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allenai / scispacy

A full spaCy pipeline and models for scientific/biomedical documents.
https://allenai.github.io/scispacy/
Apache License 2.0
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Error thrown out at LINE: from scispacy.linking import EntityLinker #446

Closed rjiang9 closed 2 years ago

rjiang9 commented 2 years ago

I am trying out scispacy on Mac M1:

1) conda env with python=3.8 OK 2) pip install scispacy OK 3) pip install the models OK 4) run sample code in section AbbreviationDetector OK

But when I run sample code in section EntityLinker, error thrown out:

zsh: illegal hardware instruction

and it looks the error is from line: from scispacy.linking import EntityLinker

Any suggestion is appreciated.

RJ

image
dakinggg commented 2 years ago

This is likely to be an issue with nmslib (see https://github.com/nmslib/nmslib/issues/476 for example). Could you see if anything over there works for you?

To verify if it is nmslib, it would also be great if you could try out some example.code from nmslib and see if that works.

Unfortunately I don't have an M1, so I can't really test anything myself.

rjiang9 commented 2 years ago

Thank you Daniel @dakinggg

It looks the solution from this thread works for me:

https://github.com/allenai/scispacy/issues/372

pip install --no-binary :all: nmslib

dakinggg commented 2 years ago

Great!