For loop indexing gpuArray

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Alex
Alex 2016-5-23
编辑： Edric Ellis 2016-5-24
I am attempting to run a for loop around an array. For each index of the loop, I extract a vector of data, apply some operations and place it into a result matrix. A compressed example of what I am doing is below.
function test_system
ll = 2^16;
ww = 256;
ol = ll-ww+1;
%Run process on CPU.
data = rand(1,ll);
out = zeros(ww,ol);
for ii = 1:ol
subdata = data(ii:ii+ww-1);
out(:,ii) = fft(subdata);
end
%Run process on GPU
out2 = gpuArray(zeros(ww,ol));
gdata = gpuArray(data);
for ii = 1:ol
subdata = data(ii:ii+ww-1);
out2(:,ii) = fft(subdata);
end
%Run process on GPU using array fun.
out3 = arrayfun(@(x) execgpu(gdata,x),1:ol,'UniformOutput',false);
end
function ret = execgpu( data,idx )
ret = fft(data(idx:idx+256-1).');
end
  • The CPU code executed in 2s.
  • The GPU code executed in 17s.
  • The arrayfun code executed in 350s.
This seems off. I only have the arrayfun version because when I googled around about this issue, a few links on the Mathworks website recommended that approach.
Note: the above is a representative subset of what I am attempting to do, not a complete subset. The other things being done require the above approach.

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回答（1 个）

Edric Ellis
Edric Ellis 2016-5-24
编辑：Edric Ellis 2016-5-24
I think the best approach here is to vectorise your code so that you're not calling fft in a loop, nor indexing the gpuArray in a loop. (It's often relatively slow to index gpuArray data). In this case, you can vectorise by forming a matrix on which you can call fft to operate down the columns, like so:
% Parameters
ll = 2^16;
ww = 256;
ol = ll-ww+1;
% Build the input data
dataGpu = gpuArray.rand(1, ll);
% Create an index matrix that we're going to use with dataGpu
idxMat = bsxfun(@plus, (1:ww)', 0:(ol-1));
% Index dataGpu to form a matrix where each column is a sub-vector
% of dataGpu
dataGpuXform = dataGpu(idxMat);
% Make a single vectorised call to fft
out = fft(dataGpuXform);
On my rather old Tesla C2070 GPU, the fft call completes in 0.09 seconds.

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