Can this GPU code snippet be redone without nested loops?
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Hello, I have two matrices: matrix1 is a logical array of 1s and 0s (1000 x 800) matrix2 is a different logical array (2000 x 800)
I am essentially taking the first row of matrix 1 and calculating the row summation of common elements / total number of elements. Both of these arrays are gpuArrays. What I finding out:
for j=gpuArray.colon(1,x)
for k=gpuArray.colon(1,y)
output(j,k)=sum(matrix1(j,:) & matrix2(k,:)) / sum(matrix1(j,:) | matrix2(k,:))
end
end
Runs very fast for small values of x and y, but once x,y is large is takes exponentially longer to run on the GPU
I am investigating the use of repmat here but I am not sure how to implement. Any ideas here? Or if there is another option for to get rid of the nested for loops?
Thanks
采纳的回答
Joss Knight
2013-11-12
The GPU isn't going to work well with your nested loops. This looks like a classic case for bsxfun:
matrix1 = permute(matrix1, [1 3 2]);
matrix2 = permute(matrix2, [3 1 2]);
output = sum( bsxfun(@and, matrix1, matrix2), 3 ) ./ ...
sum( bsxfun(@or, matrix1, matrix2), 3);
I can't promise it will run faster than on your CPU though, if you have a lot of cores.
3 个评论
Amr Ragab
2013-11-12
Jill Reese
2013-11-13
Amr, the original code was processing fewer elements at once. When Joss mentioned that "The GPU isn't going to work well with your nested loops.", he was referring to the fact that the GPU wasn't being provided enough work to keep it busy.
Joss Knight
2013-11-19
Yes, with the loop the GPU is being asked to do thousands of very small computations in series - entirely the opposite of what it's good at. Instead we created 1000x2000x800 arrays containing all possible and and or combinations (using bsxfun) and then summed along the 3rd dimension to reduce down to the 1000x2000 matrix you were after.
更多回答（1 个）
Sean de Wolski
2013-11-11
编辑：Sean de Wolski
2013-11-11
Is output preallocated?
Before the loops:
output = gpuArray.zeros(x,y);
This should speed it up dramatically.
3 个评论
Amr Ragab
2013-11-11
Sean de Wolski
2013-11-11
编辑：Sean de Wolski
2013-11-11
Do matrix1 and matrix2 already live on the gpu, i.e. are they gpuArrays?
Amr Ragab
2013-11-11
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