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Problem with parfor and matrix indexing

Asked by Guilherme Freches on 18 Sep 2019
Latest activity Answered by Edric Ellis
on 19 Sep 2019
Hey
I'm building a knn graph out of an adjacency matrix M and it seems to take some time when the number of columns is large enough.
I'm trying to paralelize the process by replacing the for on the following code snippet by a parfor
indi = zeros(1, neighbours * n);
indj = zeros(1, neighbours * n);
inds = zeros(1, neighbours * n);
parfor ii = 1:n
% Compute i-th column of distance matrix
dist = euclidean(repmat(M(:, ii), 1, n), M); %gives a euclidean distance matrix
% Sort row by distance
[s, O] = sort(dist, 'ascend');
% Save indices and value of the neighbours
indi(1, (ii-1)*neighbours+1:ii*neighbours) = ii;
indj(1, (ii-1)*neighbours+1:ii*neighbours) = O(1:neighbours);
inds(1, (ii-1)*neighbours+1:ii*neighbours) = s(1:neighbours);
end
But I keep running into the error : Valid indexes of indi, indj and inds are restricted by parfor.
Any idea what to do here?

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1 Answer

Answer by Edric Ellis
on 19 Sep 2019

In each case, you're attempting to assign neighbours elements into each of your output arrays. The restrictions on parfor sliced output variables are that must use the loop index as one subscript, and use a fixed index listing in the other positions. See the doc: https://uk.mathworks.com/help/parallel-computing/sliced-variable.html . The simplest way to fix this case is to make each of your output arrays a 2-D matrix, and assign whole rows at a time, like this:
indi = zeros(n, neighbours);
parfor ii = 1:n
indi(ii, :) = ii;
end
If you need to, you can reshape the result back later
indi = reshape(indi, 1, n * neighbours);

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