knocking can only come from ... any moving components . yours a notebook/desktop?
What brand/ Still under warranty?

does it start up fast and gradually slow down in say 5-10 mins and continue to lag? If yes

Does CHKDSK come up with any file allocation problem? If no you can rule out HD issues

I suspect is a heat related issue.. maybe fan not working/heat sink related.. when was the last time your PC was serviced? It could be very dusty inside

hmm.. did you run chkdsk?
Goto file explorer right click on your hard disk assuming is c:
>Tools>Error Checking

Normally file allocation problems arise if PC was shut down abruptly.. there may be missing data

if is hard disk checking is ok and you still have the same slow speed, I suspect is really thermal issue... cpu fan not working properly ..
a hotter than normal cpu will cause lags... may be as simple as not plugging the cpu fan leads to the motherboard/bad contact..

depending on your HDD size may take >1 hr..

if I were you I'll just let it run and goto sleep ..