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YangLabHKUST / SpatialScope

A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
https://spatialscope-tutorial.readthedocs.io/en/latest/
GNU General Public License v3.0
50 stars 6 forks source link

RAM costs of running Mouse-MOp-MERFISH.ipynb #15

Open qiaochen opened 5 months ago

qiaochen commented 5 months ago

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 commented 4 months ago

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.