Normally, the only change needed to build your application with MPI FFTW wrappers replacing original FFTW3 library is to add Intel MKL and the wrapper library at the link stage (see section "Linking Your Application with Intel® Math Kernel Library" in the Intel MKL User's Guide).
When you are recompiling your application, add subdirectory include\fftw to the search path for header files to avoid FFTW3 version conflicts.
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