add non-deterministic note
Browse files- README.md +9 -6
- configs/metadata.json +3 -2
- docs/README.md +9 -6
README.md
CHANGED
@@ -109,18 +109,21 @@ CPU: Memory: **2.3G**
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![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
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## MONAI Bundle Commands
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In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.
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For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
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#### Execute training
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```
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python -m monai.bundle run --config_file configs/train.json
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```
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#### Override the `train` config to execute multi-GPU training
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```
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torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
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@@ -128,24 +131,24 @@ torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config
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Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
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#### Override the `train` config to execute evaluation with the trained model
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```
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python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
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```
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#### Override the `train` config and `evaluate` config to execute multi-GPU evaluation
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```
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torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']"
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```
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-
#### Execute inference
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```
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python -m monai.bundle run --config_file configs/inference.json
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```
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-
#### Execute inference with Data Samples
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```
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python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
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![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
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+
Please note that this bundle is non-deterministic because of the trilinear interpolation used in the network. Therefore, reproducing the training process may not get exactly the same performance.
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+
Please refer to https://pytorch.org/docs/stable/notes/randomness.html#reproducibility for more details about reproducibility.
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+
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## MONAI Bundle Commands
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In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.
|
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For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
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+
#### Execute training:
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```
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python -m monai.bundle run --config_file configs/train.json
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```
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+
#### Override the `train` config to execute multi-GPU training:
|
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```
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torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
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Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
|
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+
#### Override the `train` config to execute evaluation with the trained model:
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```
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python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
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```
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+
#### Override the `train` config and `evaluate` config to execute multi-GPU evaluation:
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```
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torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']"
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```
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+
#### Execute inference:
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```
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python -m monai.bundle run --config_file configs/inference.json
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```
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+
#### Execute inference with Data Samples:
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```
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python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
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configs/metadata.json
CHANGED
@@ -1,13 +1,14 @@
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{
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"schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
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"version": "0.1.
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"changelog": {
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"0.1.2": "Update figure with links",
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"0.1.1": "adapt to BundleWorkflow interface and val metric",
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"0.1.0": "complete the model package",
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"0.0.1": "initialize the model package structure"
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},
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"monai_version": "1.2.
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"pytorch_version": "1.13.1",
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"numpy_version": "1.22.2",
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"optional_packages_version": {
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{
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"schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
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"version": "0.1.3",
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"changelog": {
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"0.1.3": "add non-deterministic note",
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"0.1.2": "Update figure with links",
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"0.1.1": "adapt to BundleWorkflow interface and val metric",
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"0.1.0": "complete the model package",
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"0.0.1": "initialize the model package structure"
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},
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"monai_version": "1.2.0rc4",
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"pytorch_version": "1.13.1",
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"numpy_version": "1.22.2",
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"optional_packages_version": {
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docs/README.md
CHANGED
@@ -102,18 +102,21 @@ CPU: Memory: **2.3G**
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![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
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|
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|
|
|
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|
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## MONAI Bundle Commands
|
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In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.
|
107 |
|
108 |
For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
|
109 |
|
110 |
-
#### Execute training
|
111 |
|
112 |
```
|
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python -m monai.bundle run --config_file configs/train.json
|
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```
|
115 |
|
116 |
-
#### Override the `train` config to execute multi-GPU training
|
117 |
|
118 |
```
|
119 |
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
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@@ -121,24 +124,24 @@ torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config
|
|
121 |
|
122 |
Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
|
123 |
|
124 |
-
#### Override the `train` config to execute evaluation with the trained model
|
125 |
|
126 |
```
|
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python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
|
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```
|
129 |
|
130 |
-
#### Override the `train` config and `evaluate` config to execute multi-GPU evaluation
|
131 |
|
132 |
```
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torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']"
|
134 |
```
|
135 |
|
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-
#### Execute inference
|
137 |
|
138 |
```
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python -m monai.bundle run --config_file configs/inference.json
|
140 |
```
|
141 |
-
#### Execute inference with Data Samples
|
142 |
|
143 |
```
|
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python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
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![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
|
104 |
|
105 |
+
Please note that this bundle is non-deterministic because of the trilinear interpolation used in the network. Therefore, reproducing the training process may not get exactly the same performance.
|
106 |
+
Please refer to https://pytorch.org/docs/stable/notes/randomness.html#reproducibility for more details about reproducibility.
|
107 |
+
|
108 |
## MONAI Bundle Commands
|
109 |
In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.
|
110 |
|
111 |
For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
|
112 |
|
113 |
+
#### Execute training:
|
114 |
|
115 |
```
|
116 |
python -m monai.bundle run --config_file configs/train.json
|
117 |
```
|
118 |
|
119 |
+
#### Override the `train` config to execute multi-GPU training:
|
120 |
|
121 |
```
|
122 |
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
|
|
|
124 |
|
125 |
Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove `--standalone`, modify `--nnodes`, or do some other necessary changes according to the machine used. For more details, please refer to [pytorch's official tutorial](https://pytorch.org/tutorials/intermediate/ddp_tutorial.html).
|
126 |
|
127 |
+
#### Override the `train` config to execute evaluation with the trained model:
|
128 |
|
129 |
```
|
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python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
|
131 |
```
|
132 |
|
133 |
+
#### Override the `train` config and `evaluate` config to execute multi-GPU evaluation:
|
134 |
|
135 |
```
|
136 |
torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json','configs/multi_gpu_evaluate.json']"
|
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```
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|
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+
#### Execute inference:
|
140 |
|
141 |
```
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python -m monai.bundle run --config_file configs/inference.json
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```
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144 |
+
#### Execute inference with Data Samples:
|
145 |
|
146 |
```
|
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python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
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