Why np.hypot and np.subtract.outer very fast compared to vanilla broadcast ? Using Numba for speedup numpy in parallel for distance matrix calculation
First of all, d0 and d1 takes each 50000 x 30000 x 8 = 12 GB which is pretty big. Make sure you have more than 100 GB of memory because this is what the whole script requires! This is a huge amount of memory. If you do not have enough memory, the operating system … Read more