Fix retrieval of batch indices when dataloader num_workers > 0

CHANGELOG.md

@@ -99,7 +99,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Deprecated the property `Trainer.slurm_job_id` in favor of the new `SLURMEnvironment.job_id()` method ([#10622](https://github.com/PyTorchLightning/pytorch-lightning/pull/10622))
 
 
--
+- Deprecated the access to the attribute `IndexBatchSamplerWrapper.batch_indices` in favor of `IndexBatchSamplerWrapper.seen_batch_indices` ([#10870](https://github.com/PyTorchLightning/pytorch-lightning/pull/10870))
+
 
 ### Removed
 
@@ -217,12 +218,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 - Fixed early schedule reset logic in PyTorch profiler that was causing data leak ([#10837](https://github.com/PyTorchLightning/pytorch-lightning/pull/10837))
 
 
--
+- Fixed a bug that caused incorrect batch indices to be passed to the `BasePredictionWriter` hooks when using a dataloader with `num_workers > 0` ([#10870](https://github.com/PyTorchLightning/pytorch-lightning/pull/10870))
+
 
 
 -
 
 
+
 ## [1.5.4] - 2021-11-30
 
 ### Fixed

pytorch_lightning/loops/epoch/prediction_epoch_loop.py

@@ -26,7 +26,7 @@ def __init__(self) -> None:
         self._dl_max_batches = 0
         self._num_dataloaders = 0
         self._warning_cache = WarningCache()
-        self._all_batch_indices: List[int] = []
+        self._seen_batch_indices: List[List[int]] = []
 
     @property
     def done(self) -> bool:
@@ -44,7 +44,7 @@ def connect(self, **kwargs: "Loop") -> None:
 
     def reset(self) -> None:
         """Resets the loops internal state."""
-        self._all_batch_indices = []
+        self._seen_batch_indices = []
         self.predictions = []
         self.batch_progress.reset_on_run()
 
@@ -68,6 +68,7 @@ def on_run_start(  # type: ignore[override]
         void(dataloader_iter, dataloader_idx)
         self._dl_max_batches = dl_max_batches
         self._num_dataloaders = num_dataloaders
+        self._seen_batch_indices = self._get_batch_indices(dataloader_idx)
         self.return_predictions = return_predictions
 
     def advance(  # type: ignore[override]
@@ -88,6 +89,10 @@ def advance(  # type: ignore[override]
             return_predictions: whether to return the obtained predictions
         """
         batch_idx, batch = next(dataloader_iter)
+        self._seen_batch_indices = self._get_batch_indices(dataloader_idx)
+        # we need to truncate the list of batch indicies due to prefetching in the dataloader and Lightning
+        self._seen_batch_indices = self._seen_batch_indices[: (self.batch_progress.current.completed + 1)]
+
         if batch is None:
             raise StopIteration
 
@@ -99,13 +104,10 @@ def advance(  # type: ignore[override]
         with self.trainer.profiler.profile("predict_step"):
             self._predict_step(batch, batch_idx, dataloader_idx)
 
-    def on_run_end(self) -> Tuple[List[Any], List[int]]:
+    def on_run_end(self) -> Tuple[List[Any], List[List[int]]]:
         """Returns the predictions and the corresponding batch indices."""
-        predictions = self.predictions
-        all_batch_indices = self._all_batch_indices
-        # free memory
-        self.predictions = []
-        self._all_batch_indices = []
+        predictions, all_batch_indices = self.predictions, self._seen_batch_indices
+        self.predictions, self._seen_batch_indices = [], []  # free memory
         return predictions, all_batch_indices
 
     def _predict_step(self, batch: Any, batch_idx: int, dataloader_idx: int) -> None:
@@ -121,7 +123,7 @@ def _predict_step(self, batch: Any, batch_idx: int, dataloader_idx: int) -> None
         step_kwargs = self._build_kwargs(batch, batch_idx, dataloader_idx)
 
         # extract batch_indices and store them
-        self._store_batch_indices(dataloader_idx)
+        self.current_batch_indices = self._seen_batch_indices[batch_idx] if self._seen_batch_indices else []
 
         model_ref = self.trainer.lightning_module
 
@@ -160,12 +162,12 @@ def _build_kwargs(self, batch: Any, batch_idx: int, dataloader_idx: int) -> Dict
             step_kwargs["dataloader_idx"] = dataloader_idx
         return step_kwargs
 
-    def _store_batch_indices(self, dataloader_idx: int) -> None:
-        """Stores the batch indices if the predictions should be stored."""
+    def _get_batch_indices(self, dataloader_idx: int) -> List[List[int]]:
+        """Returns a reference to the seen batch indices if the dataloader has a batch sampler wrapped by our
+        :class:`~pytorch_lightning.overrides.distributed.IndexBatchSamplerWrapper`."""
         batch_sampler = self.trainer.predict_dataloaders[dataloader_idx].batch_sampler
-        if isinstance(batch_sampler, IndexBatchSamplerWrapper):
-            self.current_batch_indices = batch_sampler.batch_indices
-            if self.should_store_predictions:
-                self._all_batch_indices.append(batch_sampler.batch_indices)
-        else:
-            warning_cache.warn("Lightning couldn't infer the indices fetched for your dataloader.")
+        if isinstance(batch_sampler, IndexBatchSamplerWrapper) and self.should_store_predictions:
+            return batch_sampler.seen_batch_indices
+
+        warning_cache.warn("Lightning couldn't infer the indices fetched for your dataloader.")
+        return []

pytorch_lightning/overrides/distributed.py

@@ -12,7 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 import itertools
-from typing import Any, cast, Iterator, List, Optional, Sized, Union
+from typing import Any, cast, Iterator, List, Sized, Union
 
 import torch
 from torch import Tensor
@@ -21,6 +21,7 @@
 
 import pytorch_lightning as pl
 from pytorch_lightning.overrides.base import _LightningModuleWrapperBase
+from pytorch_lightning.utilities import rank_zero_deprecation
 
 
 class LightningDistributedModule(_LightningModuleWrapperBase):
@@ -123,12 +124,31 @@ class IndexBatchSamplerWrapper:
     """This class is used to wrap a :class:`torch.utils.data.BatchSampler` and capture its indices."""
 
     def __init__(self, sampler: BatchSampler) -> None:
+        self.seen_batch_indices: List[List[int]] = []
         self._sampler = sampler
-        self.batch_indices: Optional[List[int]] = None
+        self._batch_indices: List[int] = []
+
+    @property
+    def batch_indices(self) -> List[int]:
+        rank_zero_deprecation(
+            "The attribute `IndexBatchSamplerWrapper.batch_indices` was deprecated in v1.5 and will be removed in"
+            " v1.7. Access the full list `seen_batch_indices` instead."
+        )
+        return self._batch_indices
+
+    @batch_indices.setter
+    def batch_indices(self, indices: List[int]) -> None:
+        rank_zero_deprecation(
+            "The attribute `IndexBatchSamplerWrapper.batch_indices` was deprecated in v1.5 and will be removed in"
+            " v1.7. Access the full list `seen_batch_indices` instead."
+        )
+        self._batch_indices = indices
 
     def __iter__(self) -> Iterator[List[int]]:
+        self.seen_batch_indices = []
         for batch in self._sampler:
-            self.batch_indices = batch
+            self._batch_indices = batch
+            self.seen_batch_indices.append(batch)
             yield batch
 
     def __len__(self) -> int:

tests/callbacks/test_prediction_writer.py

@@ -11,54 +11,98 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+from unittest.mock import ANY, call, Mock
 
 import pytest
+from torch.utils.data import DataLoader
 
 from pytorch_lightning import Trainer
 from pytorch_lightning.callbacks import BasePredictionWriter
 from pytorch_lightning.utilities.exceptions import MisconfigurationException
-from tests.helpers import BoringModel
+from tests.helpers import BoringModel, RandomDataset
+from tests.helpers.runif import RunIf
 
 
-def test_prediction_writer(tmpdir):
-    class CustomPredictionWriter(BasePredictionWriter):
-        def __init__(self, writer_interval: str):
-            super().__init__(writer_interval)
+class DummyPredictionWriter(BasePredictionWriter):
+    def write_on_batch_end(self, *args, **kwargs):
+        pass
 
-            self.write_on_batch_end_called = False
-            self.write_on_epoch_end_called = False
+    def write_on_epoch_end(self, *args, **kwargs):
+        pass
 
-        def write_on_batch_end(self, *args, **kwargs):
-            self.write_on_batch_end_called = True
-
-        def write_on_epoch_end(self, *args, **kwargs):
-            self.write_on_epoch_end_called = True
 
+def test_prediction_writer_invalid_write_interval():
+    """Test that configuring an unknown interval name raises an error."""
     with pytest.raises(MisconfigurationException, match=r"`write_interval` should be one of \['batch"):
-        CustomPredictionWriter("something")
+        DummyPredictionWriter("something")
+
+
+def test_prediction_writer_hook_call_intervals(tmpdir):
+    """Test that the `write_on_batch_end` and `write_on_epoch_end` hooks get invoked based on the defined
+    interval."""
+    DummyPredictionWriter.write_on_batch_end = Mock()
+    DummyPredictionWriter.write_on_epoch_end = Mock()
+
+    dataloader = DataLoader(RandomDataset(32, 64))
 
     model = BoringModel()
-    cb = CustomPredictionWriter("batch_and_epoch")
+    cb = DummyPredictionWriter("batch_and_epoch")
     trainer = Trainer(limit_predict_batches=4, callbacks=cb)
-    results = trainer.predict(model, dataloaders=model.train_dataloader())
+    results = trainer.predict(model, dataloaders=dataloader)
     assert len(results) == 4
-    assert cb.write_on_batch_end_called
-    assert cb.write_on_epoch_end_called
+    assert cb.write_on_batch_end.call_count == 4
+    assert cb.write_on_epoch_end.call_count == 1
 
-    cb = CustomPredictionWriter("batch_and_epoch")
+    DummyPredictionWriter.write_on_batch_end.reset_mock()
+    DummyPredictionWriter.write_on_epoch_end.reset_mock()
+
+    cb = DummyPredictionWriter("batch_and_epoch")
     trainer = Trainer(limit_predict_batches=4, callbacks=cb)
-    trainer.predict(model, dataloaders=model.train_dataloader(), return_predictions=False)
-    assert cb.write_on_batch_end_called
-    assert cb.write_on_epoch_end_called
+    trainer.predict(model, dataloaders=dataloader, return_predictions=False)
+    assert cb.write_on_batch_end.call_count == 4
+    assert cb.write_on_epoch_end.call_count == 1
+
+    DummyPredictionWriter.write_on_batch_end.reset_mock()
+    DummyPredictionWriter.write_on_epoch_end.reset_mock()
 
-    cb = CustomPredictionWriter("batch")
+    cb = DummyPredictionWriter("batch")
     trainer = Trainer(limit_predict_batches=4, callbacks=cb)
-    trainer.predict(model, dataloaders=model.train_dataloader(), return_predictions=False)
-    assert cb.write_on_batch_end_called
-    assert not cb.write_on_epoch_end_called
+    trainer.predict(model, dataloaders=dataloader, return_predictions=False)
+    assert cb.write_on_batch_end.call_count == 4
+    assert cb.write_on_epoch_end.call_count == 0
+
+    DummyPredictionWriter.write_on_batch_end.reset_mock()
+    DummyPredictionWriter.write_on_epoch_end.reset_mock()
 
-    cb = CustomPredictionWriter("epoch")
+    cb = DummyPredictionWriter("epoch")
     trainer = Trainer(limit_predict_batches=4, callbacks=cb)
-    trainer.predict(model, dataloaders=model.train_dataloader(), return_predictions=False)
-    assert not cb.write_on_batch_end_called
-    assert cb.write_on_epoch_end_called
+    trainer.predict(model, dataloaders=dataloader, return_predictions=False)
+    assert cb.write_on_batch_end.call_count == 0
+    assert cb.write_on_epoch_end.call_count == 1
+
+
+@pytest.mark.parametrize("num_workers", [0, pytest.param(2, marks=RunIf(slow=True))])
+def test_prediction_writer_batch_indices(tmpdir, num_workers):
+    DummyPredictionWriter.write_on_batch_end = Mock()
+    DummyPredictionWriter.write_on_epoch_end = Mock()
+
+    dataloader = DataLoader(RandomDataset(32, 64), batch_size=4, num_workers=num_workers)
+    model = BoringModel()
+    writer = DummyPredictionWriter("batch_and_epoch")
+    trainer = Trainer(limit_predict_batches=4, callbacks=writer)
+    trainer.predict(model, dataloaders=dataloader)
+
+    writer.write_on_batch_end.assert_has_calls(
+        [
+            call(trainer, model, ANY, [0, 1, 2, 3], ANY, 0, 0),
+            call(trainer, model, ANY, [4, 5, 6, 7], ANY, 1, 0),
+            call(trainer, model, ANY, [8, 9, 10, 11], ANY, 2, 0),
+            call(trainer, model, ANY, [12, 13, 14, 15], ANY, 3, 0),
+        ]
+    )
+
+    writer.write_on_epoch_end.assert_has_calls(
+        [
+            call(trainer, model, ANY, [[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11], [12, 13, 14, 15]]]),
+        ]
+    )

tests/deprecated_api/test_remove_1-7.py

@@ -14,6 +14,7 @@
 """Test deprecated functionality which will be removed in v1.7.0."""
 import os
 from unittest import mock
+from unittest.mock import Mock
 
 import pytest
 
@@ -23,6 +24,7 @@
 from pytorch_lightning.callbacks.progress import ProgressBar
 from pytorch_lightning.callbacks.xla_stats_monitor import XLAStatsMonitor
 from pytorch_lightning.loggers import LoggerCollection, TestTubeLogger
+from pytorch_lightning.overrides.distributed import IndexBatchSamplerWrapper
 from pytorch_lightning.plugins.environments import (
     KubeflowEnvironment,
     LightningEnvironment,
@@ -528,3 +530,12 @@ def is_using_torchelastic():
         match=f"MyClusterEnvironment.{method_name}` has been deprecated in v1.6 and will be removed in v1.7"
     ):
         MyClusterEnvironment()
+
+
+def test_v1_7_0_index_batch_sampler_wrapper_batch_indices():
+    sampler = IndexBatchSamplerWrapper(Mock())
+    with pytest.deprecated_call(match="was deprecated in v1.5 and will be removed in v1.7"):
+        _ = sampler.batch_indices
+
+    with pytest.deprecated_call(match="was deprecated in v1.5 and will be removed in v1.7"):
+        sampler.batch_indices = []

tests/deprecated_api/test_remove_1-8.py

@@ -12,6 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Test deprecated functionality which will be removed in v1.8.0."""
+
 import pytest
 import torch
 

tests/overrides/test_distributed.py

@@ -54,9 +54,7 @@ def test_index_batch_sampler(tmpdir):
     assert batch_sampler.batch_size == index_batch_sampler.batch_size
     assert batch_sampler.drop_last == index_batch_sampler.drop_last
     assert batch_sampler.sampler is sampler
-
-    for batch in index_batch_sampler:
-        assert index_batch_sampler.batch_indices == batch
+    assert list(index_batch_sampler) == index_batch_sampler.seen_batch_indices
 
 
 def test_index_batch_sampler_methods():