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Could not connect to mysql using Mysql WorkBench 5.2 CE (no replies)

Hi all,
I was able to connect to MYSQL server on Linux using MYSQL Workbench but suddenlty it stopped working and don't know how to fix - Need your help.
Here is the message that I got when I tried to connect to MYSQL
SQL Running issue
1) Check if mysql is running
Yes, MySQL is up and running. I was able to login to this server using this command:
mysql -u root -p

2) Make sure MYSQL running on port 3306
I updated the /etc/my.cnf to has port=3306 and then restart mysql but when i ran the command below
netstat -tln | grep 3306
tcp 0 0 0.0.0.0:3306 0.0.0.0:* LISTEN

So don't know why MySQL didn't use port 3306 and couldn't connect to mysql server using workbench. Would you please help to see what I have missed for MYSQL setting that gave me this connection problem

3) Check the root as rights to connect to server
already check and root has permission

4) Make sure you are both providing a password if needed and using the correct password for server connecting
from the host address you're connecting from
Should be ok

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