Lightning-Hydra-Template

A clean and scalable template to kickstart your deep learning project 🚀⚡🔥
Click on Use this template to initialize new repository.

This template is work in progress. Suggestions are always welcome!

If you use this template please add

to your README.md.

Contents

Introduction
Main Ideas Of This Template
Project Structure
Quickstart
Guide
Best Practices
Tricks
Other Repositories

Introduction

This template tries to be as general as possible - you can easily delete any unwanted features from the pipeline or rewire the configuration, by modifying behavior in src/train.py.

Effective usage of this template requires learning of a couple of technologies: PyTorch, PyTorch Lightning and Hydra. Knowledge of some experiment logging framework like Weights&Biases, Neptune or MLFlow is also recommended.

Why you should use it: it allows you to rapidly iterate over new models and scale your projects from small single experiments to large hyperparameter searches on computing clusters, without writing any boilerplate code. To my knowledge, it's one of the most, if not the most convenient all-in-one technology stack for Deep Learning research. It's also a collection of best practices for efficient workflow and reproducibility.

Why you shouldn't use it: Lightning and Hydra are not yet mature, which means you might run into some bugs sooner or later. Also, even though Lightning is very flexible, it's not well suited for every possible deep learning task.

Why PyTorch Lightning?

PyTorch Lightning is a lightweight PyTorch wrapper for high-performance AI research. It makes your code neatly organized and provides lots of useful features, like ability to run model on CPU, GPU, multi-GPU cluster and TPU.

Why Hydra?

Hydra is an open-source Python framework that simplifies the development of research and other complex applications. The key feature is the ability to dynamically create a hierarchical configuration by composition and override it through config files and the command line. It allows you to conveniently manage experiments and provides many useful plugins, like Optuna Sweeper for hyperparameter search, or Ray Launcher for running jobs on a cluster.

Main Ideas Of This Template

Predefined Structure: clean and scalable so that work can easily be extended and replicated (see #Project Structure)
Rapid Experimentation: thanks to automating pipeline with config files and hydra command line superpowers
Little Boilerplate: so pipeline can be easily modified (see src/train.py)
Main Configuration: main config file specifies default training configuration (see #Main Project Configuration)
Experiment Configurations: stored in a separate folder, they can be composed out of smaller configs, override chosen parameters or define everything from scratch (see #Experiment Configuration)
Experiment Tracking: many logging frameworks can be easily integrated! (see #Experiment Tracking)
Logs: all logs (checkpoints, data from loggers, chosen hparams, etc.) are stored in a convenient folder structure imposed by Hydra (see #Logs)
Hyperparameter Search: made easier with Hydra built in plugins like Optuna Sweeper
Best Practices: a couple of recommended tools, practices and standards (see #Best Practices)
Workflow: comes down to 4 simple steps (see #Workflow)

Project Structure

The directory structure of new project looks like this:

├── configs                 <- Hydra configuration files
│   ├── model                   <- Configurations of Lightning models
│   ├── datamodule              <- Configurations of Lightning datamodules
│   ├── callbacks               <- Configurations of Lightning callbacks
│   ├── logger                  <- Configurations of Lightning loggers
│   ├── trainer                 <- Configurations of Lightning trainers
│   ├── optimizer               <- Configurations of optimizers
│   ├── experiment              <- Configurations of experiments
│   │
│   ├── config.yaml             <- Main project configuration file
│   └── config_optuna.yaml      <- Configuration of Optuna hyperparameter search
│
├── data                    <- Project data
│
├── logs                    <- Logs generated by Hydra and PyTorch Lightning loggers
│
├── notebooks               <- Jupyter notebooks
│
├── tests                   <- Tests of any kind
│
├── src
│   ├── architectures           <- PyTorch model architectures
│   ├── datasets                <- PyTorch datasets
│   ├── pl_callbacks            <- PyTorch Lightning callbacks
│   ├── pl_datamodules          <- PyTorch Lightning datamodules
│   ├── pl_models               <- PyTorch Lightning models
│   ├── utils                   <- Utility scripts
│   │   ├── inference_example.py    <- Example of inference with trained model
│   │   └── template_utils.py       <- Some extra template utilities
│   │
│   └── train.py                <- Contains training pipeline
│
├── run.py                  <- Run training with chosen experiment configuration
│
├── .env                    <- File for storing environment variables
├── .gitignore              <- List of files/folders ignored by git
├── .pre-commit-config.yaml <- Configuration of hooks for automatic code formatting
├── conda_env_gpu.yaml      <- File for installing conda environment
├── requirements.txt        <- File for installing python dependencies
├── LICENSE
└── README.md

Quickstart

# clone project
git clone https://github.com/hobogalaxy/lightning-hydra-template
cd lightning-hydra-template

# [OPTIONAL] create conda environment
conda env create -f conda_env_gpu.yaml -n testenv
conda activate testenv

# install requirements
pip install -r requirements.txt

Template contains example with MNIST classification.
When running python run.py you should see something like this:

Your Superpowers

(click to expand)

Override any config parameter from command line

Hydra allows you to overwrite any parameter defined in your config, without writing any code!

python run.py trainer.max_epochs=20 optimizer.lr=1e-4

You can also add new parameters with + sign.

python run.py +model.new_param="uwu"

Train on CPU, GPU, TPU or even with DDP and mixed precision

PyTorch Lightning makes it really easy to train your models on different hardware.

# train on CPU
python run.py trainer.gpus=0

# train on 1 GPU
python run.py trainer.gpus=1

# train on TPU
python run.py +trainer.tpu_cores=8

# train with DDP (Distributed Data Parallel) (8 GPUs, 2 nodes)
python run.py trainer.gpus=4 +trainer.num_nodes=2 +trainer.accelerator='ddp'

# train with mixed precision
python run.py +trainer.amp_backend="apex" +trainer.amp_level="O1" +trainer.precision=16

Train model with any logger available in PyTorch Lightning, like Weights&Biases

PyTorch Lightning provides convenient integrations with most popular logging frameworks. Read more here. Using wandb requires you to setup account first. After that just complete the config as below.

# set project and entity names in `configs/logger/wandb`
wandb:
    project: "your_project_name"
    entity: "your_wandb_team_name"

# train model with Weights&Biases
# link to wandb dashboard should appear in the terminal
python run.py logger=wandb

Click here to see example wandb dashboard generated with this template.

Train model with chosen experiment config

Experiment configurations are placed in configs/experiment/.

python run.py +experiment=exp_example_simple

Attach some callbacks to run

Callbacks can be used for things such as as model checkpointing, early stopping and many more.
Callbacks configurations are placed in configs/callbacks/.

python run.py callbacks=default_callbacks

Use different tricks available in Pytorch Lightning

PyTorch Lightning provides about 40+ useful trainer flags.

# gradient clipping may be enabled to avoid exploding gradients
python run.py +trainer.gradient_clip_val=0.5

# stochastic weight averaging can make your models generalize better
python run.py +trainer.stochastic_weight_avg=True

# run validation loop 4 times during a training epoch
python run.py +trainer.val_check_interval=0.25

# accumulate gradients
python run.py +trainer.accumulate_grad_batches=10

Easily debug

# run 1 train, val and test loop, using only 1 batch
python run.py debug=true

# print full weight summary of all PyTorch modules
python run.py trainer.weights_summary="full"

# print execution time profiling after training ends
python run.py +trainer.profiler="simple"

# try overfitting to 1 batch
python run.py +trainer.overfit_batches=1 trainer.max_epochs=20

# use only 20% of the data
python run.py +trainer.limit_train_batches=0.2 \
+trainer.limit_val_batches=0.2 +trainer.limit_test_batches=0.2

Resume training from checkpoint

# checkpoint can be either path or URL
# path should be absolute!
python run.py +trainer.resume_from_checkpoint="/absolute/path/to/ckpt/name.ckpt"

Currently loading ckpt in Lightning doesn't resume logger experiment, but it will be supported in future Lightning release.

Create a sweep over hyperparameters

# this will run 6 experiments one after the other,
# each with different combination of batch_size and learning rate
python run.py -m datamodule.batch_size=32,64,128 optimizer.lr=0.001,0.0005

Currently sweeps aren't failure resistant (if one job crashes than the whole sweep crashes), but it will be supported in future Hydra release.

Create a sweep over hyperparameters with Optuna

# this will run hyperparameter search defined in `configs/config_optuna.yaml`
# over chosen experiment config
python run.py -m --config-name config_optuna.yaml +experiment=exp_example_simple

Using Optuna Sweeper plugin doesn't require you to code any boilerplate into your pipeline, everything is defined in a single config file!

Execute all experiments from folder

# execute all experiments from folder `configs/experiment/`
python run.py -m '+experiment=glob(*)'

Hydra provides special syntax for controlling behavior of multiruns. Read more here.

Execute sweep on a remote AWS cluster

This should be achievable with simple config using Ray AWS launcher for Hydra. Example is not yet implemented in this template.

Execute sweep on a Linux SLURM cluster

This should be achievable with simple config using Submitit launcher for Hydra. Example is not yet implemented in this template.

Guide

How To Learn?

First, you should probably get familiar with PyTorch Lightning
Next, go through Hydra quick start guide, basic Hydra tutorial and docs about instantiating objects with Hydra

Main Project Configuration

Location: configs/config.yaml
Main project config contains default training configuration.
It determines how config is composed when simply executing command python run.py.
It also specifies everything that shouldn't be managed by experiment configurations.

# specify here default training configuration
defaults:
    - trainer: default_trainer.yaml
    - model: mnist_model.yaml
    - optimizer: adam.yaml
    - datamodule: mnist_datamodule.yaml
    - callbacks: default_callbacks.yaml  # set this to null if you don't want to use callbacks
    - logger: null  # set logger here or use command line (e.g. `python run.py logger=wandb`)


# path to original working directory
# hydra hijacks working directory by changing it to the current log directory
# so it's useful to have this path as a special variable
# learn more here: https://hydra.cc/docs/next/tutorials/basic/running_your_app/working_directory
work_dir: ${hydra:runtime.cwd}


# path to folder with data
data_dir: ${work_dir}/data/


# use `python run.py debug=true` for easy debugging!
# (equivalent to running `python run.py trainer.fast_dev_run=True`)
debug: False


# pretty print config at the start of the run using Rich library
print_config: True


# disable python warnings if they annoy you
disable_warnings: False


# disable lightning logs if they annoy you
disable_lightning_logs: False


# output paths for hydra logs
hydra:
    run:
        dir: logs/runs/${now:%Y-%m-%d}/${now:%H-%M-%S}
    sweep:
        dir: logs/multiruns/${now:%Y-%m-%d_%H-%M-%S}
        subdir: ${hydra.job.num}

Experiment Configuration

Location: configs/experiment
You should store all your experiment configurations in this folder.
Experiment configurations allow you to overwrite parameters from main project configuration.

Simple Example

# to execute this experiment run:
# python run.py +experiment=exp_example_simple

defaults:
    - override /trainer: default_trainer.yaml
    - override /model: mnist_model.yaml
    - override /optimizer: adam.yaml
    - override /datamodule: mnist_datamodule.yaml
    - override /callbacks: default_callbacks.yaml
    - override /logger: null

# all parameters below will be merged with parameters from default configurations set above
# this allows you to overwrite only specified parameters

seed: 12345

trainer:
    max_epochs: 10
    gradient_clip_val: 0.5

model:
    lin1_size: 128
    lin2_size: 256
    lin3_size: 64

optimizer:
    lr: 0.005

datamodule:
    batch_size: 64
    train_val_test_split: [55_000, 5_000, 10_000]

Advanced Example

# to execute this experiment run:
# python run.py +experiment=exp_example_full

defaults:
    - override /trainer: null
    - override /model: null
    - override /optimizer: null
    - override /datamodule: null
    - override /callbacks: null
    - override /logger: null

# we override default configurations with nulls to prevent them from loading at all
# instead we define all modules and their paths directly in this config,
# so everything is stored in one place for more readibility

seed: 12345

trainer:
    _target_: pytorch_lightning.Trainer
    gpus: 0
    min_epochs: 1
    max_epochs: 10
    gradient_clip_val: 0.5

model:
    _target_: src.pl_models.mnist_model.MNISTLitModel
    input_size: 784
    lin1_size: 256
    lin2_size: 256
    lin3_size: 128
    output_size: 10

optimizer:
    _target_: torch.optim.Adam
    lr: 0.001
    eps: 1e-08
    weight_decay: 0.0005

datamodule:
    _target_: src.pl_datamodules.mnist_datamodule.MNISTDataModule
    data_dir: ${data_dir}
    batch_size: 64
    train_val_test_split: [55_000, 5_000, 10_000]
    num_workers: 0
    pin_memory: False

logger:
    wandb:
        _target_: pytorch_lightning.loggers.wandb.WandbLogger
        project: "lightning-hydra-template"
        tags: ["best_model", "uwu"]
        notes: "Description of this model."

Workflow

Write your PyTorch Lightning model (see mnist_model.py for example)
Write your PyTorch Lightning datamodule (see mnist_datamodule.py for example)
Write your experiment config, containing paths to your model and datamodule (see configs/experiment for examples)
Run training with chosen experiment config:
```
python run.py +experiment=experiment_name
```

Logs

Hydra creates new working directory for every executed run.
By default, logs have the following structure:

│
├── logs
│   ├── runs                    # Folder for logs generated from single runs
│   │   ├── 2021-02-15              # Date of executing run
│   │   │   ├── 16-50-49                # Hour of executing run
│   │   │   │   ├── .hydra                  # Hydra logs
│   │   │   │   ├── wandb                   # Weights&Biases logs
│   │   │   │   ├── checkpoints             # Training checkpoints
│   │   │   │   └── ...                     # Any other thing saved during training
│   │   │   ├── ...
│   │   │   └── ...
│   │   ├── ...
│   │   └── ...
│   │
│   └── multiruns               # Folder for logs generated from multiruns (sweeps)
│       ├── 2021-02-15_16-50-49     # Date and hour of executing sweep
│       │   ├── 0                       # Job number
│       │   │   ├── .hydra                  # Hydra logs
│       │   │   ├── wandb                   # Weights&Biases logs
│       │   │   ├── checkpoints             # Training checkpoints
│       │   │   └── ...                     # Any other thing saved during training
│       │   ├── 1
│       │   ├── 2
│       │   └── ...
│       ├── ...
│       └── ...
│

You can change this structure by modifying paths in main project configuration.

Experiment Tracking

PyTorch Lightning supports the most popular logging frameworks:

Weights&Biases
Neptune
Comet
MLFlow
TestTube
Tensorboard
CSV

These tools help you keep track of hyperparameters and output metrics and allow you to compare and visualize results. To use one of them simply complete its configuration in configs/logger and run:

python run.py logger=logger_name

You can use many of them at once (see configs/logger/many_loggers.yaml for example).
You can also write your own logger.

Lightning provides convenient method for logging custom metrics from inside LightningModule. Read the docs here or take a look at MNIST example.

Inference

Template contains simple example of loading model from checkpoint and running predictions.
Take a look at inference_example.py.

Callbacks

Template contains example callbacks for better Weights&Biases integration (see wandb_callbacks.py).
To support reproducibility: UploadCodeToWandbAsArtifact, UploadCheckpointsToWandbAsArtifact, WatchModelWithWandb.
To provide examples of logging custom visualisations with callbacks only: LogConfusionMatrixToWandb, LogF1PrecRecHeatmapToWandb.

Best Practices

Miniconda

Use miniconda for your python environments (it's usually unnecessary to install full anaconda environment, miniconda should be enough). It makes it easier to install some dependencies, like cudatoolkit for GPU support.
Example installation:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Automatic Code Formatting

Use pre-commit hooks to standardize code formatting of your project and save mental energy.
Simply install pre-commit package with:

pip install pre-commit

Next, install hooks from .pre-commit-config.yaml:

pre-commit install

After that your code will be automatically reformatted on every new commit.
Currently template contains configurations of Black (python code formatting) and Isort (python import sorting). You can exclude chosen files from automatic formatting, by modifying .pre-commit-config.yaml.

To format all files in the project use command:

pre-commit run --all-files

Environment Variables

System specific variables (e.g. absolute paths to datasets) should not be under version control or it will result in conflict between different users.

Template contains .env.tmp file. Change its name to .env (this name is excluded from version control in .gitignore). You should use it for storing environment variables like this:

export MY_VAR=/home/user/my_system_path

All variables from .env are loaded in run.py automatically.

Hydra allows you to reference any env variable in .yaml configs like this:

path_to_data: ${env:MY_VAR}

Data Version Control

Use DVC to version control big files, like your data or trained ML models.
To initialize the dvc repository:

dvc init

To start tracking a file or directory, use dvc add:

dvc add data/MNIST

DVC stores information about the added file (or a directory) in a special .dvc file named data/MNIST.dvc, a small text file with a human-readable format. This file can be easily versioned like source code with Git, as a placeholder for the original data:

git add data/MNIST.dvc data/.gitignore
git commit -m "Add raw data"

Support Installing Project As a Package

It allows other people to easily use your modules in their own projects. Change name of the src folder to your project name and add setup.py file:

from setuptools import find_packages, setup

setup(
    name="src",  # you should change "src" to your project name
    version="0.0.0",
    description="Describe Your Cool Project",
    author="",
    author_email="",
    # replace with your own github project link
    url="https://github.com/hobogalaxy/lightning-hydra-template",
    install_requires=["pytorch-lightning>=1.2.0", "hydra-core>=1.0.6"],
    packages=find_packages(),
)

Now your project can be installed from local files:

pip install -e .

Or directly from git repository:

pip install git+git://github.com/YourGithubName/your-repo-name.git --upgrade

So any file can be easily imported into any other file like so:

from project_name.pl_models.mnist_model import MNISTLitModel
from project_name.pl_datamodules.mnist_datamodule import MNISTDataModule

Tests

I find myself often running into bugs that come out only in edge cases or on some specific hardware/environment. To speed up the development, I usually constantly execute simple bash scripts that run a couple of quick 1 epoch experiments, like overfitting to 10 batches, training on 25% of data, etc. You can easily modify the commands in the script for your use case. If even 1 epoch is too much for your model, then you can make it run for a couple of batches instead (by using the right trainer flags).

Keep in mind those aren't real tests - it's simply executing commands one after the other, after which you need to take a look in terminal if some of them crashed. It's always best if you write real unit tests for your code.
To execute:

bash tests/smoke_tests.sh

Tricks

Accessing Datamodule Attributes In Model

The simplest way is to pass datamodule attribute directly to model on initialization:

datamodule = hydra.utils.instantiate(config.datamodule)

model = hydra.utils.instantiate(config.model, some_param=datamodule.some_param)

This is not a robust solution, since when you have many datamodules in your project, it will make them incompatible if this same parameter is not defined in each of them.

A better solution is to add Omegaconf resolver to your datamodule:

from omegaconf import OmegaConf

# you can place this snippet in your datamodule __init__()
resolver_name = "datamodule"
OmegaConf.register_new_resolver(
    resolver_name,
    lambda name: getattr(self, name),
    use_cache=False
)

This way you can reference any datamodule attribute from your config like this:

# this will get 'datamodule.some_param' field
some_parameter: ${datamodule: some_param}

When later accessing this field, say in your lightning model, it will get automatically resolved based on all resolvers that are registered. Remember not to access this field before datamodule is initialized. You also need to set resolve to false in print_config() in run.py method or it will throw errors!

template_utils.print_config(config, resolve=False)

Other Repositories

Inspirations

This template was inspired by: PyTorchLightning/deep-learninig-project-template, drivendata/cookiecutter-data-science, tchaton/lightning-hydra-seed, Erlemar/pytorch_tempest, ryul99/pytorch-project-template, lucmos/nn-template.

Useful Repositories

pytorch/hydra-torch - resources for configuring PyTorch classes with Hydra,
romesco/hydra-lightning - resources for configuring PyTorch Lightning classes with Hydra
lucmos/nn-template - similar template that's easier to start with but less scalable

Examples Of Repositories Using This Template

(TODO)

Limitations