|
- /home/aistudio/MedicalSeg
- 2022-06-13 19:21:34 [INFO]
- ------------Environment Information-------------
- platform: Linux-4.15.0-140-generic-x86_64-with-debian-stretch-sid
- Python: 3.7.4 (default, Aug 13 2019, 20:35:49) [GCC 7.3.0]
- Paddle compiled with cuda: True
- NVCC: Cuda compilation tools, release 10.1, V10.1.243
- cudnn: 7.6
- GPUs used: 1
- CUDA_VISIBLE_DEVICES: 0
- GPU: ['GPU 0: Tesla V100-SXM2-32GB']
- GCC: gcc (Ubuntu 7.5.0-3ubuntu1~16.04) 7.5.0
- PaddlePaddle: 2.2.2
- OpenCV: 4.1.1
- ------------------------------------------------
- /home/aistudio/MedicalSeg/paddleseg3d/cvlibs/config.py:434: UserWarning: Warning: The data dir now is /home/aistudio/MedicalSeg/data/, you should change the data_root in the global.yml if this directory didn't have enough space
- .format(absolute_data_dir))
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- W0613 19:21:41.270819 9028 device_context.cc:447] Please NOTE: device: 0, GPU Compute Capability: 7.0, Driver API Version: 11.2, Runtime API Version: 10.1
- W0613 19:21:41.270879 9028 device_context.cc:465] device: 0, cuDNN Version: 7.6.
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- net_numpool: 5
- 2022-06-13 19:21:48 [INFO]
- ---------------Config Information---------------
- batch_size: 2
- data_root: data/
- iters: 20
- loss:
- coef:
- - 1
- types:
- - coef:
- - 1.0
- ignore_index: 255
- losses:
- - batch_dice: false
- do_bg: false
- type: DC_and_CE_loss
- plan_path: /home/aistudio/data/preprocessed/Task006_Lung/nnUNetPlansv2.1_plans_3D.pkl
- stage: 0
- type: MultipleLoss
- lr_scheduler:
- end_lr: 0
- learning_rate: 0.01
- power: 0.9
- type: PolynomialDecay
- model:
- plans_path: /home/aistudio/data/preprocessed/Task006_Lung/nnUNetPlansv2.1_plans_3D.pkl
- stage: 0
- type: NNUNet
- optimizer:
- momentum: 0.99
- type: sgd
- use_nesterov: true
- weight_decay: 3.0e-05
- train_dataset:
- cropped_data_dir: /home/aistudio/data/cropped/Task006_Lung
- dataset_directory: 0
- dataset_root: luna16_lobe51/luna16_lobe51_phase0
- decathlon_dir: /home/aistudio/data/Task006_Lung
- fold: 0
- mode: train
- num_batches_per_epoch: 250
- output_folder: /home/aistudio/data/dataset_output
- plan2d: false
- plan3d: true
- plans_name: nnUNetPlansv2.1_plans_3D.pkl
- preprocessed_dir: /home/aistudio/data/preprocessed/Task006_Lung
- raw_data_dir: /home/aistudio/data/Task06_Lung
- result_dir: luna16_lobe51/luna16_lobe51_phase1
- stage: 0
- type: MSDDataset
- unpack_data: true
- val_dataset:
- cropped_data_dir: /home/aistudio/data/cropped/Task006_Lung
- dataset_root: luna16_lobe51/luna16_lobe51_phase0
- decathlon_dir: /home/aistudio/data/Task006_Lung
- fold: 0
- mode: val
- num_batches_per_epoch: 10
- output_folder: /home/aistudio/data/dataset_output
- plans_name: nnUNetPlansv2.1_plans_3D.pkl
- preprocessed_dir: /home/aistudio/data/preprocessed/Task006_Lung
- raw_data_dir: /home/aistudio/data/Task06_Lung
- result_dir: luna16_lobe51/luna16_lobe51_phase1
- stage: 0
- type: MSDDataset
- unpack_data: true
- ------------------------------------------------
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- <class 'paddle.nn.layer.conv.Conv3D'>'s flops has been counted
- Cannot find suitable count function for <class 'paddle.nn.layer.norm.InstanceNorm3D'>. Treat it as zero FLOPs.
- <class 'paddle.nn.layer.activation.LeakyReLU'>'s flops has been counted
- Cannot find suitable count function for <class 'paddle.fluid.dygraph.container.LayerList'>. Treat it as zero FLOPs.
- <class 'paddle.nn.layer.conv.Conv3DTranspose'>'s flops has been counted
- /opt/conda/envs/python35-paddle120-env/lib/python3.7/site-packages/paddle/tensor/creation.py:130: DeprecationWarning: `np.object` is a deprecated alias for the builtin `object`. To silence this warning, use `object` by itself. Doing this will not modify any behavior and is safe.
- Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
- if data.dtype == np.object:
- Total Flops: 625152883200 Total Params: 30785184
- Run successfully with command - nnunet - python3 train.py --config test_tipc/configs/nnunet/nnunet_3d_cascade_stage0.yml --save_interval 20 --seed 100 --num_workers 8 --save_dir=./test_tipc/output/nnunet/norm_gpus_0_autocast_null --iters=20 --batch_size=2 !
- /home/aistudio/MedicalSeg/paddleseg3d/cvlibs/config.py:434: UserWarning: Warning: The data dir now is /home/aistudio/MedicalSeg/data/, you should change the data_root in the global.yml if this directory didn't have enough space
- .format(absolute_data_dir))
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- W0613 19:23:54.512336 9254 device_context.cc:447] Please NOTE: device: 0, GPU Compute Capability: 7.0, Driver API Version: 11.2, Runtime API Version: 10.1
- W0613 19:23:54.512392 9254 device_context.cc:465] device: 0, cuDNN Version: 7.6.
- net_numpool: 5
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: val, keys: ['lung_006' 'lung_010' 'lung_033' 'lung_034' 'lung_041' 'lung_042'
- 'lung_046' 'lung_048' 'lung_059' 'lung_065' 'lung_066' 'lung_070'
- 'lung_079']
- 2022-06-13 19:23:56 [INFO]
- ---------------Config Information---------------
- batch_size: 1
- data_root: data/
- iters: 25000
- loss:
- coef:
- - 1
- types:
- - coef:
- - 1.0
- ignore_index: 255
- losses:
- - batch_dice: false
- do_bg: false
- type: DC_and_CE_loss
- plan_path: /home/aistudio/data/preprocessed/Task006_Lung/nnUNetPlansv2.1_plans_3D.pkl
- stage: 0
- type: MultipleLoss
- lr_scheduler:
- end_lr: 0
- learning_rate: 0.01
- power: 0.9
- type: PolynomialDecay
- model:
- plans_path: /home/aistudio/data/preprocessed/Task006_Lung/nnUNetPlansv2.1_plans_3D.pkl
- stage: 0
- type: NNUNet
- optimizer:
- momentum: 0.99
- type: sgd
- use_nesterov: true
- weight_decay: 3.0e-05
- train_dataset:
- cropped_data_dir: /home/aistudio/data/cropped/Task006_Lung
- dataset_directory: 0
- dataset_root: luna16_lobe51/luna16_lobe51_phase0
- decathlon_dir: /home/aistudio/data/Task006_Lung
- fold: 0
- mode: train
- num_batches_per_epoch: 250
- output_folder: /home/aistudio/data/dataset_output
- plan2d: false
- plan3d: true
- plans_name: nnUNetPlansv2.1_plans_3D.pkl
- preprocessed_dir: /home/aistudio/data/preprocessed/Task006_Lung
- raw_data_dir: /home/aistudio/data/Task06_Lung
- result_dir: luna16_lobe51/luna16_lobe51_phase1
- stage: 0
- type: MSDDataset
- unpack_data: true
- val_dataset:
- cropped_data_dir: /home/aistudio/data/cropped/Task006_Lung
- dataset_root: luna16_lobe51/luna16_lobe51_phase0
- decathlon_dir: /home/aistudio/data/Task006_Lung
- fold: 0
- mode: val
- num_batches_per_epoch: 10
- output_folder: /home/aistudio/data/dataset_output
- plans_name: nnUNetPlansv2.1_plans_3D.pkl
- preprocessed_dir: /home/aistudio/data/preprocessed/Task006_Lung
- raw_data_dir: /home/aistudio/data/Task06_Lung
- result_dir: luna16_lobe51/luna16_lobe51_phase1
- stage: 0
- type: MSDDataset
- unpack_data: true
- ------------------------------------------------
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- 2022-06-13 19:24:07 [INFO] Loading pretrained model from ./test_tipc/output/nnunet/norm_gpus_0_autocast_null/iter_20/model.pdparams
- 2022-06-13 19:24:07 [INFO] There are 98/98 variables loaded into NNUNet.
- 2022-06-13 19:24:07 [INFO] Loaded trained params of model successfully
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- start evaluating...
- val_save_folder/fold_0/validation_raw/lung_006.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_010.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_033.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_034.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_041.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_042.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_046.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_048.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_059.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_065.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_066.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_070.nii.gz already exists, skip.
- val_save_folder/fold_0/validation_raw/lung_079.nii.gz already exists, skip.
- /home/aistudio/MedicalSeg/nnunet_tools/evaluator.py:351: RuntimeWarning: Mean of empty slice
- all_scores["mean"][label][score] = float(np.nanmean(all_scores["mean"][label][score]))
- Foreground vs background
- before: 0.0
- after: 0.0
- Only one class present, no need to do each class separately as this is covered in fg vs bg
- done
- for which classes:
- []
- min_object_sizes
- None
- done
- copy gt from /home/aistudio/data/preprocessed/Task006_Lung/gt_segmentations to val_save_folder/gt_niftis.
- Run successfully with command - nnunet - python3 nnunet_tools/nnunet_fold_val.py --config test_tipc/configs/nnunet/nnunet_3d_cascade_stage0.yml --num_workers 8 --model_path=./test_tipc/output/nnunet/norm_gpus_0_autocast_null/iter_20/model.pdparams !
- /home/aistudio/MedicalSeg/paddleseg3d/cvlibs/config.py:434: UserWarning: Warning: The data dir now is /home/aistudio/MedicalSeg/data/, you should change the data_root in the global.yml if this directory didn't have enough space
- .format(absolute_data_dir))
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- W0613 19:25:02.953327 9424 device_context.cc:447] Please NOTE: device: 0, GPU Compute Capability: 7.0, Driver API Version: 11.2, Runtime API Version: 10.1
- W0613 19:25:02.957360 9424 device_context.cc:465] device: 0, cuDNN Version: 7.6.
- found unpacked dataset.
- loading dataset
- loading all case properties
- dataset split over! dataset mode: train, keys: ['lung_001' 'lung_003' 'lung_004' 'lung_005' 'lung_009' 'lung_014'
- 'lung_015' 'lung_016' 'lung_018' 'lung_020' 'lung_022' 'lung_023'
- 'lung_025' 'lung_026' 'lung_027' 'lung_028' 'lung_029' 'lung_031'
- 'lung_036' 'lung_037' 'lung_038' 'lung_043' 'lung_044' 'lung_045'
- 'lung_047' 'lung_049' 'lung_051' 'lung_053' 'lung_054' 'lung_055'
- 'lung_057' 'lung_058' 'lung_061' 'lung_062' 'lung_064' 'lung_069'
- 'lung_071' 'lung_073' 'lung_074' 'lung_075' 'lung_078' 'lung_080'
- 'lung_081' 'lung_083' 'lung_084' 'lung_086' 'lung_092' 'lung_093'
- 'lung_095' 'lung_096']
- 2022-06-13 19:25:08 [INFO] Loaded trained params of model successfully.
- /opt/conda/envs/python35-paddle120-env/lib/python3.7/site-packages/paddle/fluid/layers/utils.py:77: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working
- return (isinstance(seq, collections.Sequence) and
- 2022-06-13 19:25:11 [INFO] Model is saved in ./test_tipc/output/nnunet/norm_gpus_0_autocast_null.
- Run successfully with command - nnunet - python3 export.py --config test_tipc/configs/nnunet/nnunet_3d_cascade_stage0.yml --without_argmax --with_softmax --model_path=./test_tipc/output/nnunet/norm_gpus_0_autocast_null/iter_20/model.pdparams --save_dir=./test_tipc/output/nnunet/norm_gpus_0_autocast_null!
- ------------args parse-----------------
- infer image list: ['/home/aistudio/data/Task006_Lung/imagesTs/lung_008_0000.nii.gz']
- predictor======================
- --------------load plan over----------------------
- 2022-06-13 19:25:15 [INFO] Use GPU
- W0613 19:25:16.137565 9505 analysis_predictor.cc:795] The one-time configuration of analysis predictor failed, which may be due to native predictor called first and its configurations taken effect.
- --- Running analysis [ir_graph_build_pass]
- --- Running analysis [ir_graph_clean_pass]
- --- Running analysis [ir_analysis_pass]
- --- Running IR pass [is_test_pass]
- --- Running IR pass [simplify_with_basic_ops_pass]
- --- Running IR pass [conv_affine_channel_fuse_pass]
- --- Running IR pass [conv_eltwiseadd_affine_channel_fuse_pass]
- --- Running IR pass [conv_bn_fuse_pass]
- --- Running IR pass [conv_eltwiseadd_bn_fuse_pass]
- --- Running IR pass [embedding_eltwise_layernorm_fuse_pass]
- --- Running IR pass [multihead_matmul_fuse_pass_v2]
- --- Running IR pass [squeeze2_matmul_fuse_pass]
- --- Running IR pass [reshape2_matmul_fuse_pass]
- --- Running IR pass [flatten2_matmul_fuse_pass]
- --- Running IR pass [map_matmul_v2_to_mul_pass]
- --- Running IR pass [map_matmul_v2_to_matmul_pass]
- --- Running IR pass [map_matmul_to_mul_pass]
- --- Running IR pass [fc_fuse_pass]
- --- Running IR pass [fc_elementwise_layernorm_fuse_pass]
- --- Running IR pass [conv_elementwise_add_act_fuse_pass]
- --- Running IR pass [conv_elementwise_add2_act_fuse_pass]
- --- Running IR pass [conv_elementwise_add_fuse_pass]
- --- Running IR pass [transpose_flatten_concat_fuse_pass]
- --- Running IR pass [runtime_context_cache_pass]
- --- Running analysis [ir_params_sync_among_devices_pass]
- I0613 19:25:16.313962 9505 ir_params_sync_among_devices_pass.cc:45] Sync params from CPU to GPU
- --- Running analysis [adjust_cudnn_workspace_size_pass]
- --- Running analysis [inference_op_replace_pass]
- --- Running analysis [memory_optimize_pass]
- I0613 19:25:16.395953 9505 memory_optimize_pass.cc:216] Cluster name : x size: 4
- I0613 19:25:16.395985 9505 memory_optimize_pass.cc:216] Cluster name : leaky_relu_1.tmp_0 size: 128
- I0613 19:25:16.395989 9505 memory_optimize_pass.cc:216] Cluster name : leaky_relu_5.tmp_0 size: 512
- I0613 19:25:16.395992 9505 memory_optimize_pass.cc:216] Cluster name : conv3d_transpose_5.tmp_0 size: 1280
- I0613 19:25:16.395996 9505 memory_optimize_pass.cc:216] Cluster name : leaky_relu_7.tmp_0 size: 1024
- I0613 19:25:16.395999 9505 memory_optimize_pass.cc:216] Cluster name : concat_0.tmp_0 size: 2560
- I0613 19:25:16.396003 9505 memory_optimize_pass.cc:216] Cluster name : instance_norm_11.tmp_1 size: 4
- I0613 19:25:16.396006 9505 memory_optimize_pass.cc:216] Cluster name : leaky_relu_3.tmp_0 size: 256
- I0613 19:25:16.396009 9505 memory_optimize_pass.cc:216] Cluster name : leaky_relu_9.tmp_0 size: 1280
- I0613 19:25:16.396013 9505 memory_optimize_pass.cc:216] Cluster name : conv3d_37.tmp_1 size: 1280
- --- Running analysis [ir_graph_to_program_pass]
- I0613 19:25:16.436733 9505 analysis_predictor.cc:714] ======= optimize end =======
- I0613 19:25:16.439801 9505 naive_executor.cc:98] --- skip [feed], feed -> x
- I0613 19:25:16.441469 9505 naive_executor.cc:98] --- skip [softmax_1.tmp_0], fetch -> fetch
- W0613 19:25:34.054422 9505 device_context.cc:447] Please NOTE: device: 0, GPU Compute Capability: 7.0, Driver API Version: 11.2, Runtime API Version: 10.1
- W0613 19:25:34.058297 9505 device_context.cc:465] device: 0, cuDNN Version: 7.6.
- no separate z, order 3
- no separate z, order 1
- before: {'spacing': array([1.5 , 0.75, 0.75]), 'spacing_transposed': array([1.5 , 0.75, 0.75]), 'data.shape (data is transposed)': (1, 199, 512, 512)}
- after: {'spacing': array([2.35358718, 1.48430795, 1.48430795]), 'data.shape (data is resampled)': (1, 127, 259, 259)}
-
- debug: mirroring True mirror_axes (0, 1, 2)
- step_size: 0.5
- do mirror: True
- data shape: (1, 127, 259, 259)
- patch size: [ 80 192 160]
- steps (x, y, and z): [[0, 24, 47], [0, 67], [0, 50, 99]]
- number of tiles: 18
- computing Gaussian
- done
- initializing result array (on GPU)
- initializing result_numsamples (on GPU)
- copying results to CPU
- prediction done
- force_separate_z: None interpolation order: 1
- separate z: False lowres axis None
- no separate z, order 1
- sitk save: ./output/lung_008_0000.nii.nii.gz
- 2022-06-13 19:26:18 [INFO] Finish
- infer over!
- Run successfully with command - nnunet - python3 nnunet_tools/nnunet_infer.py --stage 0 --plan_path /home/aistudio/data/preprocessed/Task006_Lung/nnUNetPlansv2.1_plans_3D.pkl --with_argmax False --device=gpu --use_trt=False --precision=fp32 --config=./test_tipc/output/nnunet/norm_gpus_0_autocast_null//deploy.yaml --batch_size=1 --image_path=/home/aistudio/data/Task006_Lung/imagesTs/lung_008_0000.nii.gz --benchmark=False > ./test_tipc/output/nnunet/python_infer_gpu_usetrt_False_precision_fp32_batchsize_1.log 2>&1 !
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