Issue with cuda lib?

[vahluw]

GaNDLF Version

0.0.17-dev

Version information of the GaNDLF package in the virtual environment.

Desktop (please complete the following information):

• OS: [e.g. Windows/Linux (include detailed distro information)/macOS] Linux
• Version (including Build information, if any): [e.g. Fedora 22 or Windows 10.1803]

How did you install GaNDLF
Please provide all steps followed during installation.

Dataset description
Describe the data (radiology/histology/so on, dimensions, etc.).
Radiology, 3D, breast images

Describe your question/problem
A clear and concise description of what issue you are facing.
I just pulled the newest code and am starting to have issues:

"python ./gandlf_verifyInstall" had no issues

cuda version : 11.2
Command: python /home/GaNDLF/gandlf_run -c /home/config_20.yaml -i /home/train.csv -m /home/output -t True -d cuda

I am getting the following output when trying to train:

Traceback (most recent call last):
File "/cbica/home/ahluwalv/GaNDLF/gandlf_run", line 11, in
from GANDLF.cli import main_run, copyrightMessage
File "/gpfs/fs001/cbica/home/ahluwalv/GaNDLF/GANDLF/cli/init.py", line 1, in
from .patch_extraction import patch_extraction
File "/gpfs/fs001/cbica/home/ahluwalv/GaNDLF/GANDLF/cli/patch_extraction.py", line 7, in
from GANDLF.data.patch_miner.opm.patch_manager import PatchManager
File "/gpfs/fs001/cbica/home/ahluwalv/GaNDLF/GANDLF/data/init.py", line 1, in
from torch.utils.data import DataLoader
File "/cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/site-packages/torch/init.py", line 217, in
_load_global_deps()
File "/cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/site-packages/torch/init.py", line 178, in _load_global_deps
_preload_cuda_deps()
File "/cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/site-packages/torch/init.py", line 158, in _preload_cuda_deps
ctypes.CDLL(cublas_path)
File "/cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/ctypes/init.py", line 373, in init
self._handle = _dlopen(self._name, mode)
OSError: /cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/site-packages/nvidia/cublas/lib/libcublas.so.11: symbol cublasLtGetStatusString, version libcublasLt.so.11 not defined in file libcublasLt.so.11 with link time reference

[sarthakpati]

How did you install PyTorch? If you used Conda, can you try using pip [ref]?

pip install torch==1.13.1+cu116 torchvision==0.14.1+cu116 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu116

[vahluw]

What should I do if my the newest version of cuda my computer supports is 11.2?

[sarthakpati]

What should I do if my the newest version of cuda my computer supports is 11.2?

If your hardware supports CUDA 11.2, it should support 11.6. Just follow the pip installation (it should install CUDA and all required libraries into your virtual environment).

[vahluw]

So that fixed that, but now I'm getting the following:

Looping over training data for penalty calculation: 0%| | 0/2426 [00:00<?, ?it/s]/cbica/projects/DBT_AI/.conda/envs/venv_gandlf_new/lib/python3.8/site-packages/torchio/data/io.py:36: UserWarning: Error loading image with SimpleITK:
Exception thrown in SimpleITK ImageFileReader_Execute: /tmp/SimpleITK-build/ITK-prefix/include/ITK-5.2/itkImportImageContainer.hxx:192:
Failed to allocate memory for image.

Trying NiBabel...
warnings.warn(message)

Looping over training data for penalty calculation: 0%| | 0/2426 [00:00<?, ?it/s]
ERROR:

[Geeks-Sid]

Hmmmm, This seems like an interesting error. Can you please let us know your ITK version and the output of
head -n 2 data.csv for assisting you better?

[vahluw]

subjectID,channel_0,label
0,/cbica/projects/DBT_AI/Data/masks/75712684_PROC_LCC_RC_2/75712684_PROC_LCC_RC_mat.nii.gz,/cbica/projects/DBT_AI/Data/masks/75712684_PROC_LCC_RC_2/75712684_PROC_LCC_RC_mask.nii.gz

ITK verison: 3.8.0

[sarthakpati]

Can you mention the output of the following command:

# activate gandlf python environment
python -c "import SimpleITK as sitk;image=sitk.ReadImage('/cbica/projects/DBT_AI/Data/masks/75712684_PROC_LCC_RC_2/75712684_PROC_LCC_RC_mat.nii.gz');print(image.GetSize());mask=sitk.ReadImage('/cbica/projects/DBT_AI/Data/masks/75712684_PROC_LCC_RC_2/75712684_PROC_LCC_RC_mask.nii.gz');print(mask.GetSize())"

Also, it would be great if you can post at least the mask so that we can debug further.

[vahluw]

(1996, 2457, 73)
(1996, 2457, 73)

What do you mean by posting the mask?

[vahluw]

This is also at the top of the error file:
No NVIDIA kernel driver module found, skipping CUDA

[sarthakpati]

(1996, 2457, 73)
(1996, 2457, 73)

Hmm, if the piece of code I replied with is giving this output, it means that the IO is working as expected.

What do you mean by posting the mask?

I meant uploading it here for us to debug. But it doesn't matter, since the IO is working correctly (as seen from the output of the command I sent).

No NVIDIA kernel driver module found, skipping CUDA

This is not unrelated to GaNDLF, and is dependent on the host machine.

[vahluw]

I tried running the same job with 1/5 of the training data and it was able to run without an error, however, I'm getting this:
Epoch Final train loss : 1.0
Epoch Final train dice : 0.0
Epoch Final train dice_per_label : [0.0, 0.0]
Epoch Final train iou : 0.34576352043151853
Epoch Final train f1 : 0.5872102342128753

[sarthakpati]

Not technically an error. Please play around with the optimizer/scheduler/learning_rate.

[Geeks-Sid]

Also, please edit your preprocessing parameters and augmentation parameters correctly. If you are using CT vs MRI vs RGB, the preprocessing does differ for all such tasks.

[Liu7749]

I have a new problem:
When I import anndata or torch
My Terminator said
UnboundLocalError: local variable 'cublas_path' referenced before assignment

[sarthakpati]

Are you able to run nvidia-smi? If yes, can you post the output?

If the above is true, please try creating a completely new virtual environment and follow the installation instructions.