Gypsum is added to clinker during cement manufacture to 

During the manufacture of cement, towards the final process of grinding, to cool the clinker generally a small amount of gypsum is added to it. As a result, it controls the setting of the cement, that is, the cement is nicely settled down on addition of gypsum. Thus, gypsum decreases the rate of setting to avoid mixing of cement with water completely without giving a proper consistency.