[FIXED] Experiencing a problem with accessing CUDA(version 12) while using Cellbender

Issue

CUDA cannot be detected by Cellbender. I have the latest CUDA driver installed, and here is the output that confirms the same:

(CellBender) [user@server]$ nvidia-smi
Tue Jul 11 19:11:19 2023
+---------------------------------------------------------------------------------------+
| NVIDIA-SMI 535.54.03              Driver Version: 535.54.03    CUDA Version: 12.2     |
|-----------------------------------------+----------------------+----------------------+
| GPU  Name                 Persistence-M | Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp   Perf          Pwr:Usage/Cap |         Memory-Usage | GPU-Util  Compute M. |
|                                         |                      |               MIG M. |
|=========================================+======================+======================|
|   0  NVIDIA GeForce GT 1030         Off | 00000000:43:00.0 Off |                  N/A |
| 35%   28C    P8              N/A /  30W |    255MiB /  2048MiB |      0%      Default |
|                                         |                      |                  N/A |
+-----------------------------------------+----------------------+----------------------+

+---------------------------------------------------------------------------------------+
| Processes:                                                                            |
|  GPU   GI   CI        PID   Type   Process name                            GPU Memory |
|        ID   ID                                                             Usage      |
|=======================================================================================|
|    0   N/A  N/A      4396      G   /usr/libexec/Xorg                            63MiB |
|    0   N/A  N/A      4521      G   /usr/bin/gnome-shell                        190MiB |
+---------------------------------------------------------------------------------------+

I am using the following command to remove the background: cellbender remove-background --input raw_feature_bc_matrix_pDRGN_d0_r1_50.h5 --output output.h5 --cuda --expected-cells 20000 --total-droplets-included 25000 --fpr 0.01 --epochs 150

Error:

Traceback (most recent call last):
  File "/path/to/.conda/envs/CellBender/bin/cellbender", line 33, in <module>
    sys.exit(load_entry_point('cellbender', 'console_scripts', 'cellbender')())
  File "/user/CellBender/cellbender/base_cli.py", line 98, in main
    args = cli_dict[args.tool].validate_args(args)
  File "/user/CellBender/cellbender/remove_background/cli.py", line 69, in validate_args
    assert torch.cuda.is_available(), "Trying to use CUDA, " \
AssertionError: Trying to use CUDA, but CUDA is not available.

Solution

I installed torch and cuda using pip, instead of conda, and, it works for me;

Installation:

pip install torch==1.8.1+cu101 torchvision==0.9.1+cu101 torchaudio==0.8.1 -f https://download.pytorch.org/whl/torch_stable.html

Validation:

The following command should return True

# command
python -c 'import torch; print torch.cuda.is_available()'

# output
> True

Answered By - nikhil int