Add OpenMP for multiple threads, will speedup analyses further
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No need as the code is going to run on many inputs in parallel using a bash script.
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Besides it's in the range of seconds in C as opposed to death in Python.

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I've finished coding it so I know now.

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You've probably already tried this, but have you run with PyPy et al? Usually my first line of defense when Python is in a slow mood.
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I'm going to enjoy doing this in C so no worries. It's very simple, and you can totes try this code out in pypy:https://github.com/oliviaguest/pairwise_distance/blob/master/dima_version.py …
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bearing in mine I am going to run it on 50million data points.
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you got this!

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It's very fun.
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C: the power of assembly language, combined with the expressiveness of assembly language!
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