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I used the following to request my node:
srun --ntasks-per-node=4 --cpus-per-task=4 --mem=32000 --time=12:00:00 --partition=amperenodes --job-name=cell2location --gres=gpu:2
So in the training step I am getting 221/250, instead of training complete, and always I am getting error saying 'use_gpu' command is unrecognized. I would like to request you to provide memory requirement details for tutorial. I will provide any other information if required, can you please help me with this, Thank you.
Please make sure that you have installed the latest and compatible versions of packages and used the corresponding options (latest version doesn't have 'use_gpu' argument).
The tutorial can run on Google Colab with 12GB RAM given the same data. If you have larger data - you need more RAM.
Cell2location also doesn't use multiple GPUs (--gres=gpu:2) so unless you are starting two processes manually, you can request only one GPU.
There is a bug in the latest GitHub version that results in data being recorded during posterior sampling - resulting in huge RAM use. I am working on fixing this issue - however for now, you can use use_quantiles option of the posterior sampling and exclude_vars to exclude 'data_target' (if it exists).
Please use the template below to post a question to https://discourse.scverse.org/c/ecosytem/cell2location/.
Problem
I am trying to run the example in the following page:
https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html#Loading-packages
I used the following to request my node:
srun --ntasks-per-node=4 --cpus-per-task=4 --mem=32000 --time=12:00:00 --partition=amperenodes --job-name=cell2location --gres=gpu:2
So in the training step I am getting 221/250, instead of training complete, and always I am getting error saying 'use_gpu' command is unrecognized. I would like to request you to provide memory requirement details for tutorial. I will provide any other information if required, can you please help me with this, Thank you.
N_cells_per_location
anddetection_alpha
.batch_key
for reference NB regression.The text was updated successfully, but these errors were encountered: