FFTW vs Matlab FFT

Question

I posted this on matlab central but didn't get any responses so I figured I'd repost here.

I recently wrote a simple routine in Matlab that uses an FFT in a for-loop; the FFT dominates the calculations. I wrote the same routine in mex just for experimentation purposes and it calls the FFTW 3.3 library. It turns out that the matlab routine runs faster than the mex routine for very large arrays (about twice as fast). The mex routine uses wisdom and and performs the same FFT calculations. I also know matlab uses FFTW, but is it possible their version is slightly more optimized? I even used the FFTW_EXHAUSTIVE flag and its still about twice as slow for large arrays than the MATLAB counterpart. Furthermore I ensured the matlab I used was single threaded with the "-singleCompThread" flag and the mex file I used was not in debug mode. Just curious if this was the case - or if there are some optimizations matlab is using under the hood that I dont know about. Thanks.

Here's the mex portion:

void class_cg_toeplitz::analysis() { // This method computes CG iterations using FFTs     // Check for wisdom     if(fftw_import_wisdom_from_filename("cd.wis") == 0) {         mexPrintf("wisdom not loaded.\n");     } else {         mexPrintf("wisdom loaded.\n");     }      // Set FFTW Plan - use interleaved FFTW     fftw_plan plan_forward_d_buffer;         fftw_plan plan_forward_A_vec;            fftw_plan plan_backward_Ad_buffer;     fftw_complex *A_vec_fft;     fftw_complex *d_buffer_fft;     A_vec_fft = fftw_alloc_complex(n);     d_buffer_fft = fftw_alloc_complex(n);      // CREATE MASTER PLAN - Do this on an empty vector as creating a plane      // with FFTW_MEASURE will erase the contents;      // Use d_buffer     // This is somewhat dangerous because Ad_buffer is a vector; but it does not     // get resized so &Ad_buffer[0] should work     plan_forward_d_buffer = fftw_plan_dft_r2c_1d(d_buffer.size(),&d_buffer[0],d_buffer_fft,FFTW_EXHAUSTIVE);     plan_forward_A_vec = fftw_plan_dft_r2c_1d(A_vec.height,A_vec.value,A_vec_fft,FFTW_WISDOM_ONLY);     // A_vec_fft.*d_buffer_fft will overwrite d_buffer_fft     plan_backward_Ad_buffer = fftw_plan_dft_c2r_1d(Ad_buffer.size(),d_buffer_fft,&Ad_buffer[0],FFTW_EXHAUSTIVE);      // Get A_vec_fft     fftw_execute(plan_forward_A_vec);      // Find initial direction - this is the initial residual     for (int i=0;i<n;i++) {         d_buffer[i] = b.value[i];         r_buffer[i] = b.value[i];     }          // Start CG iterations     norm_ro = norm(r_buffer);     double fft_reduction = (double)Ad_buffer.size(); // Must divide by size of vector because inverse FFT does not do this     while (norm(r_buffer)/norm_ro > relativeresidual_cutoff) {                 // Find Ad - use fft         fftw_execute(plan_forward_d_buffer);             // Get A_vec_fft.*fft(d) - A_vec_fft is only real, but d_buffer_fft         // has complex elements; Overwrite d_buffer_fft                 for (int i=0;i<n;i++) {             d_buffer_fft[i][0] = d_buffer_fft[i][0]*A_vec_fft[i][0]/fft_reduction;             d_buffer_fft[i][1] = d_buffer_fft[i][1]*A_vec_fft[i][0]/fft_reduction;         }                 fftw_execute(plan_backward_Ad_buffer);           // Calculate r'*r         rtr_buffer = 0;         for (int i=0;i<n;i++) {             rtr_buffer = rtr_buffer + r_buffer[i]*r_buffer[i];         }              // Calculate alpha         alpha = 0;         for (int i=0;i<n;i++) {             alpha = alpha + d_buffer[i]*Ad_buffer[i];         }             alpha = rtr_buffer/alpha;          // Calculate new x         for (int i=0;i<n;i++) {             x[i] = x[i] + alpha*d_buffer[i];         }             // Calculate new residual         for (int i=0;i<n;i++) {             r_buffer[i] = r_buffer[i] - alpha*Ad_buffer[i];         }             // Calculate beta         beta = 0;         for (int i=0;i<n;i++) {             beta = beta + r_buffer[i]*r_buffer[i];         }           beta = beta/rtr_buffer;          // Calculate new direction vector         for (int i=0;i<n;i++) {             d_buffer[i] = r_buffer[i] + beta*d_buffer[i];         }            *total_counter = *total_counter+1;         if(*total_counter >= iteration_cutoff) {             // Set total_counter to -1, this indicates failure             *total_counter = -1;             break;         }     }      // Store Wisdom     fftw_export_wisdom_to_filename("cd.wis");      // Free fft alloc'd memory and plans     fftw_destroy_plan(plan_forward_d_buffer);     fftw_destroy_plan(plan_forward_A_vec);     fftw_destroy_plan(plan_backward_Ad_buffer);     fftw_free(A_vec_fft);     fftw_free(d_buffer_fft); }; 

Here's the matlab portion:

% Take FFT of A_vec. A_vec_fft = fft(A_vec); % Take fft once  % Find initial direction - this is the initial residual  x = zeros(n,1); % search direction r = zeros(n,1); % residual d = zeros(n+(n-2),1); % search direction; pad to allow FFT for i = 1:n     d(i) = b(i);      r(i) = b(i);  end  % Enter CG iterations total_counter = 0; rtr_buffer = 0; alpha = 0; beta = 0; Ad_buffer = zeros(n+(n-2),1); % This holds the product of A*d - calculate this once per iteration and using FFT; only 1:n is used norm_ro = norm(r);  while(norm(r)/norm_ro > 10^-6)     % Find Ad - use fft     Ad_buffer = ifft(A_vec_fft.*fft(d));       % Calculate rtr_buffer     rtr_buffer = r'*r;      % Calculate alpha         alpha = rtr_buffer/(d(1:n)'*Ad_buffer(1:n));      % Calculate new x     x = x + alpha*d(1:n);      % Calculate new residual     r = r - alpha*Ad_buffer(1:n);      % Calculate beta     beta = r'*r/(rtr_buffer);      % Calculate new direction vector     d(1:n) = r + beta*d(1:n);            % Update counter     total_counter = total_counter+1;  end 

In terms of time, for N = 50000 and b = 1:n it takes about 10.5 seconds with mex and 4.4 seconds with matlab. I'm using R2011b. Thanks

Answer 1

A few observations rather than a definite answer since I do not know any of the specifics of the MATLAB FFT implementation:

• Based on the code you have, I can see two explanations for the speed difference:
  • the speed difference is explained by differences in levels of optimization of the FFT
  • the while loop in MATLAB is executed a significantly smaller number of times

I will assume you already looked into the second issue and that the number of iterations are comparable. (If they aren't, this is most likely to some accuracy issues and worth further investigations.)

Now, regarding FFT speed comparison:

• Yes, the theory is that FFTW is faster than other high-level FFT implementations but it is only relevant as long as you compare apples to apples: here you are comparing implementations at a level further down, at the assembly level, where not only the selection of the algorithm but its actual optimization for a specific processor and by software developers with varying skills comes at play
• I have optimized or reviewed optimized FFTs in assembly on many processors over the year (I was in the benchmarking industry) and great algorithms are only part of the story. There are considerations that are very specific to the architecture you are coding for (accounting for latencies, scheduling of instructions, optimization of register usage, arrangement of data in memory, accounting for branch taken/not taken latencies, etc.) and that make differences as important as the selection of the algorithm.
• With N=500000, we are also talking about large memory buffers: yet another door for more optimizations that can quickly get pretty specific to the platform you run your code on: how well you manage to avoid cache misses won't be dictated by the algorithm so much as by how the data flow and what optimizations a software developer may have used to bring data in and out of memory efficiently.
• Though I do not know the details of the MATLAB FFT implementation, I am pretty sure that an army of DSP engineers has been (and is still) honing on its optimization as it is key to so many designs. This could very well mean that MATLAB had the right combination of developers to produce a much faster FFT.