First Take backup of all your files and database

Then go to the exact directory where you have your wordpress installed and move the directories wp-admin and wp-includes

root@server# mv wp-admin wp-admin-bk

root@server# mv wp-includes wp-includes-bk

Download the latest wordpress in the zip format.

root@server# wget http://wordpress.org/latest.zip

Unzip it

root@server# unzip wordpress-x.x.x.zip

After this go to wordpress directory

root@server# cd wordpress

Move all the latest contents to the directory where you have installed wordpress

root@server# mv * ../

Here it will ask you to overwrite below files. just press y (y for yes)

mv: overwrite `../index.php'? y mv: overwrite `../license.txt'? y mv: overwrite `../readme.html'? y mv: overwrite `../wp-activate.php'? y mv: overwrite `../wp-app.php'? y mv: overwrite `../wp-atom.php'? y mv: overwrite `../wp-blog-header.php'? y mv: overwrite `../wp-comments-post.php'? y mv: overwrite `../wp-commentsrss2.php'? y mv: overwrite `../wp-config-sample.php'? y mv: overwrite `../wp-cron.php'? y mv: overwrite `../wp-feed.php'? y mv: overwrite `../wp-links-opml.php'? y mv: overwrite `../wp-load.php'? y mv: overwrite `../wp-login.php'? y mv: overwrite `../wp-mail.php'? y mv: overwrite `../wp-pass.php'? y mv: overwrite `../wp-rdf.php'? y mv: overwrite `../wp-register.php'? y mv: overwrite `../wp-rss2.php'? y mv: overwrite `../wp-rss.php'? y mv: overwrite `../wp-settings.php'? y mv: overwrite `../wp-signup.php'? y mv: overwrite `../wp-trackback.php'? y mv: overwrite `../xmlrpc.php'? y

exit from the wordpress directory

root@server# cd ../

Now change the ownership

root@server# chown username.username * -R

run

http://yourdomain.com/wp-admin/upgrade.php

Once the link is open , click on proceed and you will have your wordpress upgraded. Thats it.