diff --git a/README.md b/README.md index 182002b48eedcbea9138c6923029126ad1bd014c..3ea6c67a8fd56eb0d76aa9af5933dca6acf4d454 100644 --- a/README.md +++ b/README.md @@ -33,18 +33,25 @@ 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 +- Pull from xuagu37 and run the image +Using singularity ``` 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 +``` +Or using enroot ``` -- Prepare BraTS dataset +enroot import 'docker://xuagu37/nvidia_nnu-net_for_pytorch:21.11.0' +enroot create --name nnunet xuagu37+nvidia_nnu-net_for_pytorch+21.11.0.sqsh +enroot start --rw --mount ${PWD}/data:/data --mount ${PWD}/results:/results nnunet +``` +- Prepare BraTS dataset (within the image) ``` 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. +You need to modify the script for e.g. the name of your reservation, number of nodes, batch_size, etc. Also, choose either singularity or enroot. ``` cd /proj/nsc/xuan/ngc/DeepLearningExamples/PyTorch/Segmentation/nnUNet sbash benchmark_nnunet_pytorch_berzelius.sh