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lmcinnes avatar lmcinnes commented on May 18, 2024

Resolved! The issue was not dimension, but rather than the numpy arrays were not contiguous in memory which interfered with cython internals in hdbscan which were using pointer arithmetic inside array buffers for efficiency. The solution was 1) mark in the cython that we need contiguous arrays! (this should later be done elsewhere too!) 2) check for contiguous arrays and duplicate to a contiguous array if it isn't before handing it off to the cython code.

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djaym7 avatar djaym7 commented on May 18, 2024

2021 - still getting this error
Cannot generate Minimum Spanning Tree; the implemented Prim's does not produce the full minimum spanning tree

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lmcinnes avatar lmcinnes commented on May 18, 2024

Is this from the current master (I think some changes to Prim's were merged recently) or the current pip release (which doesn't have those recent changes)?

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djaym7 avatar djaym7 commented on May 18, 2024

Is this from the current master (I think some changes to Prim's were merged recently) or the current pip release (which doesn't have those recent changes)?

It's from current pip release

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lmcinnes avatar lmcinnes commented on May 18, 2024

Try the current master, as it may resolve some of those issues.

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djaym7 avatar djaym7 commented on May 18, 2024

5425cd2 commit still gives the same error
image

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djaym7 avatar djaym7 commented on May 18, 2024

Any update on this ?

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lmcinnes avatar lmcinnes commented on May 18, 2024

I think you need to force not using Prim's. That may be painful.

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