http://arxiv.org/ftp/arxiv/papers/1202/1202.5260.pdf
We did an experiment like this a while back, see the paper.
If you look at figure 2, you'll see the fancy force gauge set up with the red rope and wooden handle.
To eliminate extra knots (other than the one being tested), one wraps the line around the wooden handle several times and secures it to the wooden handle with tape. The combination of friction from the wrapping and the tape secure the line without weakening it any with the tape. This is the best way to be sure only the strength of a single knot (or no knot at all) is being tested.