scnym not working; Reason: image not found

[Brunox13]

I followed the installation instructions and when I run

scnym --help

I get the following:

(scnym_env) user-comp:scnym user$ scnym --help
Traceback (most recent call last):
  File "/Users/user/anaconda3/envs/scnym_env/bin/scnym", line 11, in <module>
    load_entry_point('scnym==0.1', 'console_scripts', 'scnym')()
  File "/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 490, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2854, in load_entry_point
    return ep.load()
  File "/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2445, in load
    return self.resolve()
  File "/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/pkg_resources/__init__.py", line 2451, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/Users/user/anaconda3/scnym/scnym/__init__.py", line 8, in <module>
    from . import dataprep, model, predict, trainer, utils
  File "/Users/user/anaconda3/scnym/scnym/dataprep.py", line 1, in <module>
    import torch
  File "/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/__init__.py", line 79, in <module>
    from torch._C import *
ImportError: dlopen(/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/_C.cpython-37m-darwin.so, 9): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: /Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/lib/libshm.dylib
  Reason: image not found

I get a similar error when I open a jupyter notebook and try to import scnym:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-3-116a8c9e65d1> in <module>
----> 1 import scnym
      2 from scnym.predict import Predicter

~/anaconda3/envs/scnym_env/lib/python3.7/site-packages/scnym-0.1-py3.7.egg/scnym/__init__.py in <module>
      6 # e.g.
      7 # >> from scnym.model import CellTypeCLF
----> 8 from . import dataprep, model, predict, trainer, utils

~/anaconda3/envs/scnym_env/lib/python3.7/site-packages/scnym-0.1-py3.7.egg/scnym/dataprep.py in <module>
----> 1 import torch
      2 import numpy as np
      3 from torch.utils.data import Dataset
      4 from typing import Callable
      5 

~/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/__init__.py in <module>
     77 del _dl_flags
     78 
---> 79 from torch._C import *
     80 
     81 __all__ += [name for name in dir(_C)

ImportError: dlopen(/Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/_C.cpython-37m-darwin.so, 9): Library not loaded: /usr/local/opt/libomp/lib/libomp.dylib
  Referenced from: /Users/user/anaconda3/envs/scnym_env/lib/python3.7/site-packages/torch/lib/libshm.dylib
  Reason: image not found

[Brunox13]

I solved the problem by running the following:

brew install libomp

As suggested here: Pytorch issue #20030

[jacobkimmel]

Glad this was fixed, thanks for documenting.

Just FYI, scNym training will be very slow without a modern GPU. Most Macs are sadly lacking in that department. Inference (predicting using pre-trained models) should still be fairly fast.