monai
medical
katielink commited on
Commit
72b8d86
1 Parent(s): 52b2aaa

add non-deterministic note

Browse files
Files changed (3) hide show
  1. README.md +9 -6
  2. configs/metadata.json +3 -2
  3. 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
113
  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.
114
 
115
  For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
116
 
117
- #### Execute training
118
 
119
  ```
120
  python -m monai.bundle run --config_file configs/train.json
121
  ```
122
 
123
- #### Override the `train` config to execute multi-GPU training
124
 
125
  ```
126
  torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
@@ -128,24 +131,24 @@ torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config
128
 
129
  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).
130
 
131
- #### Override the `train` config to execute evaluation with the trained model
132
 
133
  ```
134
  python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
135
  ```
136
 
137
- #### Override the `train` config and `evaluate` config to execute multi-GPU evaluation
138
 
139
  ```
140
  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']"
141
  ```
142
 
143
- #### Execute inference
144
 
145
  ```
146
  python -m monai.bundle run --config_file configs/inference.json
147
  ```
148
- #### Execute inference with Data Samples
149
 
150
  ```
151
  python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
 
109
 
110
  ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
111
 
112
+ 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.
113
+ Please refer to https://pytorch.org/docs/stable/notes/randomness.html#reproducibility for more details about reproducibility.
114
+
115
  ## MONAI Bundle Commands
116
  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.
117
 
118
  For more details usage instructions, visit the [MONAI Bundle Configuration Page](https://docs.monai.io/en/latest/config_syntax.html).
119
 
120
+ #### Execute training:
121
 
122
  ```
123
  python -m monai.bundle run --config_file configs/train.json
124
  ```
125
 
126
+ #### Override the `train` config to execute multi-GPU training:
127
 
128
  ```
129
  torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run --config_file "['configs/train.json','configs/multi_gpu_train.json']"
 
131
 
132
  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).
133
 
134
+ #### Override the `train` config to execute evaluation with the trained model:
135
 
136
  ```
137
  python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
138
  ```
139
 
140
+ #### Override the `train` config and `evaluate` config to execute multi-GPU evaluation:
141
 
142
  ```
143
  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']"
144
  ```
145
 
146
+ #### Execute inference:
147
 
148
  ```
149
  python -m monai.bundle run --config_file configs/inference.json
150
  ```
151
+ #### Execute inference with Data Samples:
152
 
153
  ```
154
  python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
configs/metadata.json CHANGED
@@ -1,13 +1,14 @@
1
  {
2
  "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
3
- "version": "0.1.2",
4
  "changelog": {
 
5
  "0.1.2": "Update figure with links",
6
  "0.1.1": "adapt to BundleWorkflow interface and val metric",
7
  "0.1.0": "complete the model package",
8
  "0.0.1": "initialize the model package structure"
9
  },
10
- "monai_version": "1.2.0rc3",
11
  "pytorch_version": "1.13.1",
12
  "numpy_version": "1.22.2",
13
  "optional_packages_version": {
 
1
  {
2
  "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json",
3
+ "version": "0.1.3",
4
  "changelog": {
5
+ "0.1.3": "add non-deterministic note",
6
  "0.1.2": "Update figure with links",
7
  "0.1.1": "adapt to BundleWorkflow interface and val metric",
8
  "0.1.0": "complete the model package",
9
  "0.0.1": "initialize the model package structure"
10
  },
11
+ "monai_version": "1.2.0rc4",
12
  "pytorch_version": "1.13.1",
13
  "numpy_version": "1.22.2",
14
  "optional_packages_version": {
docs/README.md CHANGED
@@ -102,18 +102,21 @@ CPU: Memory: **2.3G**
102
 
103
  ![](https://developer.download.nvidia.com/assets/Clara/Images/monai_wholeBody_ct_segmentation_15mm_validation.png) <br>
104
 
 
 
 
105
  ## MONAI Bundle Commands
106
  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
  ```
113
  python -m monai.bundle run --config_file configs/train.json
114
  ```
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']"
@@ -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
  ```
127
  python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
128
  ```
129
 
130
- #### Override the `train` config and `evaluate` config to execute multi-GPU evaluation
131
 
132
  ```
133
  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
 
136
- #### Execute inference
137
 
138
  ```
139
  python -m monai.bundle run --config_file configs/inference.json
140
  ```
141
- #### Execute inference with Data Samples
142
 
143
  ```
144
  python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"
 
102
 
103
  ![](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
  ```
130
  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']"
137
  ```
138
 
139
+ #### Execute inference:
140
 
141
  ```
142
  python -m monai.bundle run --config_file configs/inference.json
143
  ```
144
+ #### Execute inference with Data Samples:
145
 
146
  ```
147
  python -m monai.bundle run --config_file configs/inference.json --datalist "['sampledata/imagesTr/s0037.nii.gz','sampledata/imagesTr/s0038.nii.gz']"