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FredHutch / easybuild-life-sciences

Howto and implementation documentation
https://fredhutch.github.io/easybuild-life-sciences/
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scanpy package broken in 3.7 (Could not load shared object file: libllvmlite.so) #382

Closed dirkpetersen closed 4 years ago

dirkpetersen commented 4 years ago 
Traceback (most recent call last):

  File "<stdin>", line 1, in <module>

  File "/app/software/scanpy/1.4.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/scanpy/__init__.py", line 36, in <module>

    from . import tools as tl

  File "/app/software/scanpy/1.4.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/scanpy/tools/__init__.py", line 1, in <module>

    from ..preprocessing._simple import pca

  File "/app/software/scanpy/1.4.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/scanpy/preprocessing/__init__.py", line 1, in <module>

    from ._recipes import recipe_zheng17, recipe_weinreb17, recipe_seurat

  File "/app/software/scanpy/1.4.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/scanpy/preprocessing/_recipes.py", line 6, in <module>

    from . import _simple as pp

  File "/app/software/scanpy/1.4.6-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/scanpy/preprocessing/_simple.py", line 8, in <module>

    import numba

  File "/app/software/numba/0.47.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/numba/__init__.py", line 15, in <module>

    from . import config, errors, _runtests as runtests, types

  File "/app/software/numba/0.47.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/numba/config.py", line 18, in <module>

    import llvmlite.binding as ll

  File "/app/software/numba/0.47.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/llvmlite/binding/__init__.py", line 6, in <module>

    from .dylib import *

  File "/app/software/numba/0.47.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/llvmlite/binding/dylib.py", line 4, in <module>

    from . import ffi

  File "/app/software/numba/0.47.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/llvmlite/binding/ffi.py", line 154, in <module>

    raise OSError("Could not load shared object file: {}".format(_lib_name))

OSError: Could not load shared object file: libllvmlite.so
fizwit commented 4 years ago

I was a very early adapter of foss-2019b. This resulted in 3 versions of LLVM for the toolchain. There are to many conflicting dependencies to resolve this issue. The individually module scanpy/1.4.6-foss-2019b-Python-3.7..4 works but when added to the "-fh1" it is broken. ScanPy for fhPython has been fixed.