Some times, it is diffcult to find the exact location of my.cnf file on linux,
using the following command we can find the diffault locations which are used by mysql server to locate its configuraton, by checking them one by one, we can locate the real my.cnf:
[ivar@fedora ~]$ sudo /usr/sbin/mysqld --verbose --help|grep -i -A 1 'Default Options'
2014-06-11 13:23:55 2617 [Note] Plugin 'FEDERATED' is disabled.
Default options are read from the following files in the given order:
/etc/my.cnf /etc/mysql/my.cnf /usr/etc/my.cnf ~/.my.cnf
--
--no-defaults Don't read default options from any option file,
except for login file.
--defaults-file=# Only read default options from the given file #.
--defaults-extra-file=# Read this file after the global files are read.
2014-06-11 13:23:56 2617 [Note] Binlog end
2014-06-11 13:23:56 2617 [Note] Shutting down plugin 'CSV'
2014-06-11 13:23:56 2617 [Note] Shutting down plugin 'MyISAM'