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SC20 Deep Learning at Scale Tutorial

This repository contains the example code material for the SC20 tutorial: Deep Learning at Scale.

The example demonstrates synchronous data-parallel distributed training of a convolutional deep neural network implemented in PyTorch on a standard computer vision problem. In particular, we are training ResNet50 on the CIFAR-100 dataset to classify images into 100 classes.

Contents

Links

Presentation slides for the tutorial can be found at: https://drive.google.com/drive/folders/1-gi1WvfQ6alDOnMwN3JqgNlrQh7MlIQr?usp=sharing

We have a nersc-dl-tutorial slack you can join. Use this link and join the #sc20-dl-tutorial channel: https://join.slack.com/t/nersc-dl-tutorial/shared_invite/zt-iwyrkhza-h_Oun~8JO9xDKZynD5hERA

Installation

If you're running these examples on the Cori GPU system at NERSC, no installation is needed; you can simply use our provided modules or shifter containers.

See the submit.slr slurm script for a simple example using our PyTorch 1.7.0 installation for GPU.

Otherwise, our package dependencies:

  • pytorch 1.7.0
  • torchvision
  • apex
  • ruamel.yaml
  • nccl

Model, data, and training code overview

The network architecture for our ResNet50 model can be found in models/resnet.py. Here we have copied the ResNet50 implementation from torchvision and made a few minor adjustments for the CIFAR dataset (e.g. reducing stride and pooling).

The data pipeline code can be found in utils/cifar100_data_loader.py. Note that the dataset code for this example is fairly simple because the torchvision package provides the dataset class which handles the image loading for us. Key ingredients:

  • We compose a sequence of data transforms for normalization and random augmentation of the images.
  • We construct a datasets.CIFAR100 dataset which will automatically download the dataset to a specified directory. We pass it our list of transforms.
  • We construct a DataLoader which orchestrates the random sampling and batching of our images.

The basic training logic can be found in train_simple.py. In this training script we have defined a simple Trainer class which implements methods for training and validation epochs. Key ingredients:

  • In the Trainer's __init__ method, we get the data loaders, construct our ResNet50 model, the SGD optimizer, and our CrossEntropyLoss objective function.
  • In the Trainer's train_one_epoch method, we implement the actual logic for training the model on batches of data.
    • Identify where we loop over data batches from our data loader.
    • Identify where we apply the forward pass of the model ("Model forward pass") and compute the loss function.
    • Identify where we call backward() on the loss value. Note the use of the grad_scaler will be explained below when enabling mixed precision.
  • Similarly, in the Trainer's validate_one_epoch, we implement the simpler logic of applying the model to a validation dataset and compute metrics like accuracy.
  • Checkpoint saving and loading are implemented in the Trainer's save_checkpoint and restore_checkpoint methods, respectively.
  • We construct and use a TensorBoard SummaryWriter for logging metrics to visualize in TensorBoard. See if you can find where our specific metrics are logged via the add_scalar call.

Besides the train_simple.py script, we have a more complex train.py script which implements the same functionality but also includes a lot of additional optimizations which will be covered in the Performance profiling and optimization section below.

Single GPU training

To run single GPU training of the baseline training script, use the following command:

$ python train.py --config=bs128

This will run the training on a single GPU using batch size of 128 (see config/cifar100.yaml for specific configuration details). Note we will use batch size 256 for the optimization work in the next section and will push beyond to larger batch sizes in the distributed training section.

In the baseline configuration, the model converges to about 75% accuracy on the validation dataset in about 80 epochs:

bs128 learning curves

Performance profiling and optimization

This is the performance of the baseline script using the NGC PyTorch 20.10 container for the first two epochs on a 16GB V100 card with batch size 256:

INFO - Starting Training Loop...
INFO - Epoch: 1, Iteration: 0, Avg img/sec: 110.19908073510402
INFO - Epoch: 1, Iteration: 20, Avg img/sec: 680.8613838734273
INFO - Epoch: 1, Iteration: 40, Avg img/sec: 682.4229819820212
INFO - Epoch: 1, Iteration: 60, Avg img/sec: 683.0516710020236
INFO - Epoch: 1, Iteration: 80, Avg img/sec: 681.2955112832597
INFO - Epoch: 1, Iteration: 100, Avg img/sec: 681.7366420029032
INFO - Epoch: 1, Iteration: 120, Avg img/sec: 680.9312458089512
INFO - Epoch: 1, Iteration: 140, Avg img/sec: 680.2227561980723
INFO - Epoch: 1, Iteration: 160, Avg img/sec: 680.6287580660272
INFO - Epoch: 1, Iteration: 180, Avg img/sec: 680.7244649829499
INFO - Time taken for epoch 1 is 79.90803146362305 sec
INFO - Epoch: 2, Iteration: 0, Avg img/sec: 297.1326786725325
INFO - Epoch: 2, Iteration: 20, Avg img/sec: 680.1821654149742
INFO - Epoch: 2, Iteration: 40, Avg img/sec: 679.7391921357676
INFO - Epoch: 2, Iteration: 60, Avg img/sec: 680.29168975637
INFO - Epoch: 2, Iteration: 80, Avg img/sec: 680.2163354650426
INFO - Epoch: 2, Iteration: 100, Avg img/sec: 680.1871635938127
INFO - Epoch: 2, Iteration: 120, Avg img/sec: 679.7543395008651
INFO - Epoch: 2, Iteration: 140, Avg img/sec: 679.708426128615
INFO - Epoch: 2, Iteration: 160, Avg img/sec: 679.2982136487756
INFO - Epoch: 2, Iteration: 180, Avg img/sec: 679.0788730107779
INFO - Time taken for epoch 2 is 78.5151789188385 sec

Profiling with Nsight Systems

Before generating a profile with Nsight, we can add NVTX ranges to the script to add context to the produced timeline. First, we can enable PyTorch's built-in NVTX annotations by using the torch.autograd.profiler.emit_nvtx context manager. We can also manually add some manually defined NVTX ranges to the code using torch.cuda.nvtx.range_push and torch.cuda.nvtx.range_pop. Search train.py for comments labeled # PROF to see where we've added code. As a quick note, we defined some simple functions to wrap the NVTX range calls in order to add synchronization:

def nvtx_range_push(name, enabled):
  if enabled:
    torch.cuda.synchronize()
    torch.cuda.nvtx.range_push(name)

def nvtx_range_pop(enabled):
  if enabled:
    torch.cuda.synchronize()
    torch.cuda.nvtx.range_pop()

As GPU operations can be asynchronous with respect to the Python thread, these syncs are necessary to create accurate ranges. Without them, the ranges will only contain the time to launch the GPU work.

To generate a timeline, run the following:

$ NSYS_NVTX_PROFILER_REGISTER_ONLY=0 nsys profile -o baseline --trace=cuda,nvtx --capture-range=nvtx --nvtx-capture=PROFILE python -m torch.distributed.launch --nproc_per_node=1 train.py --config=bs256-prof

This command will run two shortened epochs of 80 iterations of the training script and produce a file baseline.qdrep that can be opened in the Nsight System's program. The arg --trace=cuda,nvtx is optional and is used here to disable OS Runtime tracing for speed. The args --capture-range=nvtx --nvtx-capture=PROFILE and variable NSYS_NVTX_PROFILER_REGISTER_ONLY=0 will limit the profiling to the NVTX range named "PROFILE", which we've used to limit profiling to the second epoch only.

Loading this profile in Nsight Systems will look like this: Baseline

With our NVTX ranges, we can easily zoom into a single iteration and get an idea of where compute time is being spent: Baseline Zoomed

Enabling Mixed Precision Training

As a first step to improve the compute performance of this training script, we can enable automatic mixed precision (AMP) in PyTorch. AMP provides a simple way for users to convert existing FP32 training scripts to mixed FP32/FP16 precision, unlocking faster computation with Tensor Cores on NVIDIA GPUs. The AMP module in torch is composed of two main parts: torch.cuda.amp.GradScaler and torch.cuda.amp.autocast. torch.cuda.amp.GradScaler handles automatic loss scaling to control the range of FP16 gradients. The torch.cuda.amp.autocast context manager handles converting model operations to FP16 where appropriate. Search train.py for comments labeled # AMP: to see where we've added code to enable AMP in this script.

To run the script on a single GPU with AMP enabled, use the following command:

$ python -m torch.distributed.launch --nproc_per_node=1 train.py --config=bs256-amp

With AMP enabled, this is the performance of the baseline using the NGC PyTorch 20.10 container for the first two epochs on a 16GB V100 card:

INFO - Starting Training Loop...
INFO - Epoch: 1, Iteration: 0, Avg img/sec: 131.4890829860097
INFO - Epoch: 1, Iteration: 20, Avg img/sec: 1925.8088037080554
INFO - Epoch: 1, Iteration: 40, Avg img/sec: 1884.341731901802
INFO - Epoch: 1, Iteration: 60, Avg img/sec: 1796.3608488557659
INFO - Epoch: 1, Iteration: 80, Avg img/sec: 1797.1991164491794
INFO - Epoch: 1, Iteration: 100, Avg img/sec: 1794.721454602102
INFO - Epoch: 1, Iteration: 120, Avg img/sec: 1800.0616660977953
INFO - Epoch: 1, Iteration: 140, Avg img/sec: 1794.3491050370249
INFO - Epoch: 1, Iteration: 160, Avg img/sec: 1797.8587343614402
INFO - Epoch: 1, Iteration: 180, Avg img/sec: 1794.0956118635277
INFO - Time taken for epoch 1 is 33.888301610946655 sec
INFO - Epoch: 2, Iteration: 0, Avg img/sec: 397.0763949367613
INFO - Epoch: 2, Iteration: 20, Avg img/sec: 1831.3360728112361
INFO - Epoch: 2, Iteration: 40, Avg img/sec: 1804.6830246566537
INFO - Epoch: 2, Iteration: 60, Avg img/sec: 1799.7809136620713
INFO - Epoch: 2, Iteration: 80, Avg img/sec: 1793.427968035233
INFO - Epoch: 2, Iteration: 100, Avg img/sec: 1794.953670200433
INFO - Epoch: 2, Iteration: 120, Avg img/sec: 1795.3373776036665
INFO - Epoch: 2, Iteration: 140, Avg img/sec: 1791.194021111478
INFO - Epoch: 2, Iteration: 160, Avg img/sec: 1825.7166134675574
INFO - Epoch: 2, Iteration: 180, Avg img/sec: 1794.5686271249087
INFO - Time taken for epoch 2 is 33.07876420021057 sec

You can run another profile (using --config=bs256-amp-prof) with Nsight Systems. Loading this profile and zooming into a single iteration, this is what we see: AMP Zoomed

With AMP enabled, we see that the forward/loss/backward time is significatly reduced. As this is a CNN, the forward and backward convolution ops are well-suited to benefit from acceleration with tensor cores.

If we zoom into the forward section of the profile to the GPU kernels, we can see very many calls to nchwToNhwc and nhwcToNCHW kernels: AMP Zoomed Kernels

These kernels are transposing the data from PyTorch's native data layout (NCHW or channels first) to the NHWC (or channels last) format which cuDNN requires to use tensor cores. Luckily, there is a way to avoid these transposes by using the torch.channels_last memory format. To use this, we need to convert both the model and the input image tensors to this format by using the following lines:

model = model.to(memory_format=torch.channels_last)
images = images.to(memory_format=torch.channels_last)

Search train.py for comments labeled # NHWC to see where we've added these lines to run the model using NHWC format.

To run the script on a single GPU with AMP enabled using the NHWC memory format, use the following command:

$ python -m torch.distributed.launch --nproc_per_node=1 train.py --config=bs256-amp-nhwc

With AMP enabled using the NHWC memory format, this is the performance of the script using the NGC PyTorch 20.10 container for the first two epochs on a 16GB V100 card:

INFO - Starting Training Loop...
INFO - Epoch: 1, Iteration: 0, Avg img/sec: 125.35020387731124
INFO - Epoch: 1, Iteration: 20, Avg img/sec: 2089.3251919566933
INFO - Epoch: 1, Iteration: 40, Avg img/sec: 2075.2397782670346
INFO - Epoch: 1, Iteration: 60, Avg img/sec: 2078.1579609491064
INFO - Epoch: 1, Iteration: 80, Avg img/sec: 2114.314909986603
INFO - Epoch: 1, Iteration: 100, Avg img/sec: 2076.3754707171784
INFO - Epoch: 1, Iteration: 120, Avg img/sec: 2066.673609844659
INFO - Epoch: 1, Iteration: 140, Avg img/sec: 2070.3321011509784
INFO - Epoch: 1, Iteration: 160, Avg img/sec: 2107.977617868012
INFO - Epoch: 1, Iteration: 180, Avg img/sec: 2117.288989717637
INFO - Time taken for epoch 1 is 30.756738424301147 sec
INFO - Epoch: 2, Iteration: 0, Avg img/sec: 464.2617647745541
INFO - Epoch: 2, Iteration: 20, Avg img/sec: 2151.947432559358
INFO - Epoch: 2, Iteration: 40, Avg img/sec: 2208.417190923362
INFO - Epoch: 2, Iteration: 60, Avg img/sec: 2177.7232959147427
INFO - Epoch: 2, Iteration: 80, Avg img/sec: 2226.609558578422
INFO - Epoch: 2, Iteration: 100, Avg img/sec: 2253.0767957237485
INFO - Epoch: 2, Iteration: 120, Avg img/sec: 2137.2692109868517
INFO - Epoch: 2, Iteration: 140, Avg img/sec: 2214.0994804791235
INFO - Epoch: 2, Iteration: 160, Avg img/sec: 2195.9345278285564
INFO - Epoch: 2, Iteration: 180, Avg img/sec: 2162.628100059094
INFO - Time taken for epoch 2 is 28.39500093460083 sec

With the NCHW/NHWC tranposes removed, we see another modest gain in throughput. You can run another profile (using --config=bs256-amp-nhwc-prof) with Nsight Systems. Loading this profile and zooming into a single iteration, this is what we see now: AMP NHWC Zoomed

Using the NHWC memory format with AMP, we see that the forward/loss/backward times are reduced further due to no longer calling the transpose kernels. Now we can move onto some other small PyTorch-specific optimizations to deal with the remaining sections that stand out in the profile.

Applying additional PyTorch optimizations

With the forward and backward pass accelerated with AMP and NHWC memory layout, the remaining NVTX ranges we added to the profile stand out, namely the zero_grad marker and optimizer.step.

To speed up the zero_grad, we can add the following argument to the zero_grad call:

self.model.zero_grad(set_to_none=True)

This optional argument allows PyTorch to skip memset operations to zero out gradients and also allows PyTorch to set gradients with a single write (= operator) instead of a read/write (+= operator).

If we look closely at the optimizer.step range in the profile, we see that there are many indivdual pointwise operation kernels launched. To make this more efficient, we can replace the native PyTorch SGD optimizer with the FusedSGD optimizer from the Apex package, which fuses many of these pointwise operations.

Finally, as a general optimization, we add the line torch.backends.cudnn.benchmark = True to the start of training to enable cuDNN autotuning. This will allow cuDNN to test and select algorithms that run fastest on your system/model.

Search train.py for comments labeled # EXTRA to see where we've added changes for these additional optimizations.

To run the script on a single GPU with AMP enabled, NHWC memory format and these additional optimizations, use the following command:

$ python -m torch.distributed.launch --nproc_per_node=1 train.py --config=bs256-amp-nhwc-extra-opts

With all these features enabled, this is the performance of the script using the NGC PyTorch 20.10 container for the first two epochs on a 16GB V100 card:

INFO - Starting Training Loop...
INFO - Epoch: 1, Iteration: 0, Avg img/sec: 51.52879474970972
INFO - Epoch: 1, Iteration: 20, Avg img/sec: 2428.815812361664
INFO - Epoch: 1, Iteration: 40, Avg img/sec: 2471.928460752096
INFO - Epoch: 1, Iteration: 60, Avg img/sec: 2461.6635515925623
INFO - Epoch: 1, Iteration: 80, Avg img/sec: 2461.5230335547976
INFO - Epoch: 1, Iteration: 100, Avg img/sec: 2470.371590429863
INFO - Epoch: 1, Iteration: 120, Avg img/sec: 2462.8998420750218
INFO - Epoch: 1, Iteration: 140, Avg img/sec: 2567.007655538539
INFO - Epoch: 1, Iteration: 160, Avg img/sec: 2531.0173058079126
INFO - Epoch: 1, Iteration: 180, Avg img/sec: 2577.144387068793
INFO - Time taken for epoch 1 is 30.52899408340454 sec
INFO - Epoch: 2, Iteration: 0, Avg img/sec: 410.57308753695185
INFO - Epoch: 2, Iteration: 20, Avg img/sec: 2547.8182536936824
INFO - Epoch: 2, Iteration: 40, Avg img/sec: 2519.104752035505
INFO - Epoch: 2, Iteration: 60, Avg img/sec: 2529.822264348943
INFO - Epoch: 2, Iteration: 80, Avg img/sec: 2539.450348785371
INFO - Epoch: 2, Iteration: 100, Avg img/sec: 2533.167522740291
INFO - Epoch: 2, Iteration: 120, Avg img/sec: 2542.63597641221
INFO - Epoch: 2, Iteration: 140, Avg img/sec: 2502.990963521907
INFO - Epoch: 2, Iteration: 160, Avg img/sec: 2525.3185224087124
INFO - Epoch: 2, Iteration: 180, Avg img/sec: 2501.353650885946
INFO - Time taken for epoch 2 is 25.808385372161865 sec

We can run a final profile with all the optimizations enabled (using --config=bs256-amp-nhwc-extra-opts-prof) with Nsight Systems. Loading this profile and zooming into a single iteration, this is what we see now: AMP NHWC Extra Zoomed With these additional optimizations enabled in PyTorch, we see the length of the zero_grad and optimizer.step ranges are greatly reduced, as well as a small improvement in the forward/loss/backward time.

Distributed GPU training

Now that we have model training code that is optimized for training on a single GPU, we are ready to utilize multiple GPUs and multiple nodes to accelerate the workflow with distributed training. We will use the recommended DistributedDataParallel wrapper in PyTorch with the NCCL backend for optimized communication operations on systems with NVIDIA GPUs. Refer to the PyTorch documentation for additional details on the distributed package: https://pytorch.org/docs/stable/distributed.html

Code basics

We use the torch.distributed.launch utility for launching training processes on one node, one per GPU. The submit_multinode.slr script shows how we use the utility with SLURM to launch the tasks on each node in our system allocation.

In the train.py script, near the bottom in the main script execution, we set up the distributed backend. We use the environment variable initialization method, automatically configured for us when we use the torch.distributed.launch utility.

In the get_data_loader function in utils/cifar100_data_loader.py, we use the DistributedSampler from PyTorch which takes care of partitioning the dataset so that each training process sees a unique subset.

In our Trainer's __init__ method, after our ResNet50 model is constructed, we convert it to a distributed data parallel model by wrapping it as:

self.model = DistributedDataParallel(self.model, ...)

The DistributedDataParallel (DDP) model wrapper takes care of broadcasting initial model weights to all workers and performing all-reduce on the gradients in the training backward pass to properly synchronize and update the model weights in the distributed setting.

Large batch convergence

To speed up training, we try to use larger batch sizes, spread across more GPUs, with larger learning rates. In particular, we try increasing from 1 to 8 then 16 gpus, and scale the batch size similarly to 1024 and 2048. The first thing we demonstrate here is increasing the learning rate according to the square-root scaling rule. The settings for batch size 512, 1024, and 2048 are in config/cifar100.yaml under bs512-opt, bs1024-opt, and bs2048-opt, respectively. We view the accuracy plots in TensorBoard and notice that the convergence performs worse with larger batch size, i.e. we see a generalization gap:

Accuracy for bs128, bs1024, bs2048

Next, as suggested in the presentation previously, we apply a linear learning rate warmup for these batch sizes. You can see where we compute the learning rate in the warmup phase in our Trainer's train method in the train.py script. Look for the comment, "Apply learning rate warmup". As shown in configs bs1024-warmup-opt and bs2048-warmup-opt in our config/cifar100.yaml file, we use 8 and 16 epochs for the warmup, respectively.

Now we can see the generalization gap closes and the higher batch size results are as good as the original batch size 128:

Accuracy for bs128, bs1024 warmup, bs2048 warmup

Next, we can now look at the wallclock time to see that, indeed, using these tricks together result in a much faster convergence:

Accuracy vs time for bs128, bs1024 warmup, bs2048 warmup

In particular, our batch size 128 run on 1 gpu takes about 32 min to converge, while our batch size 2048 run on 16 gpus takes around 4 min.

Finally, we look at the throughput (images/second) of our training runs as we do this weak scaling of the batch size and GPUs:

Weak scaling training throughput

These plots show 81% scaling efficiency with respect to ideal scaling at 16 GPUs.