From 18c42d3f95d4d740eadac918ea9f09a3d182b504 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuagu37@gmail.com>
Date: Thu, 20 Oct 2022 15:22:21 +0200
Subject: [PATCH] Update README.md
---
README.md | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/README.md b/README.md
index 253cfae..7fb3d95 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
```
<!--
--
GitLab