From 7aef9cc3296a41998d739ae0908d96d4cbc7b011 Mon Sep 17 00:00:00 2001 From: Xuan Gu <xuan.gu@liu.se> Date: Wed, 27 Sep 2023 21:21:42 +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 | 1 + .../nnUNet/nnunet_for_pytorch_21.11.0.def | 18 ++++++++++++++---- 2 files changed, 15 insertions(+), 4 deletions(-) diff --git a/PyTorch/Segmentation/nnUNet/build.txt b/PyTorch/Segmentation/nnUNet/build.txt index 003ef31..47a7948 100644 --- a/PyTorch/Segmentation/nnUNet/build.txt +++ b/PyTorch/Segmentation/nnUNet/build.txt @@ -29,6 +29,7 @@ apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python /workspac apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode train --gpus 1 --dim 2 --batch_size 256 --amp +apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode predict --gpus 1 --dim 2 --batch_size 256 --amp # Known issue 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 c9f11ed..03f7621 100644 --- a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def +++ b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def @@ -17,10 +17,20 @@ wget --content-disposition https://api.ngc.nvidia.com/v2/resources/nvidia/nnunet 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 +#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 curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip" unzip -qq awscliv2.zip -- GitLab