diff --git a/README.md b/README.md index 253cfae03c62489a2bc911c2db2c45bd1d0521b4..7fb3d95667638a545fd1a7f1dc9a8e4a962a27dc 100644 --- a/README.md +++ b/README.md @@ -30,12 +30,24 @@ docker push xuagu37/nvidia_nnu-net_for_pytorch:21.11.0 ``` cd /proj/nsc/xuan/ngc git clone https://github.com/NVIDIA/DeepLearningExamples +cd /proj/nsc/xuan/ngc/DeepLearningExamples/PyTorch/Segmentation/nnUNet +``` +- Pull from xuagu37 and run the image +``` +singularity pull nvidia_nnu-net_for_pytorch.sif docker://xuagu37/nvidia_nnu-net_for_pytorch:21.11.0 +singularity shell -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch.sif +``` +- Prepare BraTS dataset +``` +python download.py --task 01 +python preprocess.py --task 01 --dim 2 ``` - Run the script. You need to modify the script for e.g. the name of your reservation, number of nodes, batch_size, etc. ``` cd /proj/nsc/xuan/ngc/DeepLearningExamples/PyTorch/Segmentation/nnUNet sbash benchmark_nnunet_pytorch_berzelius.sh +sbash benchmark_nnunet_pytorch_berzelius_multi_node.sh ``` <!--