Training seems to pause every N steps

[mfoglio]

I am doing feature extraction using an efficientnet_b0 model. The training process works fine but it seems to pause every once in a while. I verified this using nvidia-smi dmon. There are spikes of a few seconds where the GPU utilization is anywhere between 50% and 100%, followed by a few seconds where the GPU utilization is 0%.

Right now I am training with 4 Tesla T4, but I verified the same issue with a single GPU (T4 and V100).
I am using a batch size of 200 (per GPU). I have 48 CPUs and their usage is pretty low (I'd say 20-40%).

I noticed the training pausing at epoch 48, 96, 144,... So it pauses every 48 steps.

I thought that the pause were caused by logging so in my Trainer I set log_every_n_steps=500 and I also initialize my logger with TensorBoardLogger("tb_logs", name="vehicles", max_queue=1000, flush_secs=120). I can that the processes pauses more frequently than 120 seconds.

Originally, I thought it was a PyTorch "issue". So I opened a post here https://discuss.pytorch.org/t/gpu-usage-is-not-constant-during-training/154718 . However I am wondering whether this could be caused by torch lightning.

Thank you

[akihironitta]

@mfoglio It sounds like it's because of logging as you mentioned. To make sure if the issue sits around the logger, have you checked if you see the same behaviour by disabling it completely Trainer(logger=False)? Also, it would be easier to look into it if you could provide all of your trainer arguments (or your full script if feasible) for reproduction.

I noticed the training pausing at epoch 48, 96, 144,... So it pauses every 48 steps.

How are you checking that it happens at these exact steps? From the progress bar?
UPDATE: You mean "steps" but not "epochs", right?

[mfoglio]

Hi @akihironitta , thank you for your help. Yes, I am talking about steps, not epochs. And I am checking using the progress bar. The sleep is also confirmed by nvidia-smi dmon.

EDIT: while at the beginning the code seems to be stuck at number of steps that are multiples of 48, I also noticed the progress bar getting stuck at step 965 which is obviously not a multiple of 48.

I disabled both logging and checkpoint but I still see the same issue:

code

    # Trainer
    trainer = Trainer(
        accelerator='auto',
        gpus=-1,
        default_root_dir=checkpoint_path,
        # devices=1,  # automatically inferred
        # num_processes=os.cpu_count(),
        strategy=DDPStrategy(find_unused_parameters=True),
        precision=16 if torch.cuda.is_available() else 32,
        # max_epochs=1000,
        # max_steps=1000,
        logger=False,
        log_every_n_steps=500,
        val_check_interval=1.0,  # must be a float otherwise it's interpreted as the number of batches
        # num_sanity_val_steps=0,
        # callbacks=[
        #     feature_freeze_unfreeze,
        #     checkpoint_epoch_model,
        #     checkpoint_best_model,
        #     RichProgressBar(),
            # LearningRateMonitor(logging_interval='step'),
        # ],
        # profiler='simple',
        max_epochs=-1
    )

    # Train
    trainer.fit(
        model=model,
        datamodule=vehicles_datamodule,
        ckpt_path=sorted(
            glob.glob(os.path.join(checkpoint_epoch_path, '*.ckpt'))  # todo: edit path
        )[-1] if resume_from_checkpoint else None
    )

It's hard for me to share my entire code but I can share the model and the data module.
Model:

from collections import defaultdict
from typing import Dict, List

import seaborn as sn
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
import torchvision

from vehicles.dataset.attributes import Attribute, AttributeValue
from vehicles.dataset.splits import DatasetSplit
from vehicles.model.modules import Flatten
from utils.plots import convert_matplotlib_plot_to_torch_tensor


class MultiOutputClassifier(pl.LightningModule):

    def __init__(self, attributes: List[Attribute],
                 samples_per_attribute_value: Dict[Attribute, Dict[AttributeValue, int]],
                 batch_size: int = 64,
                 freeze_features=False,
                 verbose=False,
                 ):
        super(MultiOutputClassifier, self).__init__()
        self.attributes = attributes
        self.verbose = verbose

        # FEATURES
        # Resnet
        # resnet = torchvision.models.resnet50(pretrained=True)
        # torch.nn.Sequential(*(list(resnet.children())[:-1]))
        # EfficientNet
        efficientnet_b0 = torchvision.models.efficientnet_b0(pretrained=True)
        self.features = torch.nn.Sequential(*(list(efficientnet_b0.children())[:-1]))

        # SqueezeNet
        # self.features = torchvision.models.squeezenet1_1(pretrained=True).features  # output is [n, 512, 13, 13]

        if freeze_features is True:
            for param in self.features.parameters():
                param.requires_grad = False

        # MIDDLE LAYERS
        self.channels_fc = 128
        self.middle_layers = nn.Sequential(
            # nn.Conv2d(512, 512, 3),
            # nn.Conv2d(512, 512, 3),
            # nn.Dropout2d(p=0.1),
            # Squeezenet
            # nn.AvgPool2d(13),
            # Flatten(512),
            # EfficientDet
            Flatten(1280),
            nn.Dropout(0.25),
            nn.Linear(1280, self.channels_fc),  # 1280 for efficient det
            nn.Linear(self.channels_fc, self.channels_fc, bias=False),
            # nn.Linear(self.channels_fc, self.channels_fc, bias=False),
        )

        # OUTPUTS
        self.output_layers = nn.ModuleDict({
            f'output_{attribute.name}': nn.Sequential(
                nn.Linear(self.channels_fc, len(attribute.get_values()), bias=False),
            ) for attribute in self.attributes
        })

        # INITIALIZE WEIGHTS
        self._initialize_weights()

        # BATCH SIZE
        self.batch_size = batch_size

        # LOSSES
        self.losses = self._get_losses(self.attributes, samples_per_attribute_value)

        # METRICS
        self.accuracy_metrics = nn.ModuleDict({
            dataset_split: nn.ModuleDict({
                attribute.name: torchmetrics.Accuracy(
                    ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index,
                    average='macro',
                    num_classes=len(attribute.get_values(include_none=False))
                )
                for attribute in self.attributes
            }) for dataset_split in [DatasetSplit.TRAIN, DatasetSplit.VALIDATION, DatasetSplit.TEST]
        })
        self.precision_metrics = nn.ModuleDict({
            dataset_split: nn.ModuleDict({
                attribute.name: torchmetrics.Precision(
                    ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index,
                    average='macro',
                    num_classes=len(attribute.get_values(include_none=False))
                )
                for attribute in self.attributes
            }) for dataset_split in [DatasetSplit.TRAIN, DatasetSplit.VALIDATION, DatasetSplit.TEST]
        })
        self.recall_metrics = nn.ModuleDict({
            dataset_split: nn.ModuleDict({
                attribute.name: torchmetrics.Recall(
                    ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index,
                    average='macro',
                    num_classes=len(attribute.get_values(include_none=False))
                )
                for attribute in self.attributes
            }) for dataset_split in [DatasetSplit.TRAIN, DatasetSplit.VALIDATION, DatasetSplit.TEST]
        })
        self.f1_metrics = nn.ModuleDict({
            dataset_split: nn.ModuleDict({
                attribute.name: torchmetrics.F1Score(
                    ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index,
                    average='macro',
                    num_classes=len(attribute.get_values(include_none=False))
                )
                for attribute in self.attributes
            }) for dataset_split in [DatasetSplit.TRAIN, DatasetSplit.VALIDATION, DatasetSplit.TEST]
        })
        self.confusion_matrix_metrics = nn.ModuleDict({
            dataset_split: nn.ModuleDict({
                attribute.name: torchmetrics.ConfusionMatrix(
                    num_classes=len(attribute.get_values(include_none=False)),
                    ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index,
                    normalize='true',
                    nan_strategy='ignore'
                )
                for attribute in self.attributes
            }) for dataset_split in [DatasetSplit.TRAIN, DatasetSplit.VALIDATION, DatasetSplit.TEST]
        })

    def forward(self, x):
        # Features
        x = self.features(x)
        if self.verbose:
            print(f'Features {x.shape}')
        # Middle layers
        x = self.middle_layers(x)
        if self.verbose:
            print(f'Middle layers {x.shape}')
        # Outputs
        outputs = {attribute: output_layer(x) for attribute, output_layer in self.output_layers.items()}
        # outputs = self.output_namedtuple(**outputs)
        if self.verbose:
            print(f'Output layers' + str({attribute: output.shape for attribute, output in outputs.items()}))
        return outputs

    def configure_optimizers(self):
        def lr_lambda(epoch: int):
            if epoch < 1:
                return 1
            # elif epoch < 2:
            #     return 2
            elif epoch < 25:
                return 1
            else:
                return 0.97 ** (epoch / 2.4)  # official efficientnet decaying from paper

        # Rescaling learning rate of official paper to the used batch size
        # learning_rate = 0.1 * 0.256 / 4096 * self.batch_size * torch.cuda.device_count()
        # Optimizer used by the paper
        # TODO: check that RMSprop is properly initialized as explained in the paper
        # optimizer = torch.optim.RMSprop(
        #     self.parameters(), lr=learning_rate, alpha=0.9, momentum=0.9, weight_decay=1e-5
        # )
        optimizer = torch.optim.AdamW(self.parameters(), lr=0.1)
        # optimizer_features = torch.optim.AdamW(self.features.parameters(), lr=0.0001)
        # optimizer_middle_layers = torch.optim.AdamW(self.middle_layers.parameters(), lr=0.01)
        # optimizer_outputs = torch.optim.AdamW(self.output_layers.parameters(), lr=0.01)

        # lr_scheduler = torch.optim.lr_scheduler.LambdaLR(optimizer, lr_lambda=lr_lambda)
        lr_scheduler = torch.optim.lr_scheduler.OneCycleLR(
            optimizer, max_lr=0.25, epochs=100, steps_per_epoch=4,
            pct_start=0.1, anneal_strategy='cos', cycle_momentum=True,
            base_momentum=0.85
        )

        return [optimizer], [lr_scheduler]

    @staticmethod
    def _get_losses(attributes: List[Attribute],
                    samples_per_attribute_value: Dict[Attribute, Dict[AttributeValue, int]]):
        # Compute weights
        weights_attributes = dict()
        for attribute in attributes:
            weights_attributes[attribute]: Dict[AttributeValue, float] = dict()
            for attribute_value in attribute.get_values():
                n_samples = samples_per_attribute_value[attribute][attribute_value]
                if attribute_value is not Attribute.ATTRIBUTE_VALUE_NONE:
                    weights_attributes[attribute][attribute_value] = 1 / n_samples if n_samples != 0 else 1
        # Convert to tensors
        weights_attributes = {
            attribute: torch.tensor(list(weights_attribute.values()))
            for attribute, weights_attribute in weights_attributes.items()
        }
        losses = nn.ModuleDict({
            attribute.name: torch.nn.CrossEntropyLoss(
                weight=weights_attribute,
                ignore_index=Attribute.ATTRIBUTE_VALUE_NONE.index
            )
            for attribute, weights_attribute in weights_attributes.items()
        })
        return losses

    def training_step(self, batch, batch_id):
        inputs, labels = batch
        y_pred_attributes = self.forward(inputs)
        log_metrics = self._get_log_metrics(
            dataset_split=DatasetSplit.TRAIN,
            y_pred_attributes=y_pred_attributes,
            y_target_attributes=labels,
        )
        # self.log_dict(log_metrics, rank_zero_only=True)
        losses = {
            attribute.name: log_metrics[f'{attribute.name} Loss'][DatasetSplit.TRAIN]
            for attribute in self.attributes
        }
        sum_losses = sum([loss for loss in losses.values() if not loss.isnan()])
        return {'loss': sum_losses, 'losses': losses, 'log': log_metrics}

    def validation_step(self, batch, batch_id):
        inputs, labels = batch
        y_pred_attributes = self.forward(inputs)
        log_metrics = self._get_log_metrics(
            dataset_split=DatasetSplit.VALIDATION,
            y_pred_attributes=y_pred_attributes,
            y_target_attributes=labels,
        )
        # self.log_dict(log_metrics, sync_dist=True, rank_zero_only=True)
        losses = {
            attribute.name: log_metrics[f'{attribute.name} Loss'][DatasetSplit.VALIDATION]
            for attribute in self.attributes
        }
        sum_losses = sum([loss for loss in losses.values() if not loss.isnan()])
        return {'loss': sum_losses, 'log': log_metrics}

    def test_step(self, batch, batch_id):
        inputs, labels = batch
        y_pred_attributes = self.forward(inputs)
        log_metrics = self._get_log_metrics(
            dataset_split=DatasetSplit.TEST,
            y_pred_attributes=y_pred_attributes,
            y_target_attributes=labels,
        )
        # self.log_dict(log_metrics, sync_dist=True, rank_zero_only=True)
        losses = {
            attribute.name: log_metrics[f'{attribute.name} Loss'][DatasetSplit.TEST]
            for attribute in self.attributes
        }
        sum_losses = sum([loss for loss in losses.values() if not loss.isnan()])
        return {'loss': sum_losses, 'log': log_metrics}

    def training_epoch_end(self, outputs):
        self._log_confusion_matrix(dataset_split=DatasetSplit.TRAIN)

    def validation_epoch_end(self, outputs):
        self._log_confusion_matrix(dataset_split=DatasetSplit.VALIDATION)
        # Metric to select best model
        avg_f1 = torch.mean(torch.tensor(
            [f1_metric.compute() for f1_metric in self.f1_metrics[DatasetSplit.VALIDATION].values()]
        ))
        # self.log('val_avg_f1', avg_f1, sync_dist=True, rank_zero_only=True)

    def test_epoch_end(self, outputs):
        self._log_confusion_matrix(dataset_split=DatasetSplit.TEST)

    def _get_log_metrics(self, dataset_split: 'DatasetSplit', y_pred_attributes, y_target_attributes) \
            -> Dict[str, Dict[str, float]]:
        metrics: Dict[str, Dict[str, float]] = defaultdict(dict)
        for attribute, label in zip(self.attributes, y_target_attributes.T):
            metrics[f'{attribute.name} Loss'][dataset_split] = self.losses[attribute.name](
                y_pred_attributes[f'output_{attribute.name}'], label
            )
            if not all(label == Attribute.ATTRIBUTE_VALUE_NONE.index):  # TODO: is it ok to skip all these samples?
                y_pred_attribute = y_pred_attributes[f'output_{attribute.name}']
                # Filter out ignored index ( # TODO: torchmetrics seems to have a bug)
                # TODO: is it correct?
                filtered_label = label[label != Attribute.ATTRIBUTE_VALUE_NONE.index]
                filtered_y_pred_attribute = y_pred_attribute[label != Attribute.ATTRIBUTE_VALUE_NONE.index]
                # Compute metrics
                self.accuracy_metrics[dataset_split][attribute.name](filtered_y_pred_attribute, filtered_label)
                self.precision_metrics[dataset_split][attribute.name](filtered_y_pred_attribute, filtered_label)
                self.recall_metrics[dataset_split][attribute.name](filtered_y_pred_attribute, filtered_label)
                self.f1_metrics[dataset_split][attribute.name](filtered_y_pred_attribute, filtered_label)
                self.confusion_matrix_metrics[dataset_split][attribute.name](filtered_y_pred_attribute, filtered_label)
                metrics[f'{attribute.name} Accuracy'][dataset_split] = self.accuracy_metrics[dataset_split][attribute.name]
                metrics[f'{attribute.name} F-1'][dataset_split] = self.f1_metrics[dataset_split][attribute.name]
                metrics[f'{attribute.name} Precision'][dataset_split] = self.precision_metrics[dataset_split][attribute.name]
                metrics[f'{attribute.name} Recall'][dataset_split] = self.recall_metrics[dataset_split][attribute.name]
        return metrics

    def _log_confusion_matrix(self, dataset_split: 'DatasetSplit'):
        # Confusion matrix
        for attribute in self.attributes:
            # Compute confusion matrix
            conf_mat = self.confusion_matrix_metrics[dataset_split][attribute.name].compute().detach().cpu().numpy().astype(np.float32)
            # Convert confusion matrix to pandas dataframe
            attribute_labels = [attribute_value.label for attribute_value in attribute.get_values()]
            df_cm = pd.DataFrame(conf_mat, index=attribute_labels, columns=attribute_labels)
            # Generate plot
            figure = plt.figure(figsize=(25, 25))
            # sn.set(font_scale=1.2)
            sn.heatmap(df_cm, annot=True, annot_kws={'size': 7}, square=True, fmt='.2%')
            # Send plot to tensorboard
            image = convert_matplotlib_plot_to_torch_tensor(figure)
            # self.logger.experiment.add_image(
            #     f'{dataset_split} {attribute.name} Confusion Matrix',
            #     image,
            #     global_step=self.current_epoch
            # )

    def _initialize_weights(self):
        def init_weights(m):
            if type(m) in [nn.Linear, nn.Conv2d]:
                torch.nn.init.kaiming_uniform_(m.weight)
        self.middle_layers.apply(init_weights)
        for output_layer in self.output_layers.values():
            output_layer.apply(init_weights)

    @torch.jit.export
    def _format_single_output(self, labels: List[str], values: torch.Tensor):
        indexes = torch.argsort(values, descending=True)
        values: List[float] = values.tolist()
        sorted_labels = [labels[i] for i in indexes]
        sorted_values = [values[i] for i in indexes]
        return {label: value for label, value in zip(sorted_labels, sorted_values)}

    def freeze_feature_layers(self):
        for param in self.features.parameters():
            param.requires_grad = False

    def unfreeze_feature_layers(self):
        for param in self.features.parameters():
            param.requires_grad = True

    def freeze_middle_layers(self):
        for param in self.middle_layers.parameters():
            param.requires_grad = False

    def unfreeze_middle_layers(self):
        for param in self.middle_layers.parameters():
            param.requires_grad = True

    def to_onnx(self, **kwargs):
        # ONNX settings
        dynamic_axes = {
            'images': {0: 'batch'},
            **{
                str(output): {0: 'batch'}
                for output in self.output_layers.keys()
            }
        }
        torch_onnx_export_kwargs = dict(
            input_names=['images'],
            output_names=[str(output) for output in self.output_layers.keys()],
            dynamic_axes=dynamic_axes,
        )
        kwargs = {
            **kwargs,
            **torch_onnx_export_kwargs
        }
        super().to_onnx(**kwargs)

    def export_deepstream_label_file(self, label_file_path: str):
        # Create label file
        text = ''
        for attribute in self.attributes:
            text += ';'.join([
                f'{attribute.name}_{attribute_value.label}'
                for attribute_value in attribute.get_values(include_none=False)
            ])
            text += '\n'
        with open(label_file_path, 'w') as fp:
            fp.write(text)


class FeatureExtractorFreezeUnfreeze(pl.callbacks.BaseFinetuning):

    def __init__(self, unfreeze_at_epoch: int):
        super().__init__()
        self._unfreeze_at_epoch = unfreeze_at_epoch

    def freeze_before_training(self, pl_module):
        # freeze any module you want
        # Here, we are freezing `features`
        self.freeze(pl_module.features)

    def finetune_function(self, pl_module, current_epoch, optimizer, optimizer_idx):
        # When `current_epoch` is self._unfreeze_at_epoch, features layers will start training.
        if current_epoch == self._unfreeze_at_epoch:
            self.unfreeze_and_add_param_group(
                modules=pl_module.features,
                optimizer=optimizer,
                train_bn=True,
            )

Data module:

import os
from typing import Any, Dict, List, Optional

from torch.utils.data import DataLoader, Dataset
from pytorch_lightning import LightningDataModule

from vehicles.dataset.attributes import Attribute


class VehiclesDataModule(LightningDataModule):

    def __init__(self, train_dataset: Dataset, val_dataset: Dataset, test_dataset: Dataset,
                 attributes: List[Attribute], batch_size: int, num_workers: int):
        super().__init__()
        self.train_dataset = train_dataset
        self.val_dataset = val_dataset
        self.test_dataset = test_dataset
        self.attributes = attributes
        self.batch_size = batch_size
        self.num_workers = num_workers

    def setup(self, stage: Optional[str] = None):
        pass

    def _get_data_loaders_kwargs(self):
        return dict(
            batch_size=self.batch_size,
            num_workers=self.num_workers,
            pin_memory=True,
            persistent_workers=True,
            # drop_last=True
            prefetch_factor=2
        )

    def train_dataloader(self):
        return DataLoader(self.train_dataset, **self._get_data_loaders_kwargs())

    def val_dataloader(self):
        return DataLoader(self.val_dataset, **self._get_data_loaders_kwargs())

    def test_dataloader(self):
        return DataLoader(self.test_dataset, **self._get_data_loaders_kwargs())

    def predict_dataloader(self):
        return DataLoader(self.test_dataset, **self._get_data_loaders_kwargs())

    def teardown(self, stage: Optional[str] = None):
        # Used to clean-up when the run is finished
        pass

    def state_dict(self) -> Dict[str, Any]:
        return {
            'train_dataset': self.train_dataset.state_dict(),
            'val_dataset': self.val_dataset.state_dict(),
            'test_dataset': self.test_dataset.state_dict(),
        }

    def load_state_dict(self, state_dict: Dict[str, Any]) -> None:
        self.train_dataset.load_state_dict(state_dict['train_dataset'])
        self.val_dataset.load_state_dict(state_dict['val_dataset'])
        self.test_dataset.load_state_dict(state_dict['test_dataset'])

[mfoglio]

As a side question, the following checkpoint will be saved only at the end of every epoch, not every time there is an improvement in the metric, right? Because during the first epochs there is going to be an improvement almost every step.

    checkpoint_best_model = ModelCheckpoint(
        dirpath=checkpoint_best_path,
        filename="{epoch}-{step}-{val_avg_f1:.3f}",
        monitor="val_avg_f1",
        mode="min",
        save_top_k=10,
        save_on_train_epoch_end=True,  # to ensure the required metric is being accumulated correctly
                                       # for creating a checkpoint
    )

Again, just to be clear, in my latest test the checkpointing system was disabled.

[mfoglio]

I analyzed the problem a little bit more. I noticed that I have 48 CPUs and 48 workers. That makes the training process pausing every 48 steps. If use 12 workers, the pause happens every 12 steps.
I'd like to increase the number of workers but the RAM usage is crazy high. With 48 workers I am almost using all the 180Gb of RAM available. Is this normal for simply loading images of a few Kbytes?
Any suggestion on how to speed this up?

EDIT: I think I am facing this issue pytorch/pytorch#13246 (comment) even though I am not entirely sure. My memory consumption is of about 100-150 gb right after the training starts. I tried to used a numpy array to store the huge list of integers containing the IDs of the record in the dataset. However, this didn't reduce the RAM usage.
Suppose my dataset has a property myobject of type MyObject, and that myobject internally references a list of integers. Should I convert this list of integers to a numpy array too?

[akihironitta]

@mfoglio Very interesting! I wasn't aware of the PyTorch issue (which stems from Python's nature).

Suppose my dataset has a property myobject of type MyObject, and that myobject internally references a list of integers. Should I convert this list of integers to a numpy array too?

Definitely, yes, if I understand it correctly from the linked PyTorch issue. Let me know if it resolves your issue. (just curious 👀)

[zihaozou]

Hi @mfoglio, did you find a way to solve this problem? I am having the same problem.

[asiron]

I am facing the same issue here. Did resolving the pytorch issue help this problem ?

[asiron]

I am having the same exact issue. I tried to solve it with pytorch/pytorch#13246 (comment) but without success. For me the problem is not that it uses large amount of RAM, but that it really slows down every N steps (where N is num_workers). Things I tried (as suggested in the aforementioned issue)

• I moved the list of image paths to a numpy array so that __getitem__(idx) is looking up a numpy array instead of a Python array
• I am loading the ground truth .json file inside the __getitem__ function.
• DataLoader with pin_memory=True
  Memory usage still stays relatively low, but the pausing every N steps makes the A100 GPU basically useless.

[zihaozou]

In my case, it seems to be related to the disk i/o. I am using a cluster, which mounted the data from the storage server to the execute server through LAN. The dataloading speed is heavily influenced by the network flutuation

[damtien444]

I met the same issue and it turned out that my __getitem__ contained too many processing steps and disk reading. I solved this by caching or preprocessing everything in __getitem__.

[stolpa4]

Exactly the same issue! Still haven't found any viable solution to this. Currently in search.