Separate to the whole GPU issue: when timing code in Matlab it's best to use a more careful routine than tic/toc, like timeit.m (by a Mathworks employee): http:

Separate to the whole GPU issue: when timing code in Matlab it's best to use a more careful routine than tic/toc, like timeit.m (by a Mathworks employee): http://www.mathworks.com/matlabcentral/fileexchange/18798 http://www.mathworks.com/matlabcentral/fileexchange/18798