Numerical operations are slow on class properties versus in workspace

Question

Daniel Plotnick 2020-6-22

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编辑： per isakson 2020-6-26

Hello,

I ran into this behavior I don't really understand: simple numerical operations are order 10x+ slower on class properties than when performed in the workspace.

As an example, I will create a circular index that I want to increment by 1.

N = 2^16; % Number of times to increment
M = 2^8;  % What is our wrap point
I = 0;    % Initialize our index
t = tic;
clc
disp("Incrementing in workspace"); 
for n = 1:N
    I = mod(I+1,M); % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000); % 1000s of operations/second

Great, I am getting ~ 45,000 kOps/second.

Now, instead I will do this all in a class:

classdef speedTestClass < handle
    properties
        I = 0;
        M
    end
    
    methods
        function increment(obj)
             obj.I = mod(obj.I + 1,obj.M); % Increment, with wrapping
        end
    end
end

And then run it

ob = speedTestClass; % Make the object
ob.M = M;            % Set the wrap point
disp("Incrementing in class"); 
t = tic;
for n = 1:N
   ob.increment % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000);

Where I get 2400 kOps/second. A slowdown factor of 20x. Yikes.

So, is there a way to more efficiently perform simple operations on class properties? Is there some MEX magic working behind the scenes, and so I would need to MEX my classes?

I couldn't think of a simpler example than this basic index container; I could understand a factor of 2x speed loss, but 20x is huge, and it only gets worse when the computation is more involved and involves multiple methods/properties of the class.

I'll note that on a lark, I actually compiled this into an exe and ran it - the workspace version dropped to the speed of the class based one! Oh no.

Cheers all,

-Dan

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Matt J 2020-6-23

编辑：per isakson 2020-6-26

在 MATLAB Online 中打开

simple numerical operations are order 10x+ slower on class properties than when performed in the workspace.

The bottlenecks that you see are not indemic only to property accesses as the modified versions of your tests below will show (in R2019a). They appear to occur in method calls as well, with particularly bad performance for staitc methods.

classdef myclass < handle
    properties
        I = 0;
        M
    end
    
    methods
        function I=increment(obj,I,M)
             I = mod(I + 1,M); % Increment, with wrapping
        end
    end
    
    methods (Static)
        function  I=static_increment(I,M)
           I = mod(I + 1,M); % Increment, with wrapping
        end
    end
    
end

t = tic;
for n = 1:N
    I = mod(I+1,M); % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000); % 1000s of operations/second
ob = myclass; % Make the object
disp("Incrementing in method call"); 
t = tic;
for n = 1:N
   I=ob.increment(I,M); % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000);
disp("Incrementing in property access");
ob.I=I; ob.M=M;
t = tic;
for n = 1:N
  ob.I = mod(ob.I+1,ob.M); % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000);
disp("Incrementing in static method call");
t = tic;
for n = 1:N
  I = myclass.static_increment(I+1,M); % Increment, with wrapping
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000);

Incrementing in workspace
41935 kOps/second
Incrementing in method call
1746 kOps/second
Incrementing in property access
2758 kOps/second
Incrementing in static method call
 8 kOps/second

per isakson 2020-6-23

See Is MATLAB OOP slow or am I doing something wrong? at stackoverflow

Daniel Plotnick 2020-6-23

在 MATLAB Online 中打开

@per isakson - Wow, this is an extremely thorough analysis. I think the gist is

Yes, OOP is way slower than functional coding
No, I'm not doing something wrong and there is no current way around these speed issues.
It is unclear exactly what the bottleneck is, since closed source, but each type of access to a custom class object is going to incur some penalty.

@James Tursa - Thanks for the analysis. I continued working on it, and had planned to post the code/results here, but the Stackoverflow link has a set of benchmark code available that goes way further than I had considered.

I will note, that in the case of the buffers, the fastest solution I found was to only store the pointers and index retrieving methods for the FIFO/LIFO cases in a class; the actual buffer stays inside of the functional workspace. This reduces some of the class-based elegence I had hoped for, but bought me back a considerable speed factor.

pt = myPointer(N);
disp("Using a pointer")
t = tic;
buf = zeros(N,1);
for n = 1:N
    buf(pt.v + 1) = n;
    pt.increment;
end
fprintf("%2.0f kOps/second\n",N/toc(t)/1000);

with the pointer class

classdef myPointer < handle
    properties
        v  = 0;
        n
    end
    methods
        function obj = myPointer(n)
            obj.n = n;
        end
        
        function increment(obj)
            obj.v = mod(obj.v + 1,obj.n); 
        end
       
    end
end

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Answer 1

Matt J 2020-6-22

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/552916-numerical-operations-are-slow-on-class-properties-versus-in-workspace#answer_455605

编辑：Matt J 2020-6-22

在 MATLAB Online 中打开

It is the repeated M-coded function calls that are slowing you down. Implement the whole loop in a single function call:

        function increment(obj,N)
             M=obj.M;
             I=obj.I;
             
             for n = 1:N
                I = mod(I+1,M); % Increment, with wrapping
             end
             
             obj.I=I;
        end

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Daniel Plotnick 2020-6-22

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Thanks for the reply.

This is specifically looking at implementing this inside of a class' method, the increment is just a stand-in for the moment. As an example, consider making a buffer, where the parameter you are iterating is a pointer, and you want to return to the buffer on command:

classdef (Abstract) myBuffer < handle
    properties
        buffer  = NaN(1000,1)
        pointer = 1
    end
    methods (Abstract)
        function push(obj,v)
            
        end
        function pop(obj,n)
    end
    end
end
classdef LIFO < myBuffer
    methods
        function push(obj,v)
            obj.buffer((1:numel(v)) + obj.pointer) = v;
            obj.pointer = obj.pointer + numel(v);
        end
        function v = pop(obj,n)
            v = obj.buffer(obj.pointer:-1:obj.pointer - n)
            obj.pointer = obj.pointer - n
        end
    end
end
classdef FIFO < myBuffer
        % Write the FIFO 
end

In this example, I will be returning repeatedly to the buffer, but at arbirtary times. I used the above incrementing loop as a simpler stand in for this type of operation.

As in the incrementing loop, the push and pop operations on a preallocated buffer is MUCH faster when the buffer is in the workspace, as opposed to here in an object.

Note, I have not error checked the above buffers, but they should demonstrate one motivator for understanding where the speed bottleneck is.

Daniel Plotnick 2020-6-23

编辑：per isakson 2020-6-26

Thanks! After your initial answer, I spent some time playing with the internal structure of the class. I intentionally broke out the the increment method from the wrap/mod method. I suffered an additional 2x penalty for going into a seperate method, so it seems to me that I will suffer going into methods the same way I do going into individual m-files.

A lot of this practical excercise is to try to understand my speed penalties when taking advantage of classes and OOP versus straight function based algorithms. There are huge advantages to OOP and design pattern based coding...but at least in Matlab, based on your and Tursa's answers, there will be considerable speed penalties as a consequence of striving for the encapsulation and code maintenance advantages of OOP.

Based on Tursa's comments, it sounds like carefully MEXing the classes won't actually buy me anything. While Matlab is great for prototyping, if I want a fully class based code with high speed, I may need to go for refactoring my code into another language.

I was hoping someone had a workaround; Matlab is my go-to.

Do you know if there is any documentation on the performance penalties with going into m-files? I can't tell if it is memory access (like Tursa suggested would be an issue with MEX), or JIT, or what that causes this speed loss.

Matt J 2020-6-23

编辑：Matt J 2020-6-23

See my updated analysis above,

https://www.mathworks.com/matlabcentral/answers/552916-numerical-operations-are-slow-on-class-properties-versus-in-workspace#comment_909754

I now think you are seeing overhead from classdef's specifically, though not just from property access. I think the bottom line is one just needs to try to put loops inside functions and not the other way around. and/or to write loops that do lots of computation per iteration (esp. with vectorized commands) instead of really small and quick tasks. These were always best practices in writing efficient Matlab code, although I have to admit, I thought TMW had mananged to better optimize class operations over the years than what we're seeing now.

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