FFTW (the library responsible for all of GraphEnt's FFTs) has a mechanism for saving to disk information about how best to perform the FFT for a given array. Because chances are that if you run GraphEnt once, you will probably run it again with the same grid, GraphEnt will save a file in your HOME directory containing this information. The name of the file is .FFTW_wisdom and I would suggest that you do not delete it after the end of each GraphEnt run. There is just one thing that you shouldn't do : do not copy the .FFTW_wisdom file between different computers (even of the same company). For more information why is that so, consult the FFTW manual.