Program running killed without errors

[yilevine]

Hi,

I am trying to run SATURN on the integration of human and pig data. I successfully ran the tutorial in the Vignettes/frog_zebrafish_embryogenesis/Train SATURN.ipynb. When I ran SATURN on my data. The running was just killed without any errors.

The code I used is below:

python3 code/train-saturn.py --in_data=data/saturn/run_hu_ss.csv --in_label_col=manual_anno --ref_label_col=manual_anno --num_macrogenes=2000 --hv_genes=8000 --centroids_init_path=results/saturn/hp_centroids.pkl --score_adata --ct_map_path=data/saturn/cell_type_map_hu_ss.csv --work_dir=results/saturn --device_num=0

The running output is

Global seed set to 0 Using Device 0 Set seed to 0 After loading the anndata human View of AnnData object with n_obs × n_vars = 53686 × 17384 ... After loading the anndata pig View of AnnData object with n_obs × n_vars = 85375 × 13350 ... Killed

I am using A100 (80G)

Any idea about the error?

Thanks Yile

[Yanay1]

Hi, I think the crash could be happening because of the system running out of memory when creating the centroids, which is unrelated to the GPU.

[yilevine]

Hi,

Thanks for the reply. Okay. I will try a bigger memory on the hpc. I am closing it.

Thanks Yile