[DLMED] update based on enhancement

Signed-off-by: Nic Ma <[email protected]>

Author: Nic-Ma

modules/bundles/spleen_segmentation/configs/inference.json

@@ -3,12 +3,12 @@
         "$import glob",
         "$import os"
     ],
-    "cudnn_opt": "$setattr(torch.backends.cudnn, 'benchmark', True)",
-    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
-    "ckpt_path": "/workspace/data/tutorials/modules/bundles/spleen_segmentation/models/model.pt",
+    "bundle_root": "/workspace/data/tutorials/modules/bundles/spleen_segmentation",
+    "ckpt_path": "$@bundle_root + '/models/model.pt'",
     "download_ckpt": "$monai.apps.utils.download_url('https://huggingface.co/MONAI/example_spleen_segmentation/resolve/main/model.pt', @ckpt_path)",
     "dataset_dir": "/workspace/data/Task09_Spleen",
     "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
+    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
     "network_def": {
         "_target_": "UNet",
         "spatial_dims": 3,
@@ -120,13 +120,16 @@
     ],
     "evaluator": {
         "_target_": "SupervisedEvaluator",
-        "_requires_": "@cudnn_opt",
         "device": "@device",
         "val_data_loader": "@dataloader",
         "network": "@network",
         "inferer": "@inferer",
         "postprocessing": "@postprocessing",
         "val_handlers": "@handlers",
         "amp": true
-    }
+    },
+    "evaluating": [
+        "$setattr(torch.backends.cudnn, 'benchmark', True)",
+        "[email protected]()"
+    ]
 }

modules/bundles/spleen_segmentation/configs/train.json

@@ -4,9 +4,9 @@
         "$import os",
         "$import ignite"
     ],
-    "bundle_root": "/workspace/data/medical/tutorials/modules/bundles/spleen_segmentation",
+    "bundle_root": "/workspace/data/tutorials/modules/bundles/spleen_segmentation",
     "ckpt_dir": "$@bundle_root + '/models'",
-    "dataset_dir": "/workspace/data/medical/Task09_Spleen",
+    "dataset_dir": "/workspace/data/Task09_Spleen",
     "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))",
     "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))",
     "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",

modules/bundles/spleen_segmentation/configs/train_multi_gpu.json

@@ -5,12 +5,12 @@
         "$import ignite",
         "$import torch.distributed as dist"
     ],
-    "device": "$torch.device(f'cuda:{dist.get_rank()}')",
-    "bundle_root": "/workspace/data/medical/tutorials/modules/bundles/spleen_segmentation",
+    "bundle_root": "/workspace/data/tutorials/modules/bundles/spleen_segmentation",
     "ckpt_dir": "$@bundle_root + '/models'",
-    "dataset_dir": "/workspace/data/medical/Task09_Spleen",
+    "dataset_dir": "/workspace/data/Task09_Spleen",
     "images": "$list(sorted(glob.glob(@dataset_dir + '/imagesTr/*.nii.gz')))",
     "labels": "$list(sorted(glob.glob(@dataset_dir + '/labelsTr/*.nii.gz')))",
+    "device": "$torch.device(f'cuda:{dist.get_rank()}')",
     "network_def": {
         "_target_": "UNet",
         "spatial_dims": 3,
@@ -255,7 +255,7 @@
         }
     },
     "training": [
-        "$dist.init_process_group(backend='nccl', init_method='env://')",
+        "$dist.init_process_group(backend='nccl')",
         "$torch.cuda.set_device(@device)",
         "$monai.utils.set_determinism(seed=123)",
         "$setattr(torch.backends.cudnn, 'benchmark', True)",

modules/bundles/spleen_segmentation/docs/README.md

@@ -32,13 +32,13 @@ python -m monai.bundle run training --meta_file configs/metadata.json --config_f
 Execute multi-GPU training:
 
 ```
-torchrun --nproc_per_node=2 -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train_multi_gpu.json --logging_file configs/logging.conf
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run training --meta_file configs/metadata.json --config_file configs/train_multi_gpu.json --logging_file configs/logging.conf
 ```
 
 Execute inference:
 
 ```
-python -m monai.bundle run evaluator --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
+python -m monai.bundle run evaluating --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
 ```
 
 Verify the metadata format: