If you use fftMPI in one of your publications, please reference the URL of the fftMPI website, namely http://fftmpi.sandia.gov.
At some point we may write a new paper about fftMPI, in which case we will post a citation here.
This is an older paper which includes a discussion of the basic algorithms used in our original Parallel FFT Package, which are also still used in fftMPI:
Particle-Mesh Ewald and rRESPA for Parallel Molecular Dynamics Simulations, S. J. Plimpton, R. Pollock, M. Stevens, in Proc of the Eighth SIAM Conference on Parallel Processing for Scientific Computing, Minneapolis, MN, March 1997.