'CUDA_VISIBLE_DEVICES' question

[anishshriram]

GaNDLF Version
0.0.14-dev

Desktop
macOS Monterey
Version 12.1

How did you install GaNDLF

git clone https://github.com/CBICA/GaNDLF.git
cd GaNDLF
conda create -n venv_gandlf python=3.7 -y
conda activate venv_gandlf
conda install -c conda-forge mamba -y
mamba install -c pytorch pytorch torchvision -y
pip install -e .

Dataset description
The dataset is titled RSNA_ASNR_MICCAI_BraTS2021_TrainingData_16July2021, referring to the 2021 BraTS training data.

Description from website:
Routine clinically-acquired multi-parametric MRI (mpMRI) scans of glioma, with pathologically confirmed diagnosis and available MGMT promoter methylation status (for the glioblastoma cases with such associated data). All BraTS mpMRI scans are available as NIfTI files (.nii.gz) for Segmentation, which is the use in this issue. These mpMRI scans describe a) native (T1) and b) post-contrast T1-weighted (T1Gd), c) T2-weighted (T2), and d) T2 Fluid Attenuated Inversion Recovery (T2-FLAIR) volumes.

Describe your question/problem
I am trying to use gandlf_run.

I then executed it (with specific paths) as so:

python gandlf_run \
-c /cbica/home/shrirama/comp_space/project/meningioma/GaNDLF/samples/config_segmentation_brats.yaml \
-i /cbica/home/shrirama/comp_space/project/meningioma/data_processed.csv \
-m /cbica/home/shrirama/comp_space/project/meningioma/models \
-t True \
-d cuda \
-r True

The other error I get, though I don't exactly know if it is an error:

Please set the environment variable 'CUDA_VISIBLE_DEVICES' correctly before trying to run GANDLF on GPU

I assume this has something to do with the sge_wrapper file. I can't find in the wiki information on how to change this variable to the correct settings.

I also moved the sge_wrapper file from samples one directory up.

I would appreciate some help on this thank you so much.

[sarthakpati]

Please post a separate query per question, so that it is easier for us to address.

1. This is related to the file not getting found.
2. Setting the environment variable CUDA_VISIBLE_DEVICES is required when trying to run any GPU compute job. See a related post [ref] for details.

[sarthakpati]

I have said this in this response: #322 (reply in thread)

[sarthakpati]

Great, all the best.

[anishshriram]

What I did was call:

qsub sge_wrapper

in the command line. It did not work. How should I do this properly?

[sarthakpati]

This is not a GaNDLF question. Please post this to the CUBIC system admins for clarification.

[anishshriram]

I have emailed them thank you.