diff --git a/README.md b/README.md index 14dff974dcde2a7c458640dc8388d1e16435f7e6..28ca1e5736d9617195ff1edd61dd81164f418a37 100644 --- a/README.md +++ b/README.md @@ -43,15 +43,15 @@ Docker is not available on Berzelius. We use Apptainer or Enroot. With Apptainer ``` apptainer pull nvidia_nnu-net_for_pytorch_$VERSION.sif docker://berzeliushub/nvidia_nnu-net_for_pytorch:$VERSION -apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif bash -c "cd /workspace/nnunet_pyt && python download.py --task 01" -apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif bash -c "cd /workspace/nnunet_pyt && python preprocess.py --task 01 --dim 2" +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif cd /workspace/nnunet_pyt && python download.py --task 01 +apptainer exec --nv -B ${PWD}/data:/data -B ${PWD}/results:/results --nv nvidia_nnu-net_for_pytorch_$VERSION.sif cd /workspace/nnunet_pyt && python preprocess.py --task 01 --dim 2 ``` <!-- With Enroot ``` enroot import 'docker://berzeliushub/nvidia_nnu-net_for_pytorch:$VERSION' enroot create --name nnunet berzeliushub+nvidia_nnu-net_for_pytorch+$VERSION.sqsh -enroot start --rw --mount ${PWD}/data:/data --mount ${PWD}/results:/results nnunet bash -c "cd /workspace/nnunet_pyt && python download.py --task 01 && python preprocess.py --task 01 --dim 2" --> +enroot start --rw --mount ${PWD}/data:/data --mount ${PWD}/results:/results nnunet cd /workspace/nnunet_pyt && python download.py --task 01 && python preprocess.py --task 01 --dim 2" --> ``` <!-- - For benchmarking purpose, we use copied of a single image