EntityLinker import hangs

[mezarque]

I've been trying to import EntityLinker but running into an unusual issue where the kernel hangs for a very long time (so far I've let it run up to 93 minutes) without dying or producing an error.

I know there are some previous issues that were related to nmslib (e.g. #365, #372, #437, #446). These seemed to result in a zsh: illegal hardware instruction error, which I don't seem to be encountering.

I eventually figured out how to resolve this, but wanted to share my solution, in case anyone else runs into the same problem.

Hardware / OS

I'm using a 2021 MacBook Pro with an Apple M1 Pro chip, running macOS Ventura 13.1.

Steps

1. Create a conda environment using conda create -n scispacy python=3.9. I'm using conda 24.7.1.

2. conda activate scispacy

3. pip install scispacy

4. pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_sm-0.5.4.tar.gz

5. Start an interactive Python session with python

6. Run the following code:

   import spacy
   nlp = spacy.load("en_core_sci_sm")

   Receive warning:

   /Users/dennis/miniconda3/envs/scispacy/lib/python3.9/site-packages/spacy/language.py:2195: FutureWarning: Possible set union at position 6328
     deserializers["tokenizer"] = lambda p: self.tokenizer.from_disk(  # type: ignore[union-attr]
   

7. Continue with

   doc = nlp("Alterations in the hypocretin receptor 2 and preprohypocretin genes produce narcolepsy in some animals.")

   No problems.

8. Run the following code:

   import spacy
   
   from scispacy.abbreviation import AbbreviationDetector
   
   nlp = spacy.load("en_core_sci_sm")
   
   # Add the abbreviation pipe to the spacy pipeline.
   nlp.add_pipe("abbreviation_detector")
   
   doc = nlp("Spinal and bulbar muscular atrophy (SBMA) is an \
              inherited motor neuron disease caused by the expansion \
              of a polyglutamine tract within the androgen receptor (AR). \
              SBMA can be caused by this easily.")
   
   print("Abbreviation", "\t", "Definition")
   for abrv in doc._.abbreviations:
   	print(f"{abrv} \t ({abrv.start}, {abrv.end}) {abrv._.long_form}")

   No problems.

9. Run the following code:

   import scispacy

   No problems.

10. Run the following code:

    from scispacy.linking import EntityLinker

    Kernel hangs for a very long time without dying.

Attempts

1. I've encountered the same behavior in an interactive Python session, as well as when running the code within a Jupyter notebook.
2. I tried uninstalling nmslib with pip uninstall nmslib and reinstalling with each of the following strategies:

• pip install --no-binary :all: nmslib (suggested here)
• CFLAGS="-mavx -DWARN(a)=(a)" pip install nmslib (suggested here)

Solution

Installing nmslib using conda (I used mamba) appeared to solve the issue.

mamba install nmslib

This installed nmslib 2.1.1, which appears to be a newer version than what is specified in requirements.in and setup.py (nmslib>=1.7.3.6). Might upgrading the version there be a good idea? I'm not sure what other issues that would introduce.

[dakinggg]

Wow, thank you! This solution seems to work for me on both Windows and Linux with python 3.11, which hasn't previously worked. Thank you for sharing! I will respond to some other issues and see if it works for others and then update the installation instructions.

[dakinggg]

I just added a support matrix based on what im able to test or glean from previous github issues, so going to go ahead and close this issue. Thanks again for the suggestion!