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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process. #261

Closed alexlenail closed 12 months ago

alexlenail commented 1 year ago

I believe I'm in the step "Binarizing eGRNs AUC" but getting these warnings and errors. The job is still running, but looking at top there doesn't seem to be any computing happening.

2023-11-18 21:33:04,720 SCENIC+_wrapper INFO     Calculating TF-eGRNs AUC correlation
2023-11-18 21:36:39,817 SCENIC+_wrapper INFO     Binarizing eGRNs AUC
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
...
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.

(full log in the details)

I noticed a similar issue was reported on pySCENIC (https://github.com/aertslab/pySCENIC/issues/305), with suggestion this has to do with package version issues.

What do you recommend? 

2023-11-18 21:33:04,720 SCENIC+_wrapper INFO     Calculating TF-eGRNs AUC correlation
2023-11-18 21:36:39,817 SCENIC+_wrapper INFO     Binarizing eGRNs AUC
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
OpenBLAS warning: precompiled NUM_THREADS exceeded, adding auxiliary array for thread metadata.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Numba: Attempted to fork from a non-main thread, the TBB library may be in an invalid state in the child process.
Tripfantasy commented 12 months ago

I've ran into a similar issue on pySCENIC. I believe it has to do with how each version (pySCENIC & SCENIC+) parallelize their respective binarization functions.

In my case, I was binarizing an auc matrix downstream in pySCENIC. With that versions' binarize function, you can declare number of workers with the pool function from python's multiprocessing package.

To troubleshoot, if you have the option to set this, try not declaring a number of workers. This could force a default based on your environment. If it still doesn't work after that you could check your environments' versions of the packages. (similar to #305)

In my case running things via jupyter notebook, it seemed to just be a kernel issue, and restarting the function after interrupting the run giving the Numba: forking error allowed it to run to completion.

All this with a grain of salt though, since it was with pySCENIC. However I hope it helps you out somewhat!

alexlenail commented 12 months ago

Thanks Davin! I managed to get it to work in an older conda env. The suggestion to try without multiprocessing workers seems like a good one for future visitors of this thread.