From 0a3e326b1b4cc2b856a108e6f99f452578dff2c6 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Fri, 13 Oct 2023 17:29:08 +0000
Subject: [PATCH] Update 2 files
- /NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_latest.def
- /NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/build.txt
---
.../PyTorch/Segmentation/nnUNet/build.txt | 9 ++++++
.../nnUNet/nnunet_for_pytorch_latest.def | 29 +++++++++++++++++++
2 files changed, 38 insertions(+)
create mode 100644 NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_latest.def
diff --git a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/build.txt b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/build.txt
index 2bcba44..d7f9057 100644
--- a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/build.txt
+++ b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/build.txt
@@ -10,5 +10,14 @@ DEF_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet/
apptainer build $CONTAINER_DIR $DEF_DIR
+
+MODULE_NAME=nnunet_for_pytorch
+MODULE_VERSION=latest
+CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif
+DEF_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}_${MODULE_VERSION}.def
+
+apptainer build $CONTAINER_DIR $DEF_DIR
+
+
# Known issue
https://github.com/NVIDIA/DeepLearningExamples/issues/1113
diff --git a/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_latest.def b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_latest.def
new file mode 100644
index 0000000..fabd296
--- /dev/null
+++ b/NVIDIA/DeepLearningExamples/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_latest.def
@@ -0,0 +1,29 @@
+Bootstrap: localimage
+From: /proj/nsc_testing/xuan/containers/nvidia_pytorch_21.11-py3.sif
+
+
+%environment
+
+export PYTHONNOUSERSITE=True
+export OMP_NUM_THREADS=2
+
+%post
+
+VERSION=latest
+
+mkdir /workspace/nnunet_pyt
+cd /workspace/nnunet_pyt
+git clone https://github.com/NVIDIA/DeepLearningExamples.git
+mv DeepLearningExamples/PyTorch/Segmentation/nnUNet ./
+rm -rf DeepLearningExamples
+
+pip install --disable-pip-version-check -r requirements.txt
+pip install monai==1.0.0 --no-dependencies
+pip pip install numpy --upgrade
+
+curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
+unzip -qq awscliv2.zip
+./aws/install
+rm -rf awscliv2.zip aws
+
+cp utils/instance_norm.py /usr/local/lib/python3.8/dist-packages/apex/normalization
--
GitLab