scanpy neighbors function: LLVM ERROR: Symbol not found: __svml_sqrtf8

Question

Whenever I use sc.pp.neighbors(adata) I get this message (without any error):

I have:

scanpy==1.8.1

pynndescent==0.5.4

numba==0.54.0

umap-learn==0.5.1

anndata==0.7.6

My dataset contains only ~20,000 cells so it's quite weird that my kernel dies using this relatively small dataset.

I even tried to use scanpy's bbknn function as an alternative, and my kernel died as well.

I also encountered the same problem as an issue on github: https://github.com/theislab/scanpy/issues/1567 but it had no solution yet.

I tried to run the code on cmd instead of jupyter-notebook and got the next error:

LLVM ERROR: Symbol not found: __svml_sqrtf8

What should I do in order to properly run this function?

Answer 1

The above comment by @Iguananaut worked for me:

If you can reproduce the problem outside the Jupyter Notebook, then it's not really a problem relative to the use of Jupyter, and that tag can be avoided. The problem is somewhere else. The issue is likely related to numba, and possibly an incompatibility between a pre-compiled numba and other libraries installed on your system. I wonder if it would help if you set the environment variable NUMBA_DISABLE_INTEL_SVML=1

I created a new environmental variable as below:

• variable name: NUMBA_DISABLE_INTEL_SVML
• variable value: 1

This then allowed me to run umap. Before I was seeing the same error in a terminal window:

Symbol not found: _svml_sqrtf8

Answer 2

Had to uninstall and reinstall soundfile and librosa after changing hardware and migrating from intel to nvidia GPU. I loved my intel GPU but somebody else is using it now :)