Configure SSH Library

Not sure what you mean, CI can use the CLI by executing "php -q /path/to/index.php controller method". Like "php -q /home/user/public_html/index.php blog view" to execute the blog controller/view method.
http://www.codeigniter.com/userguide2/general/cli.html

Just remember that $_SERVER variables are set by the webserver, so if you are using CLI $_SERVER won't be present since it doesn't use the webserver and just executes php from the CLI.  So if your app uses the $_SERVER superglobal, your app probably won't work via the CLI. Also things like sessions won't work using the CLI since there's no way to store and read cookies since there's no web browser involved.

Dear CroNix,

I want to access linux server via SSH. and execute the commands from  Web Application