Add predict step accumulation (#7767)

* Add eval_accumulation_step and clean distributed eval

* Add TPU test

* Add TPU stuff

* Fix arg name

* Fix Seq2SeqTrainer

* Fix total_size

* Update src/transformers/trainer_pt_utils.py
Co-authored-by: Lysandre Debut <lysandre@huggingface.co>

* Doc and add test to TPU

* Add unit test

* Adapt name
Co-authored-by: Lysandre Debut <lysandre@huggingface.co>

docs/source/internal/trainer_utils.rst

@@ -19,3 +19,9 @@ Callbacks internals
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. autoclass:: transformers.trainer_callback.CallbackHandler
+
+Distributed Evaluation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autoclass:: transformers.trainer_pt_utils.DistributedTensorGatherer
+    :members:
\ No newline at end of file

examples/seq2seq/seq2seq_trainer.py

@@ -174,7 +174,7 @@ class Seq2SeqTrainer(Trainer):
             # Call forward again to get loss # TODO: avoidable?
             outputs = model(**inputs, use_cache=False)
             loss = self._compute_loss(outputs[1], labels_out)
-            loss = loss.mean().item()
+            loss = loss.mean().detach()
             if self.args.prediction_loss_only:
                 return (loss, None, None)
 

examples/test_xla_examples.py

@@ -81,3 +81,14 @@ class TorchXLAExamplesTests(unittest.TestCase):
 
             # Assert that the script takes less than 300 seconds to make sure it doesn't hang.
             self.assertLess(end - start, 300)
+
+    def test_trainer_tpu(self):
+        import xla_spawn
+
+        testargs = """
+            transformers/tests/test_trainer_tpu.py
+            --num_cores=8
+            transformers/tests/test_trainer_tpu.py
+            """.split()
+        with patch.object(sys, "argv", testargs):
+            xla_spawn.main()

src/transformers/trainer.py

@@ -59,6 +59,7 @@ from .trainer_callback import (
     TrainerState,
 )
 from .trainer_pt_utils import (
+    DistributedTensorGatherer,
     SequentialDistributedSampler,
     distributed_broadcast_scalars,
     distributed_concat,
@@ -1266,18 +1267,29 @@ class Trainer:
         # multi-gpu eval
         if self.args.n_gpu > 1:
             model = torch.nn.DataParallel(model)
-        else:
-            model = self.model
         # Note: in torch.distributed mode, there's no point in wrapping the model
         # inside a DistributedDataParallel as we'll be under `no_grad` anyways.
 
         batch_size = dataloader.batch_size
+        num_examples = self.num_examples(dataloader)
         logger.info("***** Running %s *****", description)
-        logger.info("  Num examples = %d", self.num_examples(dataloader))
+        logger.info("  Num examples = %d", num_examples)
         logger.info("  Batch size = %d", batch_size)
-        eval_losses: List[float] = []
-        preds: torch.Tensor = None
-        label_ids: torch.Tensor = None
+        losses_host: torch.Tensor = None
+        preds_host: Union[torch.Tensor, List[torch.Tensor]] = None
+        labels_host: Union[torch.Tensor, List[torch.Tensor]] = None
+
+        world_size = 1
+        if is_torch_tpu_available():
+            world_size = xm.xrt_world_size()
+        elif self.args.local_rank != -1:
+            world_size = torch.distributed.get_world_size()
+        world_size = max(1, world_size)
+
+        eval_losses_gatherer = DistributedTensorGatherer(world_size, num_examples, make_multiple_of=batch_size)
+        preds_gatherer = DistributedTensorGatherer(world_size, num_examples)
+        labels_gatherer = DistributedTensorGatherer(world_size, num_examples)
+
         model.eval()
 
         if is_torch_tpu_available():
@@ -1288,55 +1300,46 @@ class Trainer:
 
         self.callback_handler.eval_dataloader = dataloader
 
-        for inputs in dataloader:
+        for step, inputs in enumerate(dataloader):
             loss, logits, labels = self.prediction_step(model, inputs, prediction_loss_only)
-            batch_size = inputs[list(inputs.keys())[0]].shape[0]
             if loss is not None:
-                eval_losses.extend([loss] * batch_size)
+                losses = loss.repeat(batch_size)
+                losses_host = losses if losses_host is None else torch.cat((losses_host, losses), dim=0)
             if logits is not None:
-                preds = logits if preds is None else nested_concat(preds, logits, dim=0)
+                preds_host = logits if preds_host is None else nested_concat(preds_host, logits, dim=0)
             if labels is not None:
-                label_ids = labels if label_ids is None else nested_concat(label_ids, labels, dim=0)
+                labels_host = labels if labels_host is None else nested_concat(labels_host, labels, dim=0)
             self.control = self.callback_handler.on_prediction_step(self.args, self.state, self.control)
 
+            # Gather all tensors and put them back on the CPU if we have done enough accumulation steps.
+            if self.args.eval_accumulation_steps is not None and (step + 1) % self.args.eval_accumulation_steps == 0:
+                eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses"))
+                preds_gatherer.add_arrays(self._gather_and_numpify(preds_host, "eval_preds"))
+                labels_gatherer.add_arrays(self._gather_and_numpify(labels_host, "eval_label_ids"))
+
+                # Set back to None to begin a new accumulation
+                losses_host, preds_host, labels_host = None, None, None
+
         if self.args.past_index and hasattr(self, "_past"):
             # Clean the state at the end of the evaluation loop
             delattr(self, "_past")
 
-        if self.args.local_rank != -1:
-            # In distributed mode, concatenate all results from all nodes:
-            if preds is not None:
-                preds = distributed_concat(preds, num_total_examples=self.num_examples(dataloader))
-            if label_ids is not None:
-                label_ids = distributed_concat(label_ids, num_total_examples=self.num_examples(dataloader))
-        elif is_torch_tpu_available():
-            # tpu-comment: Get all predictions and labels from all worker shards of eval dataset
-            if preds is not None:
-                preds = nested_xla_mesh_reduce(preds, "eval_preds")
-            if label_ids is not None:
-                label_ids = nested_xla_mesh_reduce(label_ids, "eval_label_ids")
-            if eval_losses is not None:
-                eval_losses = xm.mesh_reduce("eval_losses", torch.tensor(eval_losses), torch.cat).tolist()
-
-        # Finally, turn the aggregated tensors into numpy arrays.
-        if preds is not None:
-            preds = nested_numpify(preds)
-        if label_ids is not None:
-            label_ids = nested_numpify(label_ids)
+        # Gather all remaining tensors and put them back on the CPU
+        eval_losses_gatherer.add_arrays(self._gather_and_numpify(losses_host, "eval_losses"))
+        preds_gatherer.add_arrays(self._gather_and_numpify(preds_host, "eval_preds"))
+        labels_gatherer.add_arrays(self._gather_and_numpify(labels_host, "eval_label_ids"))
+
+        eval_loss = eval_losses_gatherer.finalize()
+        preds = preds_gatherer.finalize()
+        label_ids = labels_gatherer.finalize()
 
         if self.compute_metrics is not None and preds is not None and label_ids is not None:
             metrics = self.compute_metrics(EvalPrediction(predictions=preds, label_ids=label_ids))
         else:
             metrics = {}
-        if len(eval_losses) > 0:
-            if self.args.local_rank != -1:
-                metrics["eval_loss"] = (
-                    distributed_broadcast_scalars(eval_losses, num_total_examples=self.num_examples(dataloader))
-                    .mean()
-                    .item()
-                )
-            else:
-                metrics["eval_loss"] = np.mean(eval_losses)
+
+        if eval_loss is not None:
+            metrics["eval_loss"] = eval_loss.mean().item()
 
         # Prefix all keys with eval_
         for key in list(metrics.keys()):
@@ -1345,6 +1348,20 @@ class Trainer:
 
         return PredictionOutput(predictions=preds, label_ids=label_ids, metrics=metrics)
 
+    def _gather_and_numpify(self, tensors, name):
+        """
+        Gather value of `tensors` (tensor or list/tuple of nested tensors) and convert them to numpy before
+        concatenating them to `gathered`
+        """
+        if tensors is None:
+            return
+        if is_torch_tpu_available():
+            tensors = nested_xla_mesh_reduce(tensors, name)
+        elif self.args.local_rank != -1:
+            tensors = distributed_concat(tensors)
+
+        return nested_numpify(tensors)
+
     def prediction_step(
         self, model: nn.Module, inputs: Dict[str, Union[torch.Tensor, Any]], prediction_loss_only: bool
     ) -> Tuple[Optional[float], Optional[torch.Tensor], Optional[torch.Tensor]]:
@@ -1374,8 +1391,7 @@ class Trainer:
         with torch.no_grad():
             outputs = model(**inputs)
             if has_labels:
-                # The .mean() is to reduce in case of distributed training
-                loss = outputs[0].mean().item()
+                loss = outputs[0].mean().detach()
                 logits = outputs[1:]
             else:
                 loss = None

src/transformers/trainer_pt_utils.py

@@ -21,11 +21,13 @@ import warnings
 from contextlib import contextmanager
 from typing import List, Optional, Union
 
+import numpy as np
 import torch
 from torch.utils.data.distributed import DistributedSampler
 from torch.utils.data.sampler import RandomSampler, Sampler
 
 from .file_utils import is_torch_tpu_available
+from .utils import logging
 
 
 if is_torch_tpu_available():
@@ -33,6 +35,8 @@ if is_torch_tpu_available():
 
 PT_LR_SCHEDULER_WARNING = "Please also save or load the state of the optimzer when saving or loading the scheduler."
 
+logger = logging.get_logger(__name__)
+
 
 def nested_concat(tensors, new_tensors, dim=0):
     "Concat the `new_tensors` to `tensors` on `dim`. Works for tensors or nested list/tuples of tensors."
@@ -41,7 +45,12 @@ def nested_concat(tensors, new_tensors, dim=0):
     ), f"Expected `tensors` and `new_tensors` to have the same type but found {type(tensors)} and {type(new_tensors)}."
     if isinstance(tensors, (list, tuple)):
         return type(tensors)(nested_concat(t, n, dim) for t, n in zip(tensors, new_tensors))
+    elif isinstance(tensors, torch.Tensor):
         return torch.cat((tensors, new_tensors), dim=dim)
+    elif isinstance(tensors, np.ndarray):
+        return np.concatenate((tensors, new_tensors), axis=dim)
+    else:
+        raise TypeError(f"Unsupported type for concatenation: got {type(tensors)}")
 
 
 def nested_numpify(tensors):
@@ -177,3 +186,112 @@ def get_tpu_sampler(dataset: torch.utils.data.dataset.Dataset):
     if xm.xrt_world_size() <= 1:
         return RandomSampler(dataset)
     return DistributedSampler(dataset, num_replicas=xm.xrt_world_size(), rank=xm.get_ordinal())
+
+
+def nested_new_like(arrays, num_samples):
+    """ Create the same nested structure as `arrays` with a first dimension always at `num_samples`."""
+    if isinstance(arrays, (list, tuple)):
+        return type(arrays)(nested_new_like(x, num_samples) for x in arrays)
+    return np.zeros((num_samples, *arrays.shape[1:]), dtype=arrays.dtype)
+
+
+def nested_truncate(tensors, limit):
+    "Truncate `tensors` at `limit` (even if it's a nested list/tuple of tensors)."
+    if isinstance(tensors, (list, tuple)):
+        return type(tensors)(nested_truncate(t, limit) for t in tensors)
+    return tensors[:limit]
+
+
+class DistributedTensorGatherer:
+    """
+    A class responsible for properly gathering tensors (or nested list/tuple of tensors) on the CPU
+    by chunks.
+
+    If our dataset has 16 samples with a batch size of 2 on 3 processes and we gather then transfer on
+    CPU at every step, our sampler will generate the following indices:
+
+        :obj:`[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 0, 1]`
+
+    to get something of size a multiple of 3 (so that each process gets the same dataset length). Then
+    process 0, 1 and 2 will be responsible of making predictions for the following samples:
+
+        - P0: :obj:`[0, 1, 2, 3, 4, 5]`
+        - P1: :obj:`[6, 7, 8, 9, 10, 11]`
+        - P2: :obj:`[12, 13, 14, 15, 0, 1]`
+
+    The first batch treated on each process will be
+
+        - P0: :obj:`[0, 1]`
+        - P1: :obj:`[6, 7]`
+        - P2: :obj:`[12, 13]`
+
+    So if we gather at the end of the first batch, we will get a tensor (nested list/tuple of tensor)
+    corresponding to the following indices:
+
+        :obj:`[0, 1, 6, 7, 12, 13]`
+
+    If we directly concatenate our results without taking any precautions, the user will then get
+    the predictions for the indices in this order at the end of the prediction loop:
+
+        :obj:`[0, 1, 6, 7, 12, 13, 2, 3, 8, 9, 14, 15, 4, 5, 10, 11, 0, 1]`
+
+    For some reason, that's not going to roll their boat. This class is there to solve that problem.
+
+    Args:
+
+        world_size (:obj:`int`):
+            The number of processes used in the distributed training.
+        num_samples (:obj:`int`):
+            The number of samples in our dataset.
+        make_multiple_of (:obj:`int`, `optional`):
+            If passed, the class assumes the datasets passed to each process are made to be a multiple of this argument
+            (by adding samples).
+    """
+
+    def __init__(self, world_size, num_samples, make_multiple_of=None):
+        self.world_size = world_size
+        self.num_samples = num_samples
+        total_size = world_size if make_multiple_of is None else world_size * make_multiple_of
+        self.total_samples = int(np.ceil(num_samples / total_size)) * total_size
+        self.process_length = self.total_samples // world_size
+        self._storage = None
+        self._offsets = None
+
+    def add_arrays(self, arrays):
+        """
+        Add :obj:`arrays` to the internal storage, Will initialize the storage to the full size at the first arrays
+        passed so that if we're bound to get an OOM, it happens at the beginning.
+        """
+        if arrays is None:
+            return
+        if self._storage is None:
+            self._storage = nested_new_like(arrays, self.total_samples)
+            self._offsets = list(range(0, self.total_samples, self.process_length))
+        slice_len = self._nested_set_tensors(self._storage, arrays)
+        for i in range(self.world_size):
+            self._offsets[i] += slice_len
+
+    def _nested_set_tensors(self, storage, arrays):
+        if isinstance(arrays, (list, tuple)):
+            for x, y in zip(storage, arrays):
+                slice_len = self._nested_set_tensors(x, y)
+            return slice_len
+        assert (
+            arrays.shape[0] % self.world_size == 0
+        ), f"Arrays passed should all have a first dimension multiple of {self.world_size}, found {arrays.shape[0]}."
+
+        slice_len = arrays.shape[0] // self.world_size
+        for i in range(self.world_size):
+            storage[self._offsets[i] : self._offsets[i] + slice_len] = arrays[i * slice_len : (i + 1) * slice_len]
+        return slice_len
+
+    def finalize(self):
+        """
+        Return the properly gathered arrays and truncate to the number of samples (since the sampler added some extras
+        to get each process a dataset of the same length).
+        """
+        if self._storage is None:
+            return
+        if self._offsets[0] != self.process_length:
+            logger.warn("Not all data has been set. Are you sure you passed all values?")
+        return nested_truncate(self._storage, self.num_samples)

src/transformers/training_args.py

@@ -67,7 +67,7 @@ class TrainingArguments:
             The batch size per GPU/TPU core/CPU for training.
         per_device_eval_batch_size (:obj:`int`, `optional`, defaults to 8):
             The batch size per GPU/TPU core/CPU for evaluation.
-        gradient_accumulation_steps: (:obj:`int`, `optional`, defaults to 1):
+        gradient_accumulation_steps (:obj:`int`, `optional`, defaults to 1):
             Number of updates steps to accumulate the gradients for, before performing a backward/update pass.
 
             .. warning::
@@ -75,6 +75,10 @@ class TrainingArguments:
                 When using gradient accumulation, one step is counted as one step with backward pass. Therefore,
                 logging, evaluation, save will be conducted every ``gradient_accumulation_steps * xxx_step`` training
                 examples.
+        eval_accumulation_steps (:obj:`int`, `optional`):
+            Number of predictions steps to accumulate the output tensors for, before moving the results to the CPU. If
+            left unset, the whole predictions are accumulated on GPU/TPU before being moved to the CPU (faster but
+            requires more memory).
         learning_rate (:obj:`float`, `optional`, defaults to 5e-5):
             The initial learning rate for Adam.
         weight_decay (:obj:`float`, `optional`, defaults to 0):
@@ -225,6 +229,10 @@ class TrainingArguments:
         default=1,
         metadata={"help": "Number of updates steps to accumulate before performing a backward/update pass."},
     )
+    eval_accumulation_steps: Optional[int] = field(
+        default=None,
+        metadata={"help": "Number of predictions steps to accumulate before moving the tensors to the CPU."},
+    )
 
     learning_rate: float = field(default=5e-5, metadata={"help": "The initial learning rate for Adam."})
     weight_decay: float = field(default=0.0, metadata={"help": "Weight decay if we apply some."})

tests/test_trainer.py

+# coding=utf-8
+# Copyright 2018 the HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+
 import dataclasses
 import os
 import tempfile

tests/test_trainer_distributed.py

@@ -13,15 +13,14 @@
 #   CUDA_VISIBLE_DEVICES=-1 python ./tests/test_trainer_distributed.py
 #
 
-
-import logging
 import sys
 from typing import Dict
 
 from transformers import EvalPrediction, HfArgumentParser, TrainingArguments, is_torch_available
+from transformers.utils import logging
 
 
-logger = logging.getLogger(__name__)
+logger = logging.get_logger(__name__)
 
 
 if is_torch_available():
@@ -101,4 +100,20 @@ if __name__ == "__main__":
             logger.error(p.metrics)
             exit(1)
 
+        trainer.args.eval_accumulation_steps = 2
+
+        metrics = trainer.evaluate()
+        logger.info(metrics)
+        if metrics["eval_success"] is not True:
+            logger.error(metrics)
+            exit(1)
+
+        p = trainer.predict(dataset)
+        logger.info(p.metrics)
+        if p.metrics["eval_success"] is not True:
+            logger.error(p.metrics)
+            exit(1)
+
+        trainer.args.eval_accumulation_steps = None
+
     logger.info("🔥 All distributed tests successful")

tests/test_trainer_tpu.py

+# This test is meant to be run in on an instance with TPUs like this:
+#
+#   python examples/xla_spawn.py --num_cores=8 tests/test_trainer_tpu.py
+#
+# Replace 8 with the number of TPU cores you have.
+#
+
+import sys
+from typing import Dict
+
+from transformers import EvalPrediction, HfArgumentParser, TrainingArguments, is_torch_available
+from transformers.utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+
+if is_torch_available():
+    import torch
+    from torch import nn
+    from torch.utils.data.dataset import Dataset
+
+    from transformers import Trainer
+
+    class DummyDataset(Dataset):
+        def __init__(self, length: int = 101):
+            self.length = length
+
+        def __len__(self):
+            return self.length
+
+        def __getitem__(self, i) -> int:
+            return i
+
+    class DummyDataCollator:
+        def __call__(self, features):
+            return {"input_ids": torch.tensor(features), "labels": torch.tensor(features)}
+
+    class DummyModel(nn.Module):
+        def __init__(self):
+            super().__init__()
+            # Add some (unused) params otherwise DDP will complain.
+            self.fc = nn.Linear(120, 80)
+
+        def forward(self, input_ids, labels=None):
+            if labels is not None:
+                return torch.tensor(0.0, device=input_ids.device), input_ids
+            else:
+                return input_ids
+
+
+def main():
+    parser = HfArgumentParser((TrainingArguments,))
+    sys.argv += ["--output_dir", "./examples"]
+    training_args = parser.parse_args_into_dataclasses()[0]
+
+    logger.warning(
+        "Process rank: %s, device: %s, tpu_num_cores: %s",
+        training_args.local_rank,
+        training_args.device,
+        training_args.tpu_num_cores,
+    )
+
+    # Essentially, what we want to verify in the distributed case is
+    # that we get all samples back, in the right order.
+    # (this is crucial for prediction for instance)
+    for dataset_length in [1001, 256, 15]:
+        dataset = DummyDataset(dataset_length)
+
+        def compute_metrics(p: EvalPrediction) -> Dict:
+            sequential = list(range(len(dataset)))
+            success = p.predictions.tolist() == sequential and p.label_ids.tolist() == sequential
+            return {"success": success}
+
+        trainer = Trainer(
+            model=DummyModel(),
+            args=training_args,
+            data_collator=DummyDataCollator(),
+            eval_dataset=dataset,
+            compute_metrics=compute_metrics,
+        )
+        metrics = trainer.evaluate()
+        logger.info(metrics)
+        if metrics["eval_success"] is not True:
+            logger.error(metrics)
+            exit(1)
+
+        p = trainer.predict(dataset)
+        logger.info(p.metrics)
+        if p.metrics["eval_success"] is not True:
+            logger.error(p.metrics)
+            exit(1)
+
+        trainer.args.eval_accumulation_steps = 2
+
+        metrics = trainer.evaluate()
+        logger.info(metrics)
+        if metrics["eval_success"] is not True:
+            logger.error(metrics)
+            exit(1)
+
+        p = trainer.predict(dataset)
+        logger.info(p.metrics)
+        if p.metrics["eval_success"] is not True:
+            logger.error(p.metrics)
+            exit(1)
+
+        trainer.args.eval_accumulation_steps = None
+
+    logger.info("🔥 All distributed tests successful")
+
+
+def _mp_fn(index):
+    # For xla_spawn (TPUs)
+    main()
+
+
+if __name__ == "__main__":
+    main()

tests/test_trainer_utils.py

+# coding=utf-8
+# Copyright 2018 the HuggingFace Inc. team.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+
+import unittest
+
+import numpy as np
+
+from transformers.file_utils import is_torch_available
+from transformers.testing_utils import require_torch
+
+
+if is_torch_available():
+    from transformers.trainer_pt_utils import DistributedTensorGatherer
+
+
+@require_torch
+class TrainerUtilsTest(unittest.TestCase):
+    def test_distributed_tensor_gatherer(self):
+        # Simulate a result with a dataset of size 21, 4 processes and chunks of lengths 2, 3, 1
+        world_size = 4
+        num_samples = 21
+        input_indices = [
+            [0, 1, 6, 7, 12, 13, 18, 19],
+            [2, 3, 4, 8, 9, 10, 14, 15, 16, 20, 0, 1],
+            [5, 11, 17, 2],
+        ]
+
+        predictions = np.random.normal(size=(num_samples, 13))
+        gatherer = DistributedTensorGatherer(world_size=world_size, num_samples=num_samples)
+        for indices in input_indices:
+            gatherer.add_arrays(predictions[indices])
+        result = gatherer.finalize()
+        self.assertTrue(np.array_equal(result, predictions))
+
+        # With nested tensors
+        gatherer = DistributedTensorGatherer(world_size=world_size, num_samples=num_samples)
+        for indices in input_indices:
+            gatherer.add_arrays([predictions[indices], [predictions[indices], predictions[indices]]])
+        result = gatherer.finalize()
+        self.assertTrue(isinstance(result, list))
+        self.assertTrue(len(result), 2)
+        self.assertTrue(isinstance(result[1], list))
+        self.assertTrue(len(result[1]), 2)
+        self.assertTrue(np.array_equal(result[0], predictions))
+        self.assertTrue(np.array_equal(result[1][0], predictions))
+        self.assertTrue(np.array_equal(result[1][1], predictions))