how rank is calculated in GATE?

No semester marks have no impact in the evaluation of Gate rank. Your Gate rank is calculated from your Gate exam marks. For understanding this ,I think you should be clear about three terms :  Gate Rank, Gate Score and Gate Percentile.
Gate Marks
Calculated in the same way as marks of any other exam is calculated. In case of GATE you are given +1 or +2 for every correct answer, - 1/3 or -2/3 on every wrong answer and 0 marks for no attempt. (Marking  depends on type of questions and maximum marks of the question). Gate marks are calculated out of 100 and it may even be negative if you have wrongly answered most of the questions.

Gate Rank
GATE Rank also called as AIR or All India Rank tells how far are you from top in a particular year and in a particular subject. Every GATE Qualified Candidate is given a GATE Rank. Its an integer number which tells your position in the exam and paper for the year in which you have given the exam. Example AIR-30 in CS-15 means you are at the 30th position from top in Computer Science GATE Exam conducted in year 2015.

http://www.youth4work/rank