brats_training_ddp.py

# Copyright (c) MONAI Consortium
# 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
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"""
This example shows how to execute distributed training based on PyTorch native `DistributedDataParallel` module.
It can run on several nodes with multiple GPU devices on every node.

This example is a real-world task based on Decathlon challenge Task01: Brain Tumor segmentation.
So it's more complicated than other distributed training demo examples.

Under default settings, each single GPU needs to use ~12GB memory for network training. In addition, in order to
cache the whole dataset, ~100GB GPU memory are necessary. Therefore, at least 2 NVIDIA TESLA A100 (80G) are needed.
If you do not have enough GPU memory, you can try to decrease the input parameter `cache_rate`.

Main steps to set up the distributed training:

- Execute `torchrun` to create processes on every node for every GPU.
  It receives parameters as below:
  `--nproc_per_node=NUM_GPUS_PER_NODE`
  `--nnodes=NUM_NODES`
  `--master_addr="localhost"`
  `--master_port=1234`
  For more details, refer to https://github.com/pytorch/pytorch/blob/main/torch/distributed/run.py.
  Alternatively, we can also use `torch.multiprocessing.spawn` to start program, but it that case, need to handle
  all the above parameters and compute `rank` manually, then set to `init_process_group`, etc.
  `torchrun` is even more efficient than `torch.multiprocessing.spawn` during training.
- Use `init_process_group` to initialize every process, every GPU runs in a separate process with unique rank.
  Here we use `NVIDIA NCCL` as the backend and must set `init_method="env://"` if use `torchrun`.
- Wrap the model with `DistributedDataParallel` after moving to expected device.
- Partition dataset before training, so every rank process will only handle its own data partition.

Note:
    `torchrun` will launch `nnodes * nproc_per_node = world_size` processes in total.
    Suggest setting exactly the same software environment for every node, especially `PyTorch`, `nccl`, etc.
    A good practice is to use the same MONAI docker image for all nodes directly.
    Example script to execute this program on every node:
    torchrun --nproc_per_node=NUM_GPUS_PER_NODE --nnodes=NUM_NODES
        --master_addr="localhost" --master_port=1234 brats_training_ddp.py -d DIR_OF_TESTDATA

    This example was tested with [Ubuntu 16.04/20.04], [NCCL 2.6.3].

Referring to: https://pytorch.org/tutorials/intermediate/ddp_tutorial.html

Some codes are taken from https://github.com/pytorch/examples/blob/master/imagenet/main.py

"""

import argparse
import os
import sys
import time
import warnings

import torch
import torch.distributed as dist
from torch.nn.parallel import DistributedDataParallel

from monai.apps import DecathlonDataset
from monai.data import ThreadDataLoader, partition_dataset, decollate_batch
from monai.inferers import sliding_window_inference
from monai.losses import DiceFocalLoss
from monai.metrics import DiceMetric
from monai.networks.nets import SegResNet, UNet
from monai.optimizers import Novograd
from monai.transforms import (
    Activations,
    AsDiscrete,
    Compose,
    EnsureChannelFirstd,
    LoadImaged,
    MapTransform,
    NormalizeIntensityd,
    Orientationd,
    RandFlipd,
    RandScaleIntensityd,
    RandShiftIntensityd,
    RandSpatialCropd,
    Spacingd,
    ToDeviced,
)
from monai.utils import set_determinism


class ConvertToMultiChannelBasedOnBratsClassesd(MapTransform):
    """
    Convert labels to multi channels based on brats classes:
    label 1 is the peritumoral edema
    label 2 is the GD-enhancing tumor
    label 3 is the necrotic and non-enhancing tumor core
    The possible classes are TC (Tumor core), WT (Whole tumor)
    and ET (Enhancing tumor).

    """

    def __call__(self, data):
        d = dict(data)
        for key in self.keys:
            result = []
            # merge label 2 and label 3 to construct TC
            result.append(torch.logical_or(d[key] == 2, d[key] == 3))
            # merge labels 1, 2 and 3 to construct WT
            result.append(torch.logical_or(torch.logical_or(d[key] == 2, d[key] == 3), d[key] == 1))
            # label 2 is ET
            result.append(d[key] == 2)
            d[key] = torch.stack(result, dim=0)
        return d


class BratsCacheDataset(DecathlonDataset):
    """
    Enhance the DecathlonDataset to support distributed data parallel.

    """

    def __init__(
        self,
        root_dir,
        section,
        transform=None,
        cache_rate=1.0,
        num_workers=0,
        shuffle=False,
    ) -> None:
        if not os.path.isdir(root_dir):
            raise ValueError("root directory root_dir must be a directory.")
        self.section = section
        self.shuffle = shuffle
        self.val_frac = 0.2
        self.set_random_state(seed=0)
        dataset_dir = os.path.join(root_dir, "Task01_BrainTumour")
        if not os.path.exists(dataset_dir):
            raise RuntimeError(
                f"cannot find dataset directory: {dataset_dir}, please download it from Decathlon challenge."
            )
        data = self._generate_data_list(dataset_dir)
        super(DecathlonDataset, self).__init__(data, transform, cache_rate=cache_rate, num_workers=num_workers)

    def _generate_data_list(self, dataset_dir):
        data = super()._generate_data_list(dataset_dir)
        # partition dataset based on current rank number, every rank trains with its own data
        # it can avoid duplicated caching content in each rank, but will not do global shuffle before every epoch
        return partition_dataset(
            data=data,
            num_partitions=dist.get_world_size(),
            shuffle=self.shuffle,
            seed=0,
            drop_last=False,
            even_divisible=self.shuffle,
        )[dist.get_rank()]


def main_worker(args):
    # disable logging for processes except 0 on every node
    if int(os.environ["LOCAL_RANK"]) != 0:
        f = open(os.devnull, "w")
        sys.stdout = sys.stderr = f
    if not os.path.exists(args.dir):
        raise FileNotFoundError(f"missing directory {args.dir}")

    # initialize the distributed training process, every GPU runs in a process
    dist.init_process_group(backend="nccl", init_method="env://")
    device = torch.device(f"cuda:{os.environ['LOCAL_RANK']}")
    torch.cuda.set_device(device)
    # use amp to accelerate training
    scaler = torch.cuda.amp.GradScaler()
    torch.backends.cudnn.benchmark = True

    total_start = time.time()
    train_transforms = Compose(
        [
            # load 4 Nifti images and stack them together
            LoadImaged(keys=["image", "label"]),
            ToDeviced(keys=["image", "label"], device=device),
            EnsureChannelFirstd(keys="image"),
            ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
            Orientationd(keys=["image", "label"], axcodes="RAS"),
            Spacingd(
                keys=["image", "label"],
                pixdim=(1.0, 1.0, 1.0),
                mode=("bilinear", "nearest"),
            ),
            RandSpatialCropd(keys=["image", "label"], roi_size=[224, 224, 144], random_size=False),
            RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=0),
            RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=1),
            RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=2),
            NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
            RandScaleIntensityd(keys="image", factors=0.1, prob=0.5),
            RandShiftIntensityd(keys="image", offsets=0.1, prob=0.5),
        ]
    )

    # create a training data loader
    train_ds = BratsCacheDataset(
        root_dir=args.dir,
        transform=train_transforms,
        section="training",
        num_workers=4,
        cache_rate=args.cache_rate,
        shuffle=True,
    )
    # ThreadDataLoader can be faster if no IO operations when caching all the data in memory
    train_loader = ThreadDataLoader(train_ds, num_workers=0, batch_size=args.batch_size, shuffle=True)

    # validation transforms and dataset
    val_transforms = Compose(
        [
            LoadImaged(keys=["image", "label"]),
            ToDeviced(keys=["image", "label"], device=device),
            EnsureChannelFirstd(keys="image"),
            ConvertToMultiChannelBasedOnBratsClassesd(keys="label"),
            Orientationd(keys=["image", "label"], axcodes="RAS"),
            Spacingd(
                keys=["image", "label"],
                pixdim=(1.0, 1.0, 1.0),
                mode=("bilinear", "nearest"),
            ),
            NormalizeIntensityd(keys="image", nonzero=True, channel_wise=True),
        ]
    )
    val_ds = BratsCacheDataset(
        root_dir=args.dir,
        transform=val_transforms,
        section="validation",
        num_workers=4,
        cache_rate=args.cache_rate,
        shuffle=False,
    )
    # ThreadDataLoader can be faster if no IO operations when caching all the data in memory
    val_loader = ThreadDataLoader(val_ds, num_workers=0, batch_size=args.batch_size, shuffle=False)

    # create network, loss function and optimizer
    if args.network == "SegResNet":
        model = SegResNet(
            blocks_down=[1, 2, 2, 4],
            blocks_up=[1, 1, 1],
            init_filters=16,
            in_channels=4,
            out_channels=3,
            dropout_prob=0.0,
        ).to(device)
    else:
        model = UNet(
            spatial_dims=3,
            in_channels=4,
            out_channels=3,
            channels=(16, 32, 64, 128, 256),
            strides=(2, 2, 2, 2),
            num_res_units=2,
        ).to(device)

    loss_function = DiceFocalLoss(
        smooth_nr=1e-5,
        smooth_dr=1e-5,
        squared_pred=True,
        to_onehot_y=False,
        sigmoid=True,
        batch=True,
    )
    optimizer = Novograd(model.parameters(), lr=args.lr)
    lr_scheduler = torch.optim.lr_scheduler.CosineAnnealingLR(optimizer, T_max=args.epochs)
    # wrap the model with DistributedDataParallel module
    model = DistributedDataParallel(model, device_ids=[device])

    dice_metric = DiceMetric(include_background=True, reduction="mean")
    dice_metric_batch = DiceMetric(include_background=True, reduction="mean_batch")

    post_trans = Compose([Activations(sigmoid=True), AsDiscrete(threshold=0.5)])

    # start a typical PyTorch training
    best_metric = -1
    best_metric_epoch = -1
    print(f"time elapsed before training: {time.time() - total_start}")
    train_start = time.time()
    for epoch in range(args.epochs):
        epoch_start = time.time()
        print("-" * 10)
        print(f"epoch {epoch + 1}/{args.epochs}")
        epoch_loss = train(train_loader, model, loss_function, optimizer, lr_scheduler, scaler)
        print(f"epoch {epoch + 1} average loss: {epoch_loss:.4f}")

        if (epoch + 1) % args.val_interval == 0:
            metric, metric_tc, metric_wt, metric_et = evaluate(
                model, val_loader, dice_metric, dice_metric_batch, post_trans
            )

            if metric > best_metric:
                best_metric = metric
                best_metric_epoch = epoch + 1
                if dist.get_rank() == 0:
                    torch.save(model.state_dict(), "best_metric_model.pth")
            print(
                f"current epoch: {epoch + 1} current mean dice: {metric:.4f}"
                f" tc: {metric_tc:.4f} wt: {metric_wt:.4f} et: {metric_et:.4f}"
                f"\nbest mean dice: {best_metric:.4f} at epoch: {best_metric_epoch}"
            )

        print(f"time consuming of epoch {epoch + 1} is: {(time.time() - epoch_start):.4f}")

    print(
        f"train completed, best_metric: {best_metric:.4f} at epoch: {best_metric_epoch},"
        f" total train time: {(time.time() - train_start):.4f}"
    )
    dist.destroy_process_group()


def train(train_loader, model, criterion, optimizer, lr_scheduler, scaler):
    model.train()
    step = 0
    epoch_len = len(train_loader)
    epoch_loss = 0
    step_start = time.time()
    for batch_data in train_loader:
        step += 1
        optimizer.zero_grad()
        with torch.cuda.amp.autocast():
            outputs = model(batch_data["image"])
            loss = criterion(outputs, batch_data["label"])
        scaler.scale(loss).backward()
        scaler.step(optimizer)
        scaler.update()
        epoch_loss += loss.item()
        print(f"{step}/{epoch_len}, train_loss: {loss.item():.4f}, step time: {(time.time() - step_start):.4f}")
        step_start = time.time()
    lr_scheduler.step()
    epoch_loss /= step

    return epoch_loss


def evaluate(model, val_loader, dice_metric, dice_metric_batch, post_trans):
    model.eval()
    with torch.no_grad():
        for val_data in val_loader:
            with torch.cuda.amp.autocast():
                val_outputs = sliding_window_inference(
                    inputs=val_data["image"], roi_size=(240, 240, 160), sw_batch_size=4, predictor=model, overlap=0.6
                )
            val_outputs = [post_trans(i) for i in decollate_batch(val_outputs)]
            dice_metric(y_pred=val_outputs, y=val_data["label"])
            dice_metric_batch(y_pred=val_outputs, y=val_data["label"])

        metric = dice_metric.aggregate().item()
        metric_batch = dice_metric_batch.aggregate()
        metric_tc = metric_batch[0].item()
        metric_wt = metric_batch[1].item()
        metric_et = metric_batch[2].item()
        dice_metric.reset()
        dice_metric_batch.reset()

    return metric, metric_tc, metric_wt, metric_et


def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("-d", "--dir", default="./testdata", type=str, help="directory of Brain Tumor dataset")
    parser.add_argument("--epochs", default=300, type=int, metavar="N", help="number of total epochs to run")
    parser.add_argument("--lr", default=1e-4, type=float, help="learning rate")
    parser.add_argument("-b", "--batch_size", default=1, type=int, help="mini-batch size of every GPU")
    parser.add_argument("--seed", default=None, type=int, help="seed for initializing training.")
    parser.add_argument("--cache_rate", type=float, default=1.0, help="larger cache rate relies on enough GPU memory.")
    parser.add_argument("--val_interval", type=int, default=20)
    parser.add_argument("--network", type=str, default="SegResNet", choices=["UNet", "SegResNet"])
    args = parser.parse_args()

    if args.seed is not None:
        set_determinism(seed=args.seed)
        warnings.warn(
            "You have chosen to seed training. "
            "This will turn on the CUDNN deterministic setting, "
            "which can slow down your training considerably! "
            "You may see unexpected behavior when restarting "
            "from checkpoints."
        )

    main_worker(args=args)


# usage example(refer to https://github.com/pytorch/pytorch/blob/main/torch/distributed/run.py):

# torchrun --nproc_per_node=NUM_GPUS_PER_NODE --nnodes=NUM_NODES brats_training_ddp.py -d DIR_OF_TESTDATA

if __name__ == "__main__":
    main()