This is not really a bioinformatics specific question, because the same method applies to any executable. I recommend you first search on serverfault.com or stackoverflow or google for general hints on how to track memory usage of a UNIX program over time, and then plot the values obtained with gnuplot or R. Here is one: http://stackoverflow.com/questions/131303/linux-how-to-measure-actual-memory-usage-of-an-application-or-process, http://www.cyberciti.biz/tips/howto-find-memory-used-by-program.html

https://www.google.com/search?q=tracking+memory+usage+of+program&ie=utf-8&oe=utf-8&aq=t#q=tracking+memory+usage+of+program&safe=off

You can see from the above post, that it is not at all as straight-forward as it seems. Closing, because the question is already answered in a better fashion than we can do here elsewhere.