If you installed MySQL 5.6 from the command line, the easiest way to find the temporary password is to go to the Linux command line do the following:
cd
cat `ls -la | grep mysql | grep secret | awk '{print $9}'` | awk '{print $18}'
This will quickly print the temporary password.
Try to login using that password
cd
OLDPASSFILE=`ls -la | grep mysql | grep secret | awk '{print $9}'`
PASSWORD=`cat ${OLDPASSFILE} | awk '{print $18}'
mysql -uroot -p${PASSWORD}
If the temporary password is no longer available, then you will have do the following:
NEWPASS="whateveriwant"
service mysql stop
service mysql start --skip-grant-tables
mysql -ANe"update mysql.user set password=PASSWORD('${NEWPASS}') where user='root'"
service mysql restart
Give it a Try !!!