Auto3DSeg continue training (skip trained algos) (#6310)

Second PR for issue #6291

Since the previous PR #6290
was reverted #6295

Allows to skip the already trained algos, and continue training only for
the non-trained ones.

after this PR, the default option AutoRunner(train=None) will have this
behavior, whereas manually setting AutoRunner(train=True/False) will
always train all or skip all training. Previously we can only train all
or skip all (without any option to resume)

I changed  import_bundle_algo_history() to return a better algo_dict 

previously it returned "list[dict(name: algo)]" - a list of dict, but
each dict must have a single key name "name => algo". Not it returns a
list of dicts, each with several keys dict(AlgoEnsembleKeys.ID: name,
AlgoEnsembleKeys.ALGO, algo, "is_trained": bool, etc).
this allows to put additional metadata inside of each algo_dict, and
it's easier to read it back.

previously, to get a name we had to use "name = history[0].keys()[0]",
now it's more elegant "name = history[0][AlgoEnsembleKeys.ID]".

this however required to change many files, everywhere where
import_bundle_algo_history and export_bundle_algo_history was used.

All the tests have passed, except for "integration GPU utilization
tests" , but those errors seems unrelated



After this PR, tutorials need to be updated too
Project-MONAI/tutorials#1288

---------

Signed-off-by: myron <[email protected]>

.github/workflows/integration.yml

@@ -41,27 +41,33 @@ jobs:
         python -m pip install --upgrade torch torchvision torchaudio
         python -m pip install -r requirements-dev.txt
         rm -rf /github/home/.cache/torch/hub/mmars/
-    - name: Run integration tests
+    - name: Clean directory
       run: |
         python -m pip list
         git config --global --add safe.directory /__w/MONAI/MONAI
         git clean -ffdx
         nvidia-smi
         export CUDA_VISIBLE_DEVICES=$(python -m tests.utils -c 1 | tail -n 1)
         echo $CUDA_VISIBLE_DEVICES
-        trap 'if pgrep python; then pkill python; fi;' ERR
-        python -c $'import torch\na=[torch.zeros(1,device=f"cuda:{i}") for i in range(torch.cuda.device_count())];\nwhile True:print(a)' > /dev/null &
         python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
         python -c 'import torch; print(torch.rand(5,3, device=torch.device("cuda:0")))'
 
-        # test auto3dseg
-        echo "test tag algo"
+    - name: Auto3dseg tag algo
+      shell: bash
+      env:
+        BUILD_MONAI: 0
+      run: |
         BUILD_MONAI=0 ./runtests.sh --build
         python -m tests.test_auto3dseg_ensemble
         python -m tests.test_auto3dseg_hpo
         python -m tests.test_integration_autorunner
         python -m tests.test_integration_gpu_customization
 
+    - name: Auto3dseg latest algo
+      shell: bash
+      env:
+        BUILD_MONAI: 0
+      run: |
         # test latest template
         echo "test latest algo"
         cd ../
@@ -81,14 +87,24 @@ jobs:
         python -m tests.test_integration_autorunner
         python -m tests.test_integration_gpu_customization
 
-        # the other tests
-        echo "the other tests"
+    - name: Integration tests
+      shell: bash
+      env:
+        BUILD_MONAI: 1
+      run: |
         pwd
         ls -ll
-        BUILD_MONAI=1 ./runtests.sh --build --net
-        BUILD_MONAI=1 ./runtests.sh --build --unittests
-        if pgrep python; then pkill python; fi
+        ./runtests.sh --build --net
+
+    - name: Unit tests
       shell: bash
+      env:
+        BUILD_MONAI: 1
+      run: |
+        pwd
+        ls -ll
+        ./runtests.sh --unittests
+
     - name: Add reaction
       uses: peter-evans/create-or-update-comment@v2
       if: github.event.pull_request.number != ''

monai/apps/auto3dseg/auto_runner.py

@@ -281,7 +281,7 @@ def __init__(
         # determine if we need to analyze, algo_gen or train from cache, unless manually provided
         self.analyze = not self.cache["analyze"] if analyze is None else analyze
         self.algo_gen = not self.cache["algo_gen"] if algo_gen is None else algo_gen
-        self.train = not self.cache["train"] if train is None else train
+        self.train = train
         self.ensemble = ensemble  # last step, no need to check
 
         self.set_training_params()
@@ -635,13 +635,15 @@ def _train_algo_in_sequence(self, history: list[dict[str, Any]]) -> None:
             folders under the working directory. The results include the model checkpoints, a
             progress.yaml, accuracies in CSV and a pickle file of the Algo object.
         """
-        for task in history:
-            for _, algo in task.items():
-                algo.train(self.train_params)
-                acc = algo.get_score()
-                algo_to_pickle(algo, template_path=algo.template_path, best_metrics=acc)
+        for algo_dict in history:
+            algo = algo_dict[AlgoEnsembleKeys.ALGO]
+            algo.train(self.train_params)
+            acc = algo.get_score()
 
-    def _train_algo_in_nni(self, history):
+            algo_meta_data = {str(AlgoEnsembleKeys.SCORE): acc}
+            algo_to_pickle(algo, template_path=algo.template_path, **algo_meta_data)
+
+    def _train_algo_in_nni(self, history: list[dict[str, Any]]) -> None:
         """
         Train the Algos using HPO.
 
@@ -672,40 +674,41 @@ def _train_algo_in_nni(self, history):
 
         last_total_tasks = len(import_bundle_algo_history(self.work_dir, only_trained=True))
         mode_dry_run = self.hpo_params.pop("nni_dry_run", False)
-        for task in history:
-            for name, algo in task.items():
-                nni_gen = NNIGen(algo=algo, params=self.hpo_params)
-                obj_filename = nni_gen.get_obj_filename()
-                nni_config = deepcopy(default_nni_config)
-                # override the default nni config with the same key in hpo_params
-                for key in self.hpo_params:
-                    if key in nni_config:
-                        nni_config[key] = self.hpo_params[key]
-                nni_config.update({"experimentName": name})
-                nni_config.update({"search_space": self.search_space})
-                trial_cmd = "python -m monai.apps.auto3dseg NNIGen run_algo " + obj_filename + " " + self.work_dir
-                nni_config.update({"trialCommand": trial_cmd})
-                nni_config_filename = os.path.abspath(os.path.join(self.work_dir, f"{name}_nni_config.yaml"))
-                ConfigParser.export_config_file(nni_config, nni_config_filename, fmt="yaml", default_flow_style=None)
-
-                max_trial = min(self.hpo_tasks, cast(int, default_nni_config["maxTrialNumber"]))
-                cmd = "nnictl create --config " + nni_config_filename + " --port 8088"
-
-                if mode_dry_run:
-                    logger.info(f"AutoRunner HPO is in dry-run mode. Please manually launch: {cmd}")
-                    continue
-
-                subprocess.run(cmd.split(), check=True)
-
+        for algo_dict in history:
+            name = algo_dict[AlgoEnsembleKeys.ID]
+            algo = algo_dict[AlgoEnsembleKeys.ALGO]
+            nni_gen = NNIGen(algo=algo, params=self.hpo_params)
+            obj_filename = nni_gen.get_obj_filename()
+            nni_config = deepcopy(default_nni_config)
+            # override the default nni config with the same key in hpo_params
+            for key in self.hpo_params:
+                if key in nni_config:
+                    nni_config[key] = self.hpo_params[key]
+            nni_config.update({"experimentName": name})
+            nni_config.update({"search_space": self.search_space})
+            trial_cmd = "python -m monai.apps.auto3dseg NNIGen run_algo " + obj_filename + " " + self.work_dir
+            nni_config.update({"trialCommand": trial_cmd})
+            nni_config_filename = os.path.abspath(os.path.join(self.work_dir, f"{name}_nni_config.yaml"))
+            ConfigParser.export_config_file(nni_config, nni_config_filename, fmt="yaml", default_flow_style=None)
+
+            max_trial = min(self.hpo_tasks, cast(int, default_nni_config["maxTrialNumber"]))
+            cmd = "nnictl create --config " + nni_config_filename + " --port 8088"
+
+            if mode_dry_run:
+                logger.info(f"AutoRunner HPO is in dry-run mode. Please manually launch: {cmd}")
+                continue
+
+            subprocess.run(cmd.split(), check=True)
+
+            n_trainings = len(import_bundle_algo_history(self.work_dir, only_trained=True))
+            while n_trainings - last_total_tasks < max_trial:
+                sleep(1)
                 n_trainings = len(import_bundle_algo_history(self.work_dir, only_trained=True))
-                while n_trainings - last_total_tasks < max_trial:
-                    sleep(1)
-                    n_trainings = len(import_bundle_algo_history(self.work_dir, only_trained=True))
 
-                cmd = "nnictl stop --all"
-                subprocess.run(cmd.split(), check=True)
-                logger.info(f"NNI completes HPO on {name}")
-                last_total_tasks = n_trainings
+            cmd = "nnictl stop --all"
+            subprocess.run(cmd.split(), check=True)
+            logger.info(f"NNI completes HPO on {name}")
+            last_total_tasks = n_trainings
 
     def run(self):
         """
@@ -758,7 +761,8 @@ def run(self):
             logger.info("Skipping algorithm generation...")
 
         # step 3: algo training
-        if self.train:
+        auto_train_choice = self.train is None
+        if self.train or (auto_train_choice and not self.cache["train"]):
             history = import_bundle_algo_history(self.work_dir, only_trained=False)
 
             if len(history) == 0:
@@ -767,20 +771,40 @@ def run(self):
                     "Possibly the required algorithms generation step was not completed."
                 )
 
-            if not self.hpo:
-                self._train_algo_in_sequence(history)
-            else:
-                self._train_algo_in_nni(history)
+            if auto_train_choice:
+                skip_algos = [h[AlgoEnsembleKeys.ID] for h in history if h["is_trained"]]
+                if len(skip_algos) > 0:
+                    logger.info(
+                        f"Skipping already trained algos {skip_algos}."
+                        "Set option train=True to always retrain all algos."
+                    )
+                    history = [h for h in history if not h["is_trained"]]
+
+            if len(history) > 0:
+                if not self.hpo:
+                    self._train_algo_in_sequence(history)
+                else:
+                    self._train_algo_in_nni(history)
+
             self.export_cache(train=True)
         else:
             logger.info("Skipping algorithm training...")
 
         # step 4: model ensemble and write the prediction to disks.
         if self.ensemble:
-            history = import_bundle_algo_history(self.work_dir, only_trained=True)
+            history = import_bundle_algo_history(self.work_dir, only_trained=False)
+
+            history_untrained = [h for h in history if not h["is_trained"]]
+            if len(history_untrained) > 0:
+                warnings.warn(
+                    f"Ensembling step will skip {[h['name'] for h in history_untrained]} untrained algos."
+                    "Generally it means these algos did not complete training."
+                )
+                history = [h for h in history if h["is_trained"]]
+
             if len(history) == 0:
                 raise ValueError(
-                    f"Could not find the trained results in {self.work_dir}. "
+                    f"Could not find any trained algos in {self.work_dir}. "
                     "Possibly the required training step was not completed."
                 )
 
@@ -798,4 +822,4 @@ def run(self):
                     self.save_image(pred)
                 logger.info(f"Auto3Dseg ensemble prediction outputs are saved in {self.output_dir}.")
 
-        logger.info("Auto3Dseg pipeline is complete successfully.")
+        logger.info("Auto3Dseg pipeline is completed successfully.")

monai/apps/auto3dseg/bundle_gen.py

@@ -33,6 +33,7 @@
 from monai.auto3dseg.utils import algo_to_pickle
 from monai.bundle.config_parser import ConfigParser
 from monai.utils import ensure_tuple
+from monai.utils.enums import AlgoEnsembleKeys
 
 logger = get_logger(module_name=__name__)
 ALGO_HASH = os.environ.get("MONAI_ALGO_HASH", "7758ad1")
@@ -537,4 +538,6 @@ def generate(
                     gen_algo.export_to_disk(output_folder, name, fold=f_id)
 
                 algo_to_pickle(gen_algo, template_path=algo.template_path)
-                self.history.append({name: gen_algo})  # track the previous, may create a persistent history
+                self.history.append(
+                    {AlgoEnsembleKeys.ID: name, AlgoEnsembleKeys.ALGO: gen_algo}
+                )  # track the previous, may create a persistent history

monai/apps/auto3dseg/ensemble_builder.py

@@ -267,22 +267,20 @@ class AlgoEnsembleBuilder:
 
     """
 
-    def __init__(self, history: Sequence[dict], data_src_cfg_filename: str | None = None):
+    def __init__(self, history: Sequence[dict[str, Any]], data_src_cfg_filename: str | None = None):
         self.infer_algos: list[dict[AlgoEnsembleKeys, Any]] = []
         self.ensemble: AlgoEnsemble
         self.data_src_cfg = ConfigParser(globals=False)
 
         if data_src_cfg_filename is not None and os.path.exists(str(data_src_cfg_filename)):
             self.data_src_cfg.read_config(data_src_cfg_filename)
 
-        for h in history:
+        for algo_dict in history:
             # load inference_config_paths
-            # raise warning/error if not found
-            if len(h) > 1:
-                raise ValueError(f"{h} should only contain one set of genAlgo key-value")
 
-            name = list(h.keys())[0]
-            gen_algo = h[name]
+            name = algo_dict[AlgoEnsembleKeys.ID]
+            gen_algo = algo_dict[AlgoEnsembleKeys.ALGO]
+
             best_metric = gen_algo.get_score()
             algo_path = gen_algo.output_path
             infer_path = os.path.join(algo_path, "scripts", "infer.py")

monai/apps/auto3dseg/hpo_gen.py

@@ -23,6 +23,7 @@
 from monai.bundle.config_parser import ConfigParser
 from monai.config import PathLike
 from monai.utils import optional_import
+from monai.utils.enums import AlgoEnsembleKeys
 
 nni, has_nni = optional_import("nni")
 optuna, has_optuna = optional_import("optuna")
@@ -98,8 +99,8 @@ class NNIGen(HPOGen):
             # Bundle Algorithms are already generated by BundleGen in work_dir
             import_bundle_algo_history(work_dir, only_trained=False)
             algo_dict = self.history[0]  # pick the first algorithm
-            algo_name = list(algo_dict.keys())[0]
-            onealgo = algo_dict[algo_name]
+            algo_name = algo_dict[AlgoEnsembleKeys.ID]
+            onealgo = algo_dict[AlgoEnsembleKeys.ALGO]
             nni_gen = NNIGen(algo=onealgo)
             nni_gen.print_bundle_algo_instruction()
 
@@ -237,10 +238,12 @@ def run_algo(self, obj_filename: str, output_folder: str = ".", template_path: P
         self.algo.train(self.params)
         # step 4 report validation acc to controller
         acc = self.algo.get_score()
+        algo_meta_data = {str(AlgoEnsembleKeys.SCORE): acc}
+
         if isinstance(self.algo, BundleAlgo):
-            algo_to_pickle(self.algo, template_path=self.algo.template_path, best_metrics=acc)
+            algo_to_pickle(self.algo, template_path=self.algo.template_path, **algo_meta_data)
         else:
-            algo_to_pickle(self.algo, best_metrics=acc)
+            algo_to_pickle(self.algo, **algo_meta_data)
         self.set_score(acc)
 
 
@@ -408,8 +411,9 @@ def run_algo(self, obj_filename: str, output_folder: str = ".", template_path: P
         self.algo.train(self.params)
         # step 4 report validation acc to controller
         acc = self.algo.get_score()
+        algo_meta_data = {str(AlgoEnsembleKeys.SCORE): acc}
         if isinstance(self.algo, BundleAlgo):
-            algo_to_pickle(self.algo, template_path=self.algo.template_path, best_metrics=acc)
+            algo_to_pickle(self.algo, template_path=self.algo.template_path, **algo_meta_data)
         else:
-            algo_to_pickle(self.algo, best_metrics=acc)
+            algo_to_pickle(self.algo, **algo_meta_data)
         self.set_score(acc)

monai/apps/auto3dseg/utils.py

@@ -15,13 +15,15 @@
 
 from monai.apps.auto3dseg.bundle_gen import BundleAlgo
 from monai.auto3dseg import algo_from_pickle, algo_to_pickle
+from monai.utils.enums import AlgoEnsembleKeys
 
 
 def import_bundle_algo_history(
     output_folder: str = ".", template_path: str | None = None, only_trained: bool = True
 ) -> list:
     """
-    import the history of the bundleAlgo object with their names/identifiers
+    import the history of the bundleAlgo objects as a list of algo dicts.
+    each algo_dict has keys name (folder name), algo (bundleAlgo), is_trained (bool),
 
     Args:
         output_folder: the root path of the algorithms templates.
@@ -47,11 +49,18 @@ def import_bundle_algo_history(
         if isinstance(algo, BundleAlgo):  # algo's template path needs override
             algo.template_path = algo_meta_data["template_path"]
 
-        if only_trained:
-            if "best_metrics" in algo_meta_data:
-                history.append({name: algo})
-        else:
-            history.append({name: algo})
+        best_metric = algo_meta_data.get(AlgoEnsembleKeys.SCORE, None)
+        is_trained = best_metric is not None
+
+        if (only_trained and is_trained) or not only_trained:
+            history.append(
+                {
+                    AlgoEnsembleKeys.ID: name,
+                    AlgoEnsembleKeys.ALGO: algo,
+                    AlgoEnsembleKeys.SCORE: best_metric,
+                    "is_trained": is_trained,
+                }
+            )
 
     return history
 
@@ -63,6 +72,6 @@ def export_bundle_algo_history(history: list[dict[str, BundleAlgo]]) -> None:
     Args:
         history: a List of Bundle. Typically, the history can be obtained from BundleGen get_history method
     """
-    for task in history:
-        for _, algo in task.items():
-            algo_to_pickle(algo, template_path=algo.template_path)
+    for algo_dict in history:
+        algo = algo_dict[AlgoEnsembleKeys.ALGO]
+        algo_to_pickle(algo, template_path=algo.template_path)