Update 3 files

- /PyTorch/Segmentation/nnUNet/nnunet_for_pytorch.def
- /PyTorch/Segmentation/nnUNet/build.txt
- /PyTorch/Segmentation/nnUNet/nnunet_for_pytorch_21.11.0.def

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/${MODULE_NAME}.def
+apptainer build ./containers/${MODULE_NAME}_${MODULE_VERSION}.sif ./berzelius-benchmarks/PyTorch/Segmentation/nnUNet/${MODULE_NAME}.def
 
 
 WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
@@ -18,11 +18,14 @@ cd $WORK_DIR
 mkdir -p data 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 --results $WORK_DIR/data
+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 --data $WORK_DIR/data --results $WORK_DIR/results
+apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR  python /workspace/nnunet_pyt/preprocess.py --task 01 --dim 2
  
 
 apptainer exec --nv --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode train --gpus 1 --dim 2 --batch_size 128 --amp