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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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SystemError: initialization of _internal failed without raising an exception #7

Closed snayfach closed 1 year ago

snayfach commented 1 year ago

I installed on a cori login node using conda which ran without errors: conda create -n genomad-conda -c conda-forge -c bioconda genomad

After activating and testing it produces errors:

source activate genomad-conda
genomad

Traceback (most recent call last): File "/global/homes/s/snayfach/.conda/envs/genomad-conda/bin/genomad", line 6, in from genomad.cli import cli File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/genomad/init.py", line 5, in from genomad.modules import ( File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/genomad/modules/aggregated_classification.py", line 4, in from genomad import sequence, utils File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/genomad/sequence.py", line 9, in from numba import njit File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/numba/init.py", line 42, in from numba.np.ufunc import (vectorize, guvectorize, threading_layer, File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/numba/np/ufunc/init.py", line 3, in from numba.np.ufunc.decorators import Vectorize, GUVectorize, vectorize, guvectorize File "/global/homes/s/snayfach/.conda/envs/genomad-conda/lib/python3.10/site-packages/numba/np/ufunc/decorators.py", line 3, in from numba.np.ufunc import _internal SystemError: initialization of _internal failed without raising an exception

Here's a stack overflow thread on the issue: https://github.com/numba/numba/issues/8615

From skimming that, the issue might be the latest version of numpy and installing a lower version of numpy (<1.24) may fix the problem.

snayfach commented 1 year ago

Update: that was the solution for me

conda remove --force numpy
conda install numpy=1.23.5

There was another version of numpy install with conda I had to remove as well

apcamargo commented 1 year ago

Thanks for reporting this! I'll release a new version with a numpy < 1.24 requirement. Hopefully Numba will add support for the new numpy release soon.