Update file benchmark.txt

PyTorch/Segmentation/nnUNet/benchmark.txt

+
+
+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