diff --git a/PyTorch/Segmentation/nnUNet/benchmark.txt b/PyTorch/Segmentation/nnUNet/benchmark.txt new file mode 100644 index 0000000000000000000000000000000000000000..b11aada6fe687d311874327ea3fe0d851468fe00 --- /dev/null +++ b/PyTorch/Segmentation/nnUNet/benchmark.txt @@ -0,0 +1,29 @@ + + +MODULE_NAME=nnunet_for_pytorch +MODULE_VERSION=21.11.0 + +WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet +CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif + +mkdir -p $WORK_DIR/data $WORK_DIR/results + + +export APPTAINER_BINDPATH=$WORK_DIR/data:/data,$WORK_DIR/results:/results + + +To download and preprocess the data run: + +apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python download.py --task 01 + +apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python /workspace/nnunet_pyt/preprocess.py --task 01 --dim 2 + +Start benchmarking: + +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 +https://github.com/NVIDIA/DeepLearningExamples/issues/1113