Scube.align() running slow

[DruncBread]

Hi,

I have already installed PyTorch, and I verified that CUDA is available on my system using the following code:

import torch
print(torch.cuda.is_available())

The above code returns True. But when I run Scube.align() function, it runs very slowly
And I checked the GPU usage through nvidia-smi, I found that Scube didn't use GPU.

Here's the core code I'm running:

adata_list = []
for sample_id in sample_ids:
    adata = data_reader.read_dataset(dataset,sample_id)
    adata_list.append(adata)

from SPACEL import Scube
Scube.align(adata_list,
  cluster_key='ground_truth',
  n_neighbors = 4,
  p=1,
  write_loc_path = f'{output_dir}/aligned_coordinates.csv'
 )

It took 20 minutes to align two anndata

AnnData object with n_obs × n_vars = 2378 × 254
AnnData object with n_obs × n_vars = 2423 × 254

Is this normal? Is there something I'm doing wrong during the usage, or are there some configuration or compatibility issues with Scube.align itself? I hope to get your help. Thank you!

Best regards.