I think the operation is so simple that you always see a slowdown due to the overhead of sending data to other processes and back.
I couldn't get my head around it and I guess I've exhausted myself now. 
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Yes, the slicing way is actually really tricky. I forgot pdist computes pairwise distances between ALL samples.
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yeah this is where I fell down

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Just realized you can probably use itertools.product to get all the combinations, slice the combination matrix, and do as I suggested!
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I'll try that too tomorrow! Nice idea!

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If you know of a working example I could base this off I would love a to see and be indebted. I've also thought of some more ideas to try.

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are you sure you mean itertools.product?
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you actually can use itertools.combinations as it does what I meant more directly. product would be used on lists of indices, not the matrix
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I am actually completely stuck — sorry. Maybe if you have time we could chat, but otherwise I don't understand at all.
End of conversation
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