First do:
gSystem->Load(“libGraf”);
If you link a standalone executable, see, for example, [url]Compiling Root script with g++
Just put:
LDLIBS=-lRootFftwWrapper -lfftw3 root-config --glibs
BTW. I assume you know that ROOT has a MATH FFTW module based on the TVirtualFFT class. Try “root-config --features” and see if the output contains “fftw3”, or try “root-config --has-fftw3” and see if you get “yes”. See also: ROOT Tutorials: Fast Fourier Transforms.