Mex file still too slow

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Alice Malvaldi 2015-2-11

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/177474-mex-file-still-too-slow

评论： Seyedmohammadhadi Sadati 2021-9-2

I have created a mex file for my matlab functions as follow:

% Create a MEX configuration object
cfg = coder.config('mex');
% Turn on dynamic memory allocation
cfg.DynamicMemoryAllocation = 'AllVariableSizeArrays';
% Generate MEX function
codegen -config cfg MYfunction -args {Data,Mask}
tic
result = MYfunction_mex(Data,Mask);
toc

But it is still too slow for what I want to do:

    telapsed = 2262.62 sec  % normal Matlab function
    telapsed =  670.64 sec % mex function

It is an improvement but I was expecting much higher speed up as this is running not the complete for loop I would need. The 3rd for loop is running from 1:50 instead 8760, so it would take more than 1 day to run the entire code! I know that there are certainly many ways to speed it up but I can't see them.

As "MYfunction" is about my research I cannot share the code but the basic things are:

for l = 1:4                      
      for n = 1:24
          for i = 1:50     % i shoudl go till 8760  
              INDEXvector = DataSelectionINDEX(inputs);    % function that create an array of indices to select specific data of MyData.mat file
              X = MyData(INDEXvector(:),:);
              % Covariance matrix
              [R,P] = CalcCOVARIANCEmatrix(X);   % function that calculates the covariance matrix
              %  do other minor calculations  %
              Result = "from previous calculations";
          end;
      end;
  end;

I know that the function that is more time consuming is the one in which the cross-correlations of my data are computed. But I don't understand why it is still so slow and how can I further speed it up. Thank you!

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dpb 2015-2-12

"...I cannot share much more about my code and I thing that the key things are there."

Well, I guess that's research... :) Good luck.

Ryan Livingston 2015-2-23

It is hard to tell from the example code snippet but if your code lends itself to parallelism, you could consider using PARFOR if the loop iterations are independent.

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Answer 1

Rick Rosson 2015-2-11

3
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/177474-mex-file-still-too-slow#answer_167716

在 MATLAB Online 中打开

Please try:

cfg.DynamicMemoryAllocation = 'off';

Also:

   cfg.IntegrityChecks = false;
   cfg.ResponsivenessChecks = false;

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Alice Malvaldi 2015-2-12

在 MATLAB Online 中打开

Thank you very much!

I tried it and it's better, even though I had to use

cfg.DynamicMemoryAllocation = 'Threshold';

instead of

cfg.DynamicMemoryAllocation = 'off';

because otherwise I had this error: "Computed maximum size exceeds maximum allowed number of elements etc...".

Many thanks!

Seyedmohammadhadi Sadati 2021-9-2

Thanks.

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