the !includedir /etc/mysql/conf.d/ option in my.cnf

Kill any existing MySQL Process and then start MySQL using the skip-grant-tables option.

A. Get the exact path of the mysqld daemon:

which mysqld_safe

B. Run MySQL without grant tables:

/mysqld_safe_directory/mysqld_safe --skip-grant-tables &
ex /bin/mysqld_safe

C. Make sure mysql is listening:

netstat -tlpn

you should see port 3306.

D. If so, log into MySQL:

mysql -u root -h 127.0.0.1

E. Set new password:

mysql> use mysql;
mysql> update user set password=PASSWORD("NEW-ROOT-PASSWORD") where User='root';
mysql> flush privileges;
mysql> quit

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The two answers given from @RickJames and @drogart are essentially the remedies. (+1 for each).

Right from the error log you present, the last two lines say:

InnoDB: Error: log file ./ib_logfile0 is of different size 0 134217728 bytes

InnoDB: than specified in the .cnf file 0 268435456 bytes! `

At that point, it was evident that you set innodb_log_file_size to 256M (268435456) in my.cnf while the InnoDB Transaction Logs (ib_logfile0,ib_logfile1) were respectively 128M (134217728) each. Looking back at the link to my StackOverflow answer in your question, you had to do the following:

Step 01) Add this to my.cnf:

[mysqld]
innodb_buffer_pool_size=4G
innodb_log_file_size=1G

Step 02) Run these command in the OS

mysql -u... -p... -e"SET GLOBAL innodb_fast_shutdown = 1"
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Your management configuration seems fine to me. It sounds like ndb_mgmd didn't quite die or there is a problem with the contents in the /var/lib/mysql-cluster directory on the management server.

You might also want to make sure that ndb_mgmd isn't starting automatically, like through some startup script in /etc/init.d/.

To try and resolve the issue, I'd start with these steps first.

Since you are just getting started and don't have any real data yet.

Kill any left over ndb_mgmd processes with: killall ndb_mgmd or by rebooting if killall doesn't help.
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Start the cluster process again: ndb_mgmd -f /etc/config.ini --initial
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$> netstat -tlpn

Active Internet connections (only servers) Proto Recv-Q Send-Q Local Address Foreign Address State PID/Program name
tcp 0 0 0.0.0.0:1186 0.0.0.0:* LISTEN 3251/ndb_mgmd

Connect to management node

$> ndb_mgm
ndb_mgm> show
Connected to Management Server at: localhost:1186
Cluster Configuration


[ndb_mgmd(MGM)] 1 node(s)
id=1    @192.168.9.26  (mysql-5.1.61 ndb-7.1.22)

Update

Here is a Quick Start guide from Oracle with all nodes, management, mysql and data running on one server.

http://downloads.mysql.com/tutorials/cluster/GetMySQLClusterRunning-LINUX.pdf

Best Answer

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