diff --git a/PyTorch/Segmentation/nnUNet/benchmark.txt b/PyTorch/Segmentation/nnUNet/benchmark.txt index 7ee89dfc9857a996e31add10fece2aeaae500454..5aa121aef8c9b1757449fdc9203706405f2660cd 100644 --- a/PyTorch/Segmentation/nnUNet/benchmark.txt +++ b/PyTorch/Segmentation/nnUNet/benchmark.txt @@ -25,4 +25,5 @@ apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/be # Known issue +# ImportError: cannot import name 'get_num_classes' from 'torchmetrics.utilities.data' (/opt/conda/lib/python3.8/site-packages/torchmetrics/utilities/data.py) https://github.com/NVIDIA/DeepLearningExamples/issues/1113 diff --git a/PyTorch/Segmentation/nnUNet/build.txt b/PyTorch/Segmentation/nnUNet/build.txt index 258b49152ae283c08d44ae1f6bbae9f7505005b2..1a679dabd10f3fb4cb20e1b5054bd66370d207b9 100644 --- a/PyTorch/Segmentation/nnUNet/build.txt +++ b/PyTorch/Segmentation/nnUNet/build.txt @@ -3,12 +3,13 @@ https://catalog.ngc.nvidia.com/orgs/nvidia/resources/nnunet_for_pytorch/quick-st apptainer build containers/nvidia_pytorch_21.11-py3.sif docker://nvcr.io/nvidia/pytorch:21.11-py3 export APPTAINER_BINDPATH= -gotesting MODULE_NAME=nnunet_for_pytorch MODULE_VERSION=21.11.0 +CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif +DEF_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}_${MODULE_VERSION}.def -apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}_${MODULE_VERSION}.def +apptainer build $CONTAINER_DIR $DEF_DIR # Known issue diff --git a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def index 31fa8fe6ab5fc4a64505adc961e9bd3a3ead0c70..abaedb402d4590879b54581058b0efb8d18e13a5 100644 --- a/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def +++ b/PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def @@ -16,7 +16,7 @@ cd /workspace/nnunet_pyt wget --content-disposition https://api.ngc.nvidia.com/v2/resources/nvidia/nnunet_for_pytorch/versions/$VERSION/zip -O nnunet_for_pytorch_$VERSION.zip unzip nnunet_for_pytorch_21.11.0.zip -#sed 's/pytorch-lightning==1.3.8/pytorch-lightning==1.5.0/g' requirements.txt > temp_file && mv temp_file requirements.txt +sed 's/pytorch-lightning==1.3.8/pytorch-lightning==1.6.0/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