How do I make this function run faster?

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Apurva 2020-5-21

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https://ww2.mathworks.cn/matlabcentral/answers/529118-how-do-i-make-this-function-run-faster

评论： Apurva 2020-5-22

What this function does:

I have variables defined on a mesh. Given one of the variables (called 'fieldvar'), this function iterates over every cell of the mesh, iterates over every face of a cell, finds the neighbouring cell. Fetches data of that cell and interpolates to a required degree (given by 'order_new'). Finally, assigns one its faces to 'neigb' and returns it.

Problem:

This funtion is called many times and is unusably slow.

Function definition:

function neighb = neighbour2D(fieldvar)
% function neighb = neighbour2D(fieldvar)
% Purpose: Compute the neighbouring values of fieldvar for every cell commensurate to the order
% demanded. Return array equivalent to e.g. Ez(vmapP), i.e. values of the
% neighbouring cells as a flat array, where every cell contributes
% Nfp*Nfaces no. of entries. Here, the Nfp is acc. to order_new.
Globals2D;
neighb=zeros(length(vmapM),1);
count=0;
for k=1:K
    kself1=fI(k,1); kself2=fI(k,2);
    one=ones(1,Nfp(order_new(k)));
    fmask_local = Fmask{order_new(k)};
    for f=1:Nfaces
        % find neighbor
        kneigh = EToE(k,f); fneigh = EToF(k,f);
        knei1 = fI(kneigh,1); knei2 = fI(kneigh,2);
        val=interp{order_new(kneigh),order_new(k)}*fieldvar(knei1:knei2);
        val=val(fmask_local); val=val(:,fneigh);
    
        % reference length of edge
        v1 = EToV(k,f); v2 = EToV(k, 1+mod(f,Nfaces));
        refd = sqrt( (VX(v1)-VX(v2))^2 + (VY(v1)-VY(v2))^2 );
    
        % find volume node numbers of left and right nodes 
        xself = x(kself1:kself2); yself = y(kself1:kself2);
        xneig = x(knei1:knei2); yneig = y(knei1:knei2);
        x1=xself(fmask_local); x1=x1(:,f);
        x2=interp{order_new(kneigh),order_new(k)}*xneig;
        x2=x2(fmask_local); x2=x2(:,fneigh);
        y1=yself(fmask_local); y1=y1(:,f);
        y2=interp{order_new(kneigh),order_new(k)}*yneig;
        y2=y2(fmask_local); y2=y2(:,fneigh);
        x1=x1*one; x2=x2*one; y1=y1*one; y2=y2*one;
    
        % Compute distance matrix
        D = (x1-x2').^2 + (y1-y2').^2;
        
        [row,~]=find(sqrt(abs(D))<NODETOL*refd);
        neighb(count+1:count+length(val(row)))=val(row);
        count=count+length(val(row));
    end
end
return

Here's what the profiler says:

Lines where the most time was spent

Line Number Code Calls Total Time % Time Time Plot

43 neighb(count+1:count+length(va... 776520 2.198 s 15.3%

42 [row,~]=find(sqrt(abs(D))<N... 776520 1.601 s 11.1%

21 val=interp{order_new(kneigh),o... 776520 1.020 s 7.1%

22 val=val(fmask_local); val=val(... 776520 0.982 s 6.8%

36 y2=y2(fmask_local); y2=y2(:,fn... 776520 0.974 s 6.8%

All other lines 7.611 s 52.9%

6 个评论
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Rik 2020-5-22

The point is that you are storing data in that vector. If it is not large enough yet, Matlab will have to copy the array to extend it, which is very slow.

A=zeros(1,3);
A(1:4)=1:4;%A was too small

Apurva 2020-5-22

Oh, got it. Yes, I've prealloacted it to the correct size. No implicit expansion should be required.

neighb=zeros(length(vmapM),1);

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