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It's not quite right to say Java's performance is better than Python or viceversa, as one is better than other in different areas.
I would like to repeat the following things again -
It is good to think in your terms where memory is getting wasted, but "not here". I am a game developer and believe me I know exactly when one should be worrying about memory.
I agree to the point of yours that saving a value into a single register is better than reading n^2 values as a chunk. But, is it arguably bad? Though we have better readability, and also it is easy to code. Again, believe me it is not!
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Diagonal Difference
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It's not quite right to say Java's performance is better than Python or viceversa, as one is better than other in different areas. I would like to repeat the following things again -