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I've changed my.ini with port=3308 but after restart the service mysql 5.6 is working in the same default port 3306.

I've tried in mysql 5.5 and it worked fine.

C:\Archivos de programa\MySQL\MySQL Server 5.6


# For advice on how to change settings please see
# *** DO NOT EDIT THIS FILE. It's a template which will be copied to the
# *** default location during install, and will be replaced if you
# *** upgrade to a newer version of MySQL.


# Remove leading # and set to the amount of RAM for the most important data
# cache in MySQL. Start at 70% of total RAM for dedicated server, else 10%.
# innodb_buffer_pool_size = 128M

# Remove leading # to turn on a very important data integrity option: logging
# changes to the binary log between backups.
# log_bin

# These are commonly set, remove the # and set as required.
# basedir = .....
# datadir = .....
port = 3309
# server_id = .....

What am I missing? Is there any bug?

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No, that should basically work. Is there any information in the server log? – Felix Frank Jun 17 '14 at 13:05
I think I found the problem, the path in mysql 5.6 is not that. It is using the path where the data is stored intead of where mysql is installed. :s. This must be new on this version of mysql – Joe Jun 17 '14 at 13:15

MySQL 5.6 my.ini file is in the path where the data is stored, in my case

C:\Documents and Settings\All Users\Datos de programa\MySQL\MySQL Server 5.6 

instead of the path where mysql is install

C:\Archivos de programa\MySQL\MySQL Server 5.6

, like older versions.

We have to change C:\Documents and Settings\All Users\Datos de programa\MySQL\MySQL Server 5.6 \my.ini file to the changes take effect, and restart the service.

On Windows, MySQL programs read startup options from the following files, in the specified order

enter image description here

More info Using options files

You can see configuration options through the following command and look up 'Default options' to see the paths where configuration .ini and .cnf are.

> mysqld --verbose --help

And with this other command you can see mysql variables

> mysqladmin variables
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