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Created July 16, 2026 00:18
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Fixing openslide-python error on Slurm Cluster (AllianceCan)
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openslide-python.md

AllianceCan clusters have openslide available as a loadable module, but openslide-python cannot normally resolve it, throwing an error like:

ModuleNotFoundError: Couldn't locate OpenSlide shared library. Try `pip install openslide-bin`. https://openslide.org/api/python/#installing

To fix this, you need to help the linker resolve the library. To do so, load the module:

module load openslide

and then then locate the library via:

find ${EBROOTOPENSLIDE:-/nonexistent} ${OPENSLIDE_ROOT:-/nonexistent} ${OPENSLIDE_HOME:-/nonexistent} -name 'libopenslide.so*' 2>/dev/null

Finally, append the exact path to LD_LIBRARY_PATH so openslide-python can resolve it. For example:

export LD_LIBRARY_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/openslide/4.0.0/lib:$LD_LIBRARY_PATH
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