Like all arrays in MATLAB, gpuArray data is stored in "column-major" order. One consequence of this is that it is much more efficient to extract individual columns from a matrix than individual rows - this is true on the CPU, and doubly true on the GPU. Extracting a column is equivalent to a simple memory block copy. Extracting a row requires a "strided" copy operation. You can take advantage of this by performing a single up-front transpose on your array, and then use efficient column indexing operations:
tst_t = tst.';
for n = 1:100
tst1 = tst_t(:, 1).';
tst2 = tst_t(:, 2).';
tst3 = tst_t(:, 3).';
[th, phi, r] = cart2sph(tst1, tst2, tst3);
end
On my machine with a now rather old Tesla K20c, this approach takes 0.015 seconds compared with 5.3 seconds for your first approach and 2.0 seconds for your second approach. (Note that transposing vectors can be extremely effficient because the memory layout is identical)
