Mex file still too slow

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Alice Malvaldi
Alice Malvaldi 2015-2-11
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!
  4 个评论
显示 2更早的评论
dpb
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
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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回答（1 个）

Rick Rosson
Rick Rosson 2015-2-11
Please try:
cfg.DynamicMemoryAllocation = 'off';
Also:
cfg.IntegrityChecks = false;
cfg.ResponsivenessChecks = false;
  2 个评论
Alice Malvaldi
Alice Malvaldi 2015-2-12
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!

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