PyTorch消除训练瓶颈提速技巧

2024-03-06 12:01:43

【GiantPandaCV导读】训练大型的数据集的速度受很多因素影响，由于数据集比较大，每个优化带来的时间提升就不可小觑。硬件方面，CPU、内存大小、GPU、机械硬盘orSSD存储等都会有一定的影响。软件实现方面，PyTorch本身的DataLoader有时候会不够用，需要额外操作，比如使用混合精度、数据预读取、多线程读取数据、多卡并行优化等策略也会给整个模型优化带来非常巨大的作用。那什么时候需要采取这篇文章的策略呢？那就是明明GPU显存已经占满，但是显存的利用率很低。

本文将搜集到的资源进行汇总，由于目前笔者训练的GPU利用率已经很高，所以并没有实际实验，可以在参考文献中看一下其他作者做的实验。同时感谢作者群各位大佬的指点，yyds。

1. 硬件层面
2. 如何测试训练过程的瓶颈
3. 图片解码
4. 数据增强加速
5. data Prefetch
6. 多GPU并行处理
7. 混合精度训练
8. 其他细节
参考文献

1. 硬件层面

CPU的话尽量看主频比较高的，缓存比较大的，核心数也是比较重要的参数。

显卡尽可能选现存比较大的，这样才能满足大batch训练，多卡当让更好。

内存要求64G，4根16G的内存条插满绝对够用了。

主板性能也要跟上，否则装再好的CPU也很难发挥出全部性能。

电源供电要充足，GPU运行的时候会对功率有一定要求，全力运行的时候如果电源供电不足对性能影响还是比较大的。

存储如果有条件，尽量使用SSD存放数据，SSD和机械硬盘的在训练的时候的读取速度不是一个量级。笔者试验过，相同的代码，将数据移动到SSD上要比在机械硬盘上快10倍。

操作系统尽量用Ubuntu就可以（实验室用）

如何实时查看Ubuntu下各个资源利用情况呢？

GPU使用 watch -n 1 nvidia-smi 来动态监控
IO情况，使用iostat命令来监控
CPU情况，使用htop命令来监控

笔者对硬件了解很有限，欢迎补充，如有问题轻喷。

2. 如何测试训练过程的瓶颈

如果现在程序运行速度很慢，那应该如何判断瓶颈在哪里呢？PyTorch中提供了工具，非常方便的可以查看设计的代码在各个部分运行所消耗的时间。

瓶颈测试：https://pytorch.org/docs/stable/bottleneck.html

可以使用PyTorch中bottleneck工具，具体使用方法如下：

python -m torch.utils.bottleneck /path/to/source/script.py [args]

详细内容可以看上面给出的链接。

当然，也可用cProfile这样的工具来测试瓶颈所在,先运行以下命令。

python -m cProfile -o 100_percent_gpu_utilization.prof train.py

这样就得到了文件100_percent_gpu_utilization.prof

对其进行可视化（用到了snakeviz包，pip install snakeviz即可）

snakeviz 100_percent_gpu_utilization.prof

可视化的结果如下图所示：

其他方法：

# Profile CPU bottlenecks
python -m cProfile training_script.py --profiling
# Profile GPU bottlenecks
nvprof --print-gpu-trace python train_mnist.py
# Profile system calls bottlenecks
strace -fcT python training_script.py -e trace=open,close,read

还可以用以下代码分析：

def test_loss_profiling():
    loss = nn.BCEWithLogitsLoss()
    with torch.autograd.profiler.profile(use_cuda=True) as prof:
        input = torch.randn((8, 1, 128, 128)).cuda()
        input.requires_grad = True

        target = torch.randint(1, (8, 1, 128, 128)).cuda().float()

        for i in range(10):
            l = loss(input, target)
            l.backward()
    print(prof.key_averages().table(sort_by="self_cpu_time_total"))

3. 图片解码

PyTorch中默认使用的是Pillow进行图像的解码，但是其效率要比Opencv差一些，如果图片全部是JPEG格式，可以考虑使用TurboJpeg库解码。具体速度对比如下图所示：

对于jpeg读取也可以考虑使用jpeg4py库（pip install jpeg4py）,重写一个loader即可。

存bmp图也可以降低解码耗时，其他方案还有recordIO,hdf5,pth,n5,lmdb等格式

4. 数据增强加速

在PyTorch中，通常使用transformer做图片分类任务的数据增强，而其调用的是CPU做一些Crop、Flip、Jitter等操作。

如果你通过观察发现你的CPU利用率非常高，GPU利用率比较低，那说明瓶颈在于CPU预处理，可以使用Nvidia提供的DALI库在GPU端完成这部分数据增强操作。

Dali链接：https://github.com/NVIDIA/DALI

文档也非常详细：

Dali文档：https://docs.nvidia.com/deeplearning/sdk/dali-developer-guide/index.html

当然，Dali提供的操作比较有限，仅仅实现了常用的方法，有些新的方法比如cutout需要自己搞。

具体实现可以参考这一篇：https://zhuanlan.zhihu.com/p/77633542

5. data Prefetch

Nvidia Apex中提供的解决方案

　参考来源：https://zhuanlan.zhihu.com/p/66145913

Apex提供的策略就是预读取下一次迭代需要的数据。

class data_prefetcher():
    def __init__(self, loader):
        self.loader = iter(loader)
        self.stream = torch.cuda.Stream()
        self.mean = torch.tensor([0.485 * 255, 0.456 * 255, 0.406 * 255]).cuda().view(1,3,1,1)
        self.std = torch.tensor([0.229 * 255, 0.224 * 255, 0.225 * 255]).cuda().view(1,3,1,1)
        # With Amp, it isn't necessary to manually convert data to half.
        # if args.fp16:
        #     self.mean = self.mean.half()
        #     self.std = self.std.half()
        self.preload()

    def preload(self):
        try:
            self.next_input, self.next_target = next(self.loader)
        except StopIteration:
            self.next_input = None
            self.next_target = None
            return
        with torch.cuda.stream(self.stream):
            self.next_input = self.next_input.cuda(non_blocking=True)
            self.next_target = self.next_target.cuda(non_blocking=True)
            # With Amp, it isn't necessary to manually convert data to half.
            # if args.fp16:
            #     self.next_input = self.next_input.half()
            # else:
            self.next_input = self.next_input.float()
            self.next_input = self.next_input.sub_(self.mean).div_(self.std)

在训练函数中进行如下修改：

原先是：

training_data_loader = DataLoader(
    dataset=train_dataset,
    num_workers=opts.threads,
    batch_size=opts.batchSize,
    pin_memory=True,
    shuffle=True,
)
for iteration, batch in enumerate(training_data_loader, 1):
    # 训练代码

修改以后：

data, label = prefetcher.next()
iteration = 0
while data is not None:
    iteration += 1
    # 训练代码
    data, label = prefetcher.next()

用prefetch库实现

https://zhuanlan.zhihu.com/p/97190313

安装：

pip install prefetch_generator

使用：

from torch.utils.data import DataLoader
from prefetch_generator import BackgroundGenerator

class DataLoaderX(DataLoader):

    def __iter__(self):
        return BackgroundGenerator(super().__iter__())

然后用DataLoaderX替换原本的DataLoader

cuda.Steam加速拷贝过程

https://zhuanlan.zhihu.com/p/97190313

实现：

class DataPrefetcher():
    def __init__(self, loader, opt):
        self.loader = iter(loader)
        self.opt = opt
        self.stream = torch.cuda.Stream()
        # With Amp, it isn't necessary to manually convert data to half.
        # if args.fp16:
        #     self.mean = self.mean.half()
        #     self.std = self.std.half()
        self.preload()

    def preload(self):
        try:
            self.batch = next(self.loader)
        except StopIteration:
            self.batch = None
            return
        with torch.cuda.stream(self.stream):
            for k in self.batch:
                if k != 'meta':
                    self.batch[k] = self.batch[k].to(device=self.opt.device, non_blocking=True)

            # With Amp, it isn't necessary to manually convert data to half.
            # if args.fp16:
            #     self.next_input = self.next_input.half()
            # else:
            #     self.next_input = self.next_input.float()

    def next(self):
        torch.cuda.current_stream().wait_stream(self.stream)
        batch = self.batch
        self.preload()
        return batch

调用：

# ----改造前----
for iter_id, batch in enumerate(data_loader):
    if iter_id >= num_iters:
        break
    for k in batch:
        if k != 'meta':
            batch[k] = batch[k].to(device=opt.device, non_blocking=True)
    run_step()
    
# ----改造后----
prefetcher = DataPrefetcher(data_loader, opt)
batch = prefetcher.next()
iter_id = 0
while batch is not None:
    iter_id += 1
    if iter_id >= num_iters:
        break
    run_step()
    batch = prefetcher.next()

国外大佬实现

数据加载部分

import threading
import numpy as np
import cv2
import random 

class threadsafe_iter:
  """Takes an iterator/generator and makes it thread-safe by
  serializing call to the `next` method of given iterator/generator.
  """
  def __init__(self, it):
    self.it = it
    self.lock = threading.Lock()

  def __iter__(self):
    return self

  def next(self):
    with self.lock:
      return self.it.next()

def get_path_i(paths_count):
  """Cyclic generator of paths indice
  """
  current_path_id = 0
  while True:
    yield current_path_id
    current_path_id    = (current_path_id + 1) % paths_count

class InputGen:
  def __init__(self, paths, batch_size):
    self.paths = paths
    self.index = 0
    self.batch_size = batch_size
    self.init_count = 0
    self.lock = threading.Lock() #mutex for input path
    self.yield_lock = threading.Lock() #mutex for generator yielding of batch
    self.path_id_generator = threadsafe_iter(get_path_i(len(self.paths))) 
    self.images = []
    self.labels = []
    
  def get_samples_count(self):
    """ Returns the total number of images needed to train an epoch """
    return len(self.paths)

  def get_batches_count(self):
    """ Returns the total number of batches needed to train an epoch """
    return int(self.get_samples_count() / self.batch_size)

  def pre_process_input(self, im,lb):
    """ Do your pre-processing here
                Need to be thread-safe function"""
    return im, lb

  def next(self):
    return self.__iter__()

  def __iter__(self):
    while True:
      #In the start of each epoch we shuffle the data paths            
      with self.lock: 
        if (self.init_count == 0):
          random.shuffle(self.paths)
          self.images, self.labels, self.batch_paths = [], [], []
          self.init_count = 1
      #Iterates through the input paths in a thread-safe manner
      for path_id in self.path_id_generator: 
        img, label = self.paths[path_id]
        img = cv2.imread(img, 1)
        label_img = cv2.imread(label,1)
        img, label = self.pre_process_input(img,label_img)
        #Concurrent access by multiple threads to the lists below
        with self.yield_lock: 
          if (len(self.images)) < self.batch_size:
            self.images.append(img)
            self.labels.append(label)
          if len(self.images) % self.batch_size == 0:                    
            yield np.float32(self.images), np.float32(self.labels)
            self.images, self.labels = [], []
      #At the end of an epoch we re-init data-structures
      with self.lock: 
        self.init_count = 0
  def __call__(self):
    return self.__iter__()

使用方法：

class thread_killer(object):
  """Boolean object for signaling a worker thread to terminate
  """
  def __init__(self):
    self.to_kill = False
  
  def __call__(self):
    return self.to_kill
  
  def set_tokill(self,tokill):
    self.to_kill = tokill
  
def threaded_batches_feeder(tokill, batches_queue, dataset_generator):
  """Threaded worker for pre-processing input data.
  tokill is a thread_killer object that indicates whether a thread should be terminated
  dataset_generator is the training/validation dataset generator
  batches_queue is a limited size thread-safe Queue instance.
  """
  while tokill() == False:
    for batch, (batch_images, batch_labels) \
      in enumerate(dataset_generator):
        #We fill the queue with new fetched batch until we reach the max       size.
        batches_queue.put((batch, (batch_images, batch_labels))\
                , block=True)
        if tokill() == True:
          return

def threaded_cuda_batches(tokill,cuda_batches_queue,batches_queue):
  """Thread worker for transferring pytorch tensors into
  GPU. batches_queue is the queue that fetches numpy cpu tensors.
  cuda_batches_queue receives numpy cpu tensors and transfers them to GPU space.
  """
  while tokill() == False:
    batch, (batch_images, batch_labels) = batches_queue.get(block=True)
    batch_images_np = np.transpose(batch_images, (0, 3, 1, 2))
    batch_images = torch.from_numpy(batch_images_np)
    batch_labels = torch.from_numpy(batch_labels)

    batch_images = Variable(batch_images).cuda()
    batch_labels = Variable(batch_labels).cuda()
    cuda_batches_queue.put((batch, (batch_images, batch_labels)), block=True)
    if tokill() == True:
      return

if __name__ =='__main__':
  import time
  import Thread
  import sys
  from Queue import Empty,Full,Queue
  
  num_epoches=1000
  #model is some Pytorch CNN model
  model.cuda()
  model.train()
  batches_per_epoch = 64
  #Training set list suppose to be a list of full-paths for all
  #the training images.
  training_set_list = None
  #Our train batches queue can hold at max 12 batches at any given time.
  #Once the queue is filled the queue is locked.
  train_batches_queue = Queue(maxsize=12)
  #Our numpy batches cuda transferer queue.
  #Once the queue is filled the queue is locked
  #We set maxsize to 3 due to GPU memory size limitations
  cuda_batches_queue = Queue(maxsize=3)


  training_set_generator = InputGen(training_set_list,batches_per_epoch)
  train_thread_killer = thread_killer()
  train_thread_killer.set_tokill(False)
  preprocess_workers = 4


  #We launch 4 threads to do load && pre-process the input images
  for _ in range(preprocess_workers):
    t = Thread(target=threaded_batches_feeder, \
           args=(train_thread_killer, train_batches_queue, training_set_generator))
    t.start()
  cuda_transfers_thread_killer = thread_killer()
  cuda_transfers_thread_killer.set_tokill(False)
  cudathread = Thread(target=threaded_cuda_batches, \
           args=(cuda_transfers_thread_killer, cuda_batches_queue, train_batches_queue))
  cudathread.start()

  
  #We let queue to get filled before we start the training
  time.sleep(8)
  for epoch in range(num_epoches):
    for batch in range(batches_per_epoch):
      
      #We fetch a GPU batch in 0's due to the queue mechanism
      _, (batch_images, batch_labels) = cuda_batches_queue.get(block=True)
            
      #train batch is the method for your training step.
      #no need to pin_memory due to diminished cuda transfers using queues.
      loss, accuracy = train_batch(batch_images, batch_labels)

  train_thread_killer.set_tokill(True)
  cuda_transfers_thread_killer.set_tokill(True)    
  for _ in range(preprocess_workers):
    try:
      #Enforcing thread shutdown
      train_batches_queue.get(block=True,timeout=1)
                  cuda_batches_queue.get(block=True,timeout=1)    
    except Empty:
      pass
  print "Training done"

6. 多GPU并行处理

PyTorch中提供了分布式训练API, nn.DistributedDataParallel, 推理的时候也可以使用nn.DataParallel或者nn.DistributedDataParallel。

推荐一个库，里面实现了多种分布式训练的demo: https://github.com/tczhangzhi/pytorch-distributed 其中包括：

nn.DataParallel
torch.distributed
torch.multiprocessing
apex再加速
horovod实现
slurm GPU集群分布式

7. 混合精度训练

mixed precision yyds，之前分享过mixed precision论文阅读，实现起来非常简单。在PyTorch中，可以使用Apex库。如果用的是最新版本的PyTorch，其自身已经支持了混合精度训练，非常nice。

简单来说，混合精度能够让你在精度不掉的情况下，batch提升一倍。其原理就是将原先float point32精度的数据变为float point16的数据，不管是数据传输还是训练过程，都极大提升了训练速度，炼丹必备。

8. 其他细节

batch_images = batch_images.pin_memory() 
Batch_labels = Variable(batch_labels).cuda(non_blocking=True)

PyTorch的DataLoader有一个参数pin_memory，使用固定内存，并使用non_blocking=True来并行处理数据传输。
torch.backends.cudnn.benchmark=True
及时释放掉不需要的显存、内存。
如果数据集比较小，直接将数据复制到内存中，从内存中读取可以极大加快数据读取的速度。
调整workers数量，过少的线程读取数据会导致速度非常慢，过多线程读取数据可能会由于阻塞也导致速度非常慢。所以需要根据自己机器的情况，尝试不同数量的workers，选择最合适的数量。一般设置为 cpu 核心数或gpu数量
编码的时候要注意尽可能减少CPU和GPU之间的数据传输，使用类似numpy的编码方式，通过并行的方式来处理，可以提高性能。
使用TFRecord或者LMDB等，减少小文件的读写