Build CTF, provide include and lib path to config.mk and run make.
Easiest way to do above is to install CTF with ./configure --no-dynamic && make install globally with sudo make install, but local build would also work fine.
To test with default parameters, just run ./jaccard or mpirun -np 4 ./jaccard.
To run, use e.g. ./jaccard -m 4000 -n 100 -p .01 -nbatch 10, which would generate a 4000-by-100 k-mer bit matrix with 1% nonzeros, then compute a 100-by-100 similarity matrix by accumulating batches of 400 rows at a time.