Update 2 files

- /PyTorch/Segmentation/nnUNet/benchmark.txt
- /PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh

PyTorch/Segmentation/nnUNet/benchmark.txt

@@ -8,20 +8,17 @@ CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}
 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 -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --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
+apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --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 -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --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
+apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --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

PyTorch/Segmentation/nnUNet/run_benchmark_single_node.sh

@@ -25,7 +25,7 @@ WORK_DIR=/proj/nsc_testing/xuan/berzelius-benchmarks/PyTorch/Segmentation/nnUNet
 CONTAINER_DIR=/proj/nsc_testing/xuan/containers/${MODULE_NAME}_${MODULE_VERSION}.sif
 
 rm -f $WORK_DIR/results/$LOG_DIR
-apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results $CONTAINER_DIR bash -c "cd /workspace/nnunet_pyt && python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --nodes ${2} --amp --logname='$LOG_DIR'" 
+apptainer exec --nv -B ${WORK_DIR}/data:/data -B ${WORK_DIR}/results:/results --pwd /workspace/nnunet_pyt $CONTAINER_DIR python scripts/benchmark.py --mode train --gpus ${3} --dim ${1} --batch_size ${4} --nodes ${2} --amp --logname='$LOG_DIR'
 
 
 EOT