How do I know which configuration file is used by MySQL currently? Is there any command or something to find it out?
You should find them by default in a folder like /etc/my.cnf, maybe also depends on versions. From MySQL Configuration File:
Interestingly, the scope of this file can be set according to its location. The settings will be considered global to all MySQL servers if stored in /etc/my.cnf. It will be global to a specific server if located in the directory where the MySQL databases are stored (/usr/local/mysql/data for a binary installation, or /usr/local/var for a source installation). Finally, its scope could be limited to a specific user if located in the home directory of the MySQL user (~/.my.cnf). Keep in mind that even if MySQL does locate a my.cnf file in /etc/my.cnf (global to all MySQL servers on that machine), it will continue its search for a server-specific file, and then a user-specific file. You can think of the final configuration settings as being the result of the /etc/my.cnf, mysql-data-dir/my.cnf, and ~/.my.cnf files.
There are a few switches to package managers to list specific files.
RPM Sytems:
There are switches to rpm command, -q for query, and -c or --configfiles to list config files. There is also -l or --list
The --configfiles one didn't quiet work for me, but --list did list a few .cnf files held by mysql-server
rpm -q --list mysql-server
DEB Systems:
Also with limited success: dpkg --listfiles mysql-server