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GuangyuWangLab2021 / cellDancer

Predict RNA velocity through deep learning
https://guangyuwanglab2021.github.io/cellDancer_website/
BSD 3-Clause "New" or "Revised" License
60 stars 11 forks source link

Memory cap? #7

Closed cnk113 closed 1 year ago

cnk113 commented 1 year ago

Hello,

I've been trying to run cellDancer for about 150K cells, but during velocity estimation the memory explodes no matter the gene list size input. I was wondering if there was a way to cap the memory usage?

Thanks, Chang

Abclisy commented 1 year ago

Hi Chang, cellDancer uses joblib.Parallel to allow the prediction for multiple genes at the same time. _njobs is set to -1 by default, which means all CPUs are used. Could you please start with _njobs=1 for cd.velocity to see if it works or not?

If it still doesn't work, could you provide us with your usage of cd.velocity along with parameters and error message? Or, if possible, providing a small subset of your data could let us repeat your problem. Thank you!

Abclisy commented 1 year ago

Hello, it's been a while since we heard back from you regarding this issue. We will be closing this issue. However, please don't hesitate to reopen it or create a new issue if you have further questions or concerns. Thank you for your understanding.