Error in running large dataset about harmonypy HOT 2 CLOSED

It's solved. when I used harmony_integrate function of scanpy, it's worked.

sce.pp.harmony_integrate(adata, 'aligned_dataset',basis='X_uce')

from harmonypy.

Thanks for sharing your experience.

If we search the web for "precompiled NUM_THREADS exceeded" we can find many results with suggestions for how to solve this issue.

For example, this Stackoverflow post suggests that we can set the NUM_THREADS option like this:

os.environ['OPENBLAS_NUM_THREADS'] = '1'

and then the sklearn.KMeans function should run without error.

I do not know whether or not this will fix your issue, because I don't know your system environment (python version, package versions, etc.).

from harmonypy.