There's no size limit -- for example, just today I had to convert a 50 MB comic book from ePub to azw3, and the run time for it (I just checked) is 32 seconds.
Is your computer lagging in anything else? If so, the problem may not be calibre.
You could try restarting calibre and seeing if it still lags.
Or else, the file may be broken in some way and calibre choked on it. Try submitting a bug report if nothing else works, at
http://calibre-ebook.com/bugs, and make sure to include/attach the job log and the input file.