For indexing in gpuArray, how can I improve my code?

          
function dists = compute_distances(obj,X)%X is a matrix with 10000 X 1024
    num_test=size(X, 1);
    num_train=size(obj.x_train,1);
    temp_dists=double(zeros(num_test,num_train));
    gpu_X=gpuArray(X);
    gpu_xtrain=gpuArray(obj.x_train);%obj.x_train is a matrix with 1000 X 1024
    for i = 1:num_test
      for j =1:num_train
        tmp=X(i,:)-obj.x_train(j,:);
        temp_dists(i,j)=sqrt(sum(tmp.*tmp));
      end
    end
    dists=temp_dists;
end

My CPU code executed in 5 mins.

The GPU code executed in 25mins.

I am trying to calculate the distance, but I noticed that I can use gpuArray to improve the speed.

I have no idea why it doesn't work.

Answer 1

[Joss Knight]

Firstly, use pdist2.

Secondly, say no to loops:

Y = reshape(obj.x_train',1,[],num_train);
delta = X-Y;
dists = squeeze(sqrt(sum(delta.*delta,2)));