on godaddy hosting i have following structure

/var/chroot/home/content/xx/xxxxxxx/html/website/master(Master site)
/var/chroot/home/content/xx/xxxxxxx/html/website/slave/public(Slave site)

Default primary domain maps to html directory on godaddy /var/chroot/home/content/xx/xxxxxxx/html/


Now, how do i map the primary domain to the slave site directory?

i.e, when www.myDomain.com is typed, it should go to the slave site(/var/chroot/home/content/xx/xxxxxxx/html/website/slave/public)

I have tried using alias(/var/chroot/home/content/xx/xxxxxxx/html/) but, i'm getting error as path in use already.

You can not use an "alias" because the "html" directory can not be replaced by a symbolic link.
In godaddy (shared hosting), you have no choice to put all the websites in a subdirectory of html.
A potential solution that I didn't experiment would be to add a .htaccess in your html directory and setup a "rewritebase" with the directory of your slave site that contain your website.

I would test the following thing
Create a .htacces that contain

Options +FollowSymLinks
RewriteEngine On
RewriteBase /website/slave/public/

Becarefull that if you put a .htaccess in the /html directory, it is probable that it will also be used by the subdirectories. So you may also need to create .htacces in the subdirectories to "discard" the special RewriteBase parameter.