Support checkpoint save and load with Stochastic Weight Averaging (Li…

…ghtning-AI#9938)

Co-authored-by: thomas chaton <thomas@grid.ai>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adrian Wälchli <aedu.waelchli@gmail.com>
Co-authored-by: Carlos Mocholi <carlossmocholi@gmail.com>
Co-authored-by: Kushashwa Ravi Shrimali <kushashwaravishrimali@gmail.com>
Co-authored-by: Jirka <jirka.borovec@seznam.cz>
Co-authored-by: Rohit Gupta <rohitgr1998@gmail.com>

src/pytorch_lightning/CHANGELOG.md

@@ -73,6 +73,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Fixed incorrect `precision="mixed"` being used with `DeepSpeedStrategy` and `IPUStrategy` ([#14041](https://github.com/Lightning-AI/lightning/pull/14041))
 
 
+- Fixed resuming from a checkpoint when using Stochastic Weight Averaging (SWA) ([#9938](https://github.com/Lightning-AI/lightning/pull/9938))
+
+
 - Fixed dtype inference during gradient norm computation ([#14051](https://github.com/Lightning-AI/lightning/pull/14051))
 
 

src/pytorch_lightning/callbacks/stochastic_weight_avg.py

@@ -16,14 +16,15 @@
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 """
 from copy import deepcopy
-from typing import Any, Callable, cast, List, Optional, Union
+from typing import Any, Callable, cast, Dict, List, Optional, Union
 
 import torch
 from torch import nn, Tensor
 from torch.optim.swa_utils import SWALR
 
 import pytorch_lightning as pl
 from pytorch_lightning.callbacks.callback import Callback
+from pytorch_lightning.strategies import DDPFullyShardedStrategy, DeepSpeedStrategy
 from pytorch_lightning.utilities.exceptions import MisconfigurationException
 from pytorch_lightning.utilities.rank_zero import rank_zero_info, rank_zero_warn
 from pytorch_lightning.utilities.types import _LRScheduler, LRSchedulerConfig
@@ -112,15 +113,22 @@ def __init__(
         if device is not None and not isinstance(device, (torch.device, str)):
             raise MisconfigurationException(f"device is expected to be a torch.device or a str. Found {device}")
 
+        self.n_averaged: Optional[torch.Tensor] = None
         self._swa_epoch_start = swa_epoch_start
         self._swa_lrs = swa_lrs
         self._annealing_epochs = annealing_epochs
         self._annealing_strategy = annealing_strategy
         self._avg_fn = avg_fn or self.avg_fn
         self._device = device
-        self._max_epochs: int
-        self._model_contains_batch_norm: bool
+        self._model_contains_batch_norm: Optional[bool] = None
         self._average_model: "pl.LightningModule"
+        self._initialized = False
+        self._swa_scheduler: Optional[_LRScheduler] = None
+        self._scheduler_state: Optional[Dict] = None
+        self._init_n_averaged = 0
+        self._latest_update_epoch = -1
+        self.momenta: Optional[Dict[nn.modules.batchnorm._BatchNorm, float]] = None
+        self._max_epochs: int
 
     @property
     def swa_start(self) -> int:
@@ -147,6 +155,9 @@ def on_fit_start(self, trainer: "pl.Trainer", pl_module: "pl.LightningModule") -
         if len(trainer.lr_scheduler_configs) > 1:
             raise MisconfigurationException("SWA currently not supported for more than 1 `lr_scheduler`.")
 
+        if isinstance(trainer.strategy, (DDPFullyShardedStrategy, DeepSpeedStrategy)):
+            raise MisconfigurationException("SWA does not currently support sharded models.")
+
         if isinstance(self._swa_epoch_start, float):
             self._swa_epoch_start = int(trainer.max_epochs * self._swa_epoch_start)
 
@@ -158,8 +169,13 @@ def on_fit_start(self, trainer: "pl.Trainer", pl_module: "pl.LightningModule") -
             assert trainer.fit_loop.max_epochs is not None
             trainer.fit_loop.max_epochs += 1
 
+        if self._scheduler_state is not None:
+            self._clear_schedulers(trainer)
+
     def on_train_epoch_start(self, trainer: "pl.Trainer", pl_module: "pl.LightningModule") -> None:
-        if trainer.current_epoch == self.swa_start:
+        if (not self._initialized) and (self.swa_start <= trainer.current_epoch <= self.swa_end):
+            self._initialized = True
+
             # move average model to request device.
             self._average_model = self._average_model.to(self._device or pl_module.device)
 
@@ -180,6 +196,17 @@ def on_train_epoch_start(self, trainer: "pl.Trainer", pl_module: "pl.LightningMo
                     last_epoch=trainer.max_epochs if self._annealing_strategy == "cos" else -1,
                 ),
             )
+            if self._scheduler_state is not None:
+                # Restore scheduler state from checkpoint
+                self._swa_scheduler.load_state_dict(self._scheduler_state)
+            elif trainer.current_epoch != self.swa_start:
+                # Log a warning if we're initializing after start without any checkpoint data,
+                # as behaviour will be different compared to having checkpoint data.
+                rank_zero_warn(
+                    "SWA is initializing after swa_start without any checkpoint data. "
+                    "This may be caused by loading a checkpoint from an older version of PyTorch Lightning."
+                )
+
             # We assert that there is only one optimizer on fit start, so know opt_idx is always 0
             default_scheduler_cfg = LRSchedulerConfig(self._swa_scheduler, opt_idx=0)
             assert default_scheduler_cfg.interval == "epoch" and default_scheduler_cfg.frequency == 1
@@ -196,14 +223,18 @@ def on_train_epoch_start(self, trainer: "pl.Trainer", pl_module: "pl.LightningMo
             else:
                 trainer.lr_scheduler_configs.append(default_scheduler_cfg)
 
-            self.n_averaged = torch.tensor(0, dtype=torch.long, device=pl_module.device)
+            if self.n_averaged is None:
+                self.n_averaged = torch.tensor(self._init_n_averaged, dtype=torch.long, device=pl_module.device)
 
-        if self.swa_start <= trainer.current_epoch <= self.swa_end:
+        if (self.swa_start <= trainer.current_epoch <= self.swa_end) and (
+            trainer.current_epoch > self._latest_update_epoch
+        ):
+            assert self.n_averaged is not None
             self.update_parameters(self._average_model, pl_module, self.n_averaged, self._avg_fn)
+            self._latest_update_epoch = trainer.current_epoch
 
         # Note: No > here in case the callback is saved with the model and training continues
         if trainer.current_epoch == self.swa_end + 1:
-
             # Transfer weights from average model to pl_module
             self.transfer_weights(self._average_model, pl_module)
 
@@ -265,6 +296,7 @@ def reset_batch_norm_and_save_state(self, pl_module: "pl.LightningModule") -> No
 
     def reset_momenta(self) -> None:
         """Adapted from https://github.com/pytorch/pytorch/blob/v1.7.1/torch/optim/swa_utils.py#L164-L165."""
+        assert self.momenta is not None
         for bn_module in self.momenta:
             bn_module.momentum = self.momenta[bn_module]
 
@@ -285,3 +317,35 @@ def update_parameters(
     def avg_fn(averaged_model_parameter: Tensor, model_parameter: Tensor, num_averaged: Tensor) -> Tensor:
         """Adapted from https://github.com/pytorch/pytorch/blob/v1.7.1/torch/optim/swa_utils.py#L95-L97."""
         return averaged_model_parameter + (model_parameter - averaged_model_parameter) / (num_averaged + 1)
+
+    def state_dict(self) -> Dict[str, Any]:
+        return {
+            "n_averaged": 0 if self.n_averaged is None else self.n_averaged.item(),
+            "latest_update_epoch": self._latest_update_epoch,
+            "scheduler_state": None if self._swa_scheduler is None else self._swa_scheduler.state_dict(),
+            "average_model_state": None if self._average_model is None else self._average_model.state_dict(),
+        }
+
+    def load_state_dict(self, state_dict: Dict[str, Any]) -> None:
+        self._init_n_averaged = state_dict["n_averaged"]
+        self._latest_update_epoch = state_dict["latest_update_epoch"]
+        self._scheduler_state = state_dict["scheduler_state"]
+        self._load_average_model_state(state_dict["average_model_state"])
+
+    @staticmethod
+    def _clear_schedulers(trainer: "pl.Trainer") -> None:
+        # If we have scheduler state saved, clear the scheduler configs so that we don't try to
+        # load state into the wrong type of schedulers when restoring scheduler checkpoint state.
+        # We'll configure the scheduler and re-load its state in on_train_epoch_start.
+        # Note that this relies on the callback state being restored before the scheduler state is
+        # restored, and doesn't work if restore_checkpoint_after_setup is True, but at the time of
+        # writing that is only True for deepspeed which is already not supported by SWA.
+        # See https://github.com/PyTorchLightning/pytorch-lightning/issues/11665 for background.
+        if trainer.lr_scheduler_configs:
+            assert len(trainer.lr_scheduler_configs) == 1
+            trainer.lr_scheduler_configs.clear()
+
+    def _load_average_model_state(self, model_state: Any) -> None:
+        if self._average_model is None:
+            return
+        self._average_model.load_state_dict(model_state)

tests/tests_pytorch/callbacks/test_stochastic_weight_avg.py

@@ -12,11 +12,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 import logging
+import os
+from pathlib import Path
+from typing import ContextManager, Optional
 from unittest import mock
 
 import pytest
 import torch
 from torch import nn
+from torch.optim.lr_scheduler import LambdaLR
 from torch.optim.swa_utils import SWALR
 from torch.utils.data import DataLoader
 
@@ -30,7 +34,9 @@
 
 
 class SwaTestModel(BoringModel):
-    def __init__(self, batchnorm: bool = True, interval: str = "epoch", iterable_dataset: bool = False):
+    def __init__(
+        self, batchnorm: bool = True, interval: str = "epoch", iterable_dataset: bool = False, crash_on_epoch=None
+    ):
         super().__init__()
         layers = [nn.Linear(32, 32)]
         if batchnorm:
@@ -39,17 +45,18 @@ def __init__(self, batchnorm: bool = True, interval: str = "epoch", iterable_dat
         self.layer = nn.Sequential(*layers)
         self.interval = interval
         self.iterable_dataset = iterable_dataset
+        self.crash_on_epoch = crash_on_epoch
 
     def training_step(self, batch, batch_idx):
+        if self.crash_on_epoch and self.trainer.current_epoch >= self.crash_on_epoch:
+            raise Exception("SWA crash test")
         output = self.forward(batch)
         loss = self.loss(batch, output)
         return {"loss": loss}
 
     def train_dataloader(self):
-
         dset_cls = RandomIterableDataset if self.iterable_dataset else RandomDataset
         dset = dset_cls(32, 64)
-
         return DataLoader(dset, batch_size=2)
 
     def configure_optimizers(self):
@@ -66,6 +73,8 @@ def configure_optimizers(self):
 class SwaTestCallback(StochasticWeightAveraging):
     update_parameters_calls: int = 0
     transfer_weights_calls: int = 0
+    # Record the first epoch, as if we are resuming from a checkpoint this may not be equal to 0
+    first_epoch: Optional[int] = None
 
     def update_parameters(self, *args, **kwargs):
         self.update_parameters_calls += 1
@@ -77,6 +86,11 @@ def transfer_weights(self, *args, **kwargs):
 
     def on_train_epoch_start(self, trainer, *args):
         super().on_train_epoch_start(trainer, *args)
+        if self.first_epoch is None and not trainer.fit_loop.restarting:
+            # since the checkpoint loaded was saved `on_train_epoch_end`, the first `FitLoop` iteration will
+            # not update the model and just call the epoch-level hooks, for that reason, we check that we are not
+            # restarting before choosing the first epoch
+            self.first_epoch = trainer.current_epoch
         assert trainer.fit_loop._skip_backward == (trainer.current_epoch > self.swa_end)
         if self.swa_start <= trainer.current_epoch:
             assert isinstance(trainer.lr_scheduler_configs[0].scheduler, SWALR)
@@ -88,6 +102,7 @@ def on_train_epoch_end(self, trainer, *args):
         if self.swa_start <= trainer.current_epoch <= self.swa_end:
             swa_epoch = trainer.current_epoch - self.swa_start
             assert self.n_averaged == swa_epoch + 1
+            assert self._swa_scheduler is not None
             # Scheduler is stepped once on initialization and then at the end of each epoch
             assert self._swa_scheduler._step_count == swa_epoch + 2
         elif trainer.current_epoch > self.swa_end:
@@ -103,10 +118,13 @@ def on_train_end(self, trainer, pl_module):
 
         if not isinstance(trainer.strategy, DDPSpawnStrategy):
             # check backward call count. the batchnorm update epoch should not backward
-            assert trainer.strategy.backward.call_count == trainer.max_epochs * trainer.limit_train_batches
+            assert trainer.strategy.backward.call_count == (
+                (trainer.max_epochs - self.first_epoch) * trainer.limit_train_batches
+            )
 
         # check call counts
-        assert self.update_parameters_calls == trainer.max_epochs - (self._swa_epoch_start - 1)
+        first_swa_epoch = max(self.first_epoch, self.swa_start)
+        assert self.update_parameters_calls == trainer.max_epochs - first_swa_epoch
         assert self.transfer_weights_calls == 1
 
 
@@ -140,7 +158,7 @@ def train_with_swa(
         devices=devices,
     )
 
-    with mock.patch.object(Strategy, "backward", wraps=trainer.strategy.backward):
+    with _backward_patch(trainer):
         trainer.fit(model)
 
     # check the model is the expected
@@ -226,9 +244,10 @@ def test_swa_multiple_lrs(tmpdir):
 
     class TestModel(BoringModel):
         def __init__(self):
-            super(BoringModel, self).__init__()
+            super().__init__()
             self.layer1 = torch.nn.Linear(32, 32)
             self.layer2 = torch.nn.Linear(32, 2)
+            self.on_train_epoch_start_called = False
 
         def forward(self, x):
             x = self.layer1(x)
@@ -255,3 +274,98 @@ def on_train_epoch_start(self):
     )
     trainer.fit(model)
     assert model.on_train_epoch_start_called
+
+
+def _swa_resume_training_from_checkpoint(tmpdir, model, resume_model, ddp=False):
+    swa_start = 3
+    trainer_kwargs = {
+        "default_root_dir": tmpdir,
+        "max_epochs": 5,
+        "accelerator": "cpu",
+        "strategy": "ddp_spawn_find_unused_parameters_false" if ddp else None,
+        "devices": 2 if ddp else 1,
+        "limit_train_batches": 5,
+        "limit_val_batches": 0,
+        "accumulate_grad_batches": 2,
+        "enable_progress_bar": False,
+    }
+    trainer = Trainer(callbacks=SwaTestCallback(swa_epoch_start=swa_start, swa_lrs=0.1), **trainer_kwargs)
+
+    with _backward_patch(trainer), pytest.raises(Exception, match="SWA crash test"):
+        trainer.fit(model)
+
+    checkpoint_dir = Path(tmpdir) / "lightning_logs" / "version_0" / "checkpoints"
+    checkpoint_files = os.listdir(checkpoint_dir)
+    assert len(checkpoint_files) == 1
+    ckpt_path = str(checkpoint_dir / checkpoint_files[0])
+
+    trainer = Trainer(callbacks=SwaTestCallback(swa_epoch_start=swa_start, swa_lrs=0.1), **trainer_kwargs)
+
+    with _backward_patch(trainer):
+        trainer.fit(resume_model, ckpt_path=ckpt_path)
+
+
+class CustomSchedulerModel(SwaTestModel):
+    def configure_optimizers(self):
+        optimizer = torch.optim.SGD(self.layer.parameters(), lr=0.1)
+
+        def lr_lambda(current_step: int):
+            return 0.1
+
+        scheduler = LambdaLR(optimizer, lr_lambda, -1)
+        return {
+            "optimizer": optimizer,
+            "lr_scheduler": {
+                "scheduler": scheduler,
+                "interval": self.interval,
+            },
+        }
+
+
+@pytest.mark.parametrize("crash_on_epoch", [1, 3])
+def test_swa_resume_training_from_checkpoint(tmpdir, crash_on_epoch):
+    model = SwaTestModel(crash_on_epoch=crash_on_epoch)
+    resume_model = SwaTestModel()
+    _swa_resume_training_from_checkpoint(tmpdir, model, resume_model)
+
+
+@pytest.mark.parametrize("crash_on_epoch", [1, 3])
+def test_swa_resume_training_from_checkpoint_custom_scheduler(tmpdir, crash_on_epoch):
+    # Reproduces the bug reported in https://github.com/PyTorchLightning/pytorch-lightning/issues/11665
+    model = CustomSchedulerModel(crash_on_epoch=crash_on_epoch)
+    resume_model = CustomSchedulerModel()
+    _swa_resume_training_from_checkpoint(tmpdir, model, resume_model)
+
+
+@RunIf(skip_windows=True)
+def test_swa_resume_training_from_checkpoint_ddp(tmpdir):
+    model = SwaTestModel(crash_on_epoch=3)
+    resume_model = SwaTestModel()
+    _swa_resume_training_from_checkpoint(tmpdir, model, resume_model, ddp=True)
+
+
+@pytest.mark.parametrize(
+    "strategy",
+    [
+        pytest.param("fsdp", marks=RunIf(fairscale_fully_sharded=True, min_cuda_gpus=1)),
+        pytest.param("deepspeed", marks=RunIf(deepspeed=True, min_cuda_gpus=1)),
+    ],
+)
+def test_misconfiguration_error_with_sharded_model(tmpdir, strategy: str):
+    model = SwaTestModel()
+    swa_callback = SwaTestCallback(swa_epoch_start=2, swa_lrs=0.1)
+    trainer = Trainer(
+        default_root_dir=tmpdir,
+        enable_progress_bar=False,
+        max_epochs=5,
+        callbacks=[swa_callback],
+        strategy=strategy,
+        accelerator="gpu",
+        devices=1,
+    )
+    with pytest.raises(MisconfigurationException, match="SWA does not currently support sharded models"):
+        trainer.fit(model)
+
+
+def _backward_patch(trainer: Trainer) -> ContextManager:
+    return mock.patch.object(Strategy, "backward", wraps=trainer.strategy.backward)