ctheodoris

/

Geneformer

like 266

Thank you for your great work in geneformer!
However, when I redid the disease classification, I found a series of problems:

1. "File "/home/.../anaconda3/envs/geneformer3/lib/python3.9/site-packages/torch/serialization.py", line 166, in validate_cuda_device
   raise RuntimeError('Attempting to deserialize object on a CUDA '
   RuntimeError: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False."
   Another:
   "File "/home/.../anaconda3/envs/geneformer3/lib/python3.9/site-packages/ray/worker.py", line 1833, in get
   raise value
   ray.exceptions.RaySystemError: System error: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False. If you are running on a CPU-only machine, please use torch.load with map_location=torch.device('cpu') to map your storages to the CPU."

It is really strange because I do have a CUDA device.

"
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 525.60.13 Driver Version: 525.60.13 CUDA Version: 12.0 |
|-------------------------------+----------------------+----------------------+
| 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 Tesla V100-SXM2... On | 00000000:3B:00.0 Off | 0 |
| N/A 30C P0 55W / 300W | 903MiB / 32768MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
| 1 Tesla V100-SXM2... On | 00000000:86:00.0 Off | 0 |
| N/A 27C P0 51W / 300W | 25MiB / 32768MiB | 0% Default |
| | | N/A |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=============================================================================|
| 0 N/A N/A 196221 C python 900MiB |
| 1 N/A N/A 196692 C ray::ImplicitFunc.train() 24MiB |
+-----------------------------------------------------------------------------+
"

2. "During handling of the above exception, another exception occurred:
   ...
   File "/home/.../envs/geneformer3/lib/python3.9/site-packages/transformers/configuration_utils.py", line 693, in _get_config_dict
   raise EnvironmentError(
   OSError: Can't load the configuration of 'path/to/pretrained_model/'. If you were trying to load it from 'https://huggingface.co/models', make sure you don't have a local directory with the same name. Otherwise, make sure 'path/to/pretrained_model/' is the correct path to a directory containing a config.json file"
   It's also strange because I can load the pretrained_model in the cell classification and gene classification task by the same "path/to".

3. "File "/home/jdhan_pkuhpc/profiles/yeyaxuan/lustre2/anaconda3/envs/geneformer3/lib/python3.9/site-packages/huggingface_hub/utils/_validators.py", line 158, in validate_repo_id
   raise HFValidationError(
   huggingface_hub.utils._validators.HFValidationError: Repo id must be in the form 'repo_name' or 'namespace/repo_name': 'path/to/pretrained_model/'. Use repo_type argument if needed."

I wonder whether it is caused by version conflict. I currently use the ray of version '1.13.0'.
I would appreciate it if you can offer me some help!