Asked by Theron FARRELL
on 28 May 2019

Hi there,

Here goes a piece of testing code, yet arrayfun runs more slowly. Any thoughts? Many thanks.

function Test_GPU1()

EP = gpuArray(eps*ones(10000, 1, 'single'));

ONE = gpuArray(ones(10000, 1, 'single'));

ZERO = gpuArray(zeros(10000, 1, 'single'));

Cur_FF_Output = gpuArray(0.5*ones(10000, 1, 'single'));

Cur_Desired_Output = gpuArray(0.5*ones(10000, 1, 'single'));

for iter = 1:1000

% In output layer, Cur_Delta = Del(C)/Del(z) = Del(C)/Del(a) * Del(a)/Del(z)

% [~, Cur_Delta0] = Cost_Function_GPU(Cur_FF_Output, Cur_Desired_Output, Hyper_Para);

temp00 = Cur_FF_Output + eps;

temp11 = log(temp00);

temp22 = log(1-Cur_FF_Output+eps);

temp33 = Cur_Desired_Output.*temp11;

temp44 = 1-Cur_FF_Output.*temp22;

Cur_Delta = Cur_FF_Output-Cur_Desired_Output;

Cost = 0-sum(temp33+temp44);

temp00 = arrayfun(@plus, Cur_FF_Output, EP);

temp11 = arrayfun(@log, temp00);

temp22 = arrayfun(@log, arrayfun(@minus, ONE, arrayfun(@plus, Cur_FF_Output, EP)));

temp33 = arrayfun(@times, Cur_Desired_Output, temp11);

temp44 = arrayfun(@minus, ONE, arrayfun(@times, Cur_FF_Output, temp22));

Cur_Delta = arrayfun(@minus, Cur_FF_Output, Cur_Desired_Output);

Cost = arrayfun(@minus, ZERO, sum(temp33+temp44));

end

end

Answer by Joss Knight
on 28 May 2019

Accepted Answer

You are misunderstanding the use of arrayfun for gpuArray. Combine all those operations into a single function.

temp00 = arrayfun(@plus, Cur_FF_Output, EP);

temp11 = arrayfun(@log, temp00);

temp22 = arrayfun(@log, arrayfun(@minus, ONE, arrayfun(@plus, Cur_FF_Output, EP)));

temp33 = arrayfun(@times, Cur_Desired_Output, temp11);

temp44 = arrayfun(@minus, ONE, arrayfun(@times, Cur_FF_Output, temp22));

Cur_Delta = arrayfun(@minus, Cur_FF_Output, Cur_Desired_Output);

Cost = arrayfun(@minus, ZERO, sum(temp33+temp44));

becomes

function Cur_Delta = stuff(Cur_FF_Output, Cur_Desired_Output, EP)

temp00 = Cur_FF_Output + EP;

temp11 = log(temp00);

temp22 = log(1 - (Cur_FF_Output + EP));

temp33 = Cur_Desired_Output .* temp11;

temp44 = 1 - (Cur_FF_Output .* temp22);

Cur_Delta = Cur_FF_Output - Cur_Desired_Output;

end

Cur_Delta = arrayfun(@stuff, Cur_FF_Output, Cur_Desired_Output, EP);

Obviously, this can be extremely simplified. I've made a start, by removing the unnecessary ONE and ZERO variables.

After this, question whether you really need arrayfun, or should just call this function directly? MATLAB uses some clever optimisations that, for most sequences of element-wise operations, make using arrayfun unnecessary.

Theron FARRELL
on 1 Jun 2019

I see. 'If you know what you're doing', 'At fast as', and 'no fun' are the key phrases, as I sense. *_^

To be candid, MATLAB, being the de facto most powerful, miraculous, as well as user-friendly scientific and technical SIMULATION and PROTOTYPING tool since 1984--I would not use the word computing here (let's forget MATLAB coder, embedded coder etc originally designed for auto industry at the moment), enjoys her AUTOMATIC optimisation without users' heavy involvement. One of the most typical examples is element-wise (vectorised) operations. That being said, my point is that a user should not take too many efforts on seeking THE most optimised code in lieu of concentrating on algorithmic designs and prototyping, which I do not think most users will do. Consequently, some notifications about pros and cons of using functions as well as PRACTICAL examples such as arrayfun() would be better to be given in the Help page, for example a more formal statement of your words above. Especially , in the advent of DNN, MATLAB would be better prepared for competing with loads of well-optimised, open-sourced code, tensorflow, theano, Caffe etc...

Joss Knight
on 1 Jun 2019

Theron FARRELL
on 3 Jun 2019

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Answer by Jan
on 28 May 2019

Edited by Jan
on 28 May 2019

Of course arrayfun has a certain overhead. It is expected to run slower than calling the operators directly with arrays as inputs. In addition, in

Cur_FF_Output + eps

the second operand is a scalar, while in

arrayfun(@plus, Cur_FF_Output, EP)

Matlab has to process a vector. Addressing the elements of an array needs to access memory using a loop. Accessing a scalar is much cheaper.

What is the purpose of:

arrayfun(@minus, ZERO, sum(temp33+temp44))

? This is faster:

-sum(temp33+temp44)

Joss Knight
on 29 May 2019

Theron FARRELL
on 30 May 2019

No, it is not a bug. Maybe somewhere I wrote the code mistakenly. My bad, sorry.

Jan
on 31 May 2019

Even arrayfun(@minus, 0, sum(temp33+temp44)) is too complicated compared to

-sum(temp33+temp44)

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