You aren't going to like the answer, but WEKA can't handle it. The implementation uses a full SVD no matter what. So if you have more than a few thousand data points, just doing the full SVD is going to take an enormous amount of time.
Not to mention that WEKA uses far more memory than needed in general.
Ontop of all that, Weka creates a dense matrix to do the SVD from. You are probably using it for sparse data, and thats going to destroy any hope you ever have of using Weka for LSA.
The fact is you are going to have to use something other than Weka to get LSA done.