C++ code generated by Matlab coder too slow

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I have an algorithm written in matlab, which detects some artefatcs in blood pulsewave. These algorithm is converted to C++ by maltab coder and I use these C++ files in my C# SW. It works fine.
But, I use several FIRs in my code, one of them is 10000 order FIR. The signal length is around 1M samples, so it take too much time to count it with filter(...) function or conv(..) function. I have tried to count the FIR with convolution theorem, I have used this:
fftLen = 2^nextpow2(length(values));
filteredValues = ifft(fft(values,fftLen).*fft(coefs,fftLen));
It works more then 30x faster in matlab. But if I convert the code to C++ by matlab Coder, it is not so fast. It is more then 10x slower than the matlab version. I use matlab 2017b. Why?
Walter Roberson
Walter Roberson on 13 Feb 2019
Multithreaded was added in R2007a according to Loren's blog of March 1, 2007.

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Accepted Answer

Ryan Livingston
Ryan Livingston on 13 Feb 2019
Edited: Ryan Livingston on 13 Feb 2019
If the bottleneck in the generated code is in fft or other MATLAB builtin functions, I'd suggest taking a look at this answer:
In short, those functions use highly optimized libraries in MATLAB as Walter mentioned and also for computing FFTs. The default generated code may be less optimized in favor of portability.
The answer describes that as of R2017b you can instruct MATLAB Coder and Simulink Coder to generate calls to FFTW to improve FFT performance:
There are similar capabilities to generate calls to BLAS and LAPACK for matrix operations and linear algebra:
Note: When generating C++ code that calls FFTW there is a bug in R2017b that was fixed in R2017b_update5:
So if you would like to use FFTW with Coder and generate C++ in R2017b, I'd suggest installing that update.

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