RAM costs of running Mouse-MOp-MERFISH.ipynb

[qiaochen]

Hi Authors,

Thanks for sharing your project. I am trying to replicate the results in the Mouse-MOp-MERFISH.ipynb. My process seems to be killed when runing Deomposition.py for gene imputation, because of exceeding RAM usage limit.

I am using one a100 40G gpu & 128GB RAM, may I know the environment of your running the notebook?
Thanks

Best

[JiaShun-Xiao]

Hi Authors,

Thanks for sharing your project. I am trying to replicate the results in the Mouse-MOp-MERFISH.ipynb. My process seems to be killed when runing Deomposition.py for gene imputation, because of exceeding RAM usage limit.

I am using one a100 40G gpu & 128GB RAM, may I know the environment of your running the notebook? Thanks

Best

Hi, one GPUs is really not enough, you can try to use a smaller batch (e.g., 500 cells) when runing Deomposition.py for gene imputation.