Gert Hulselmans

Looking at: https://researchcomputing.princeton.edu/support/knowledge-base/memory is seems that you specified the `mem-per-cpu` wrong (should be `3G` instead of `3GB`) In the memory allocation error you got, you can also see that you...

Which version of pySCENIC do you have installed? The latter is not a bug (see the dask webpage).

> About the stochastic nature of the pyscenic, I was wondering if whether it is only related to the first step(grn) of SCENIC or it is for whole of the...

You can try with a more recent version of python than 3.7, which does not use fork but spawn when using mulitprocessing.

Did you use the latest git version of pySCENIC?

@lindaseong Could you try in a new virtual environment and installing pySCENIC from scratch? The `gene_names` variable is defined in main, so it shouldn't be undefined: ```python ❯ arboreto_with_multiprocessing.py ${f_loom_path_scenic}...

Are you running it on MacOSby any chance? We run pySCENIC exclusively on Linux (x86_64), so it is possible that it doesn't work on MacOS.

It should be fixed in master: https://github.com/aertslab/pySCENIC/commit/692132a097cd9533524e943cc67495231242c960

You can add `--mode dask_multiprocessing`. But probably you should limit the number of workers to a lower value (`--num_workers`) so you wouldn't run out of RAM in the first place.

Why not give the proper amount from the start? Are you running it in a VM?