From 4da2fb3c9d545d77b98d4add1c67c3331077b811 Mon Sep 17 00:00:00 2001
From: Xuan Gu <xuan.gu@liu.se>
Date: Wed, 27 Sep 2023 21:42:11 +0000
Subject: [PATCH] Update 2 files
- /PyTorch/Segmentation/nnUNet/build.txt
- /PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
---
PyTorch/Segmentation/nnUNet/build.txt | 2 +-
.../nnUNet/nnunet_for_pytorch_21.11.0.def | 17 ++++-------------
2 files changed, 5 insertions(+), 14 deletions(-)
diff --git a/PyTorch/Segmentation/nnUNet/build.txt b/PyTorch/Segmentation/nnUNet/build.txt
index 47a7948..e3e069b 100644
--- a/PyTorch/Segmentation/nnUNet/build.txt
+++ b/PyTorch/Segmentation/nnUNet/build.txt
@@ -8,7 +8,7 @@ gotesting
MODULE_NAME=nnunet_for_pytorch
MODULE_VERSION=21.11.0
-apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}.def
+apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}_${MODULE_VERSION}.def
WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
diff --git a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
index 03f7621..99b03ea 100644
--- a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
+++ b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def
@@ -18,19 +18,10 @@ unzip nnunet_for_pytorch_21.11.0.zip
# Fix for https://github.com/NVIDIA/DeepLearningExamples/issues/1113
#sed 's/pytorch-lightning==1.3.8/pytorch-lightning==1.5.10/g' requirements.txt > temp_file && mv temp_file requirements.txt
-#pip install --disable-pip-version-check -r requirements.txt
-#pip install monai==0.8.0 --no-dependencies
-#pip uninstall -y torchtext
-
-conda install -y nibabel==3.2.1 \
-joblib==1.0.1 \
-pytorch-lightning==1.3.8 \
-scikit-learn==1.0 \
-scikit-image==0.18.3 \
-pynvml==11.0.0 \
-monai==0.8.0
-
-conda remove -y torchtext
+pip install --disable-pip-version-check -r requirements.txt
+pip install monai==0.8.0 --no-dependencies
+pip uninstall -y torchtext torchmetrics
+pip install torchmetrics==0.6.0
curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
unzip -qq awscliv2.zip
--
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