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aertslab / SCENICprotocol

A scalable SCENIC workflow for single-cell gene regulatory network analysis
GNU General Public License v3.0
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Memory required for running pyscenic #57

Open sidrahmaryam-cyber opened 2 years ago

sidrahmaryam-cyber commented 2 years ago

Hello, I am trying to run the dummy dataset using the given pyscenic workflow on the cluster using slurm script. However, when I assigned 180G memory usage, still it is giving me the error for memory exhaustion. When I submitted the job without any slurm script, it gave an overconsumption issue.

Showing you a glimpse of the error generated:

distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting distributed.nanny - WARNING - Worker exceeded 95% memory budget. Restarting

Can I please be suggested an alternative for it? Or can I please get to know how much the memory will be needed for running? This is a sample data given in the tutorial.

I will be grateful for your help. Thanks.

Erfan1369 commented 2 years ago

Hello, Did you find out answer or not? I want to run on the clusters too, Thanks

sidrahmaryam-cyber commented 2 years ago

Hello, No I could not find any answers yet. Trying to find alternatives still.