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A Year in Review: Quansight’s Contributions to PyTorch in 2021

Published April 13, 2022

Ralf
rgommers

Ralf Gommers

This post was co-written between Mario Lezcano & Ralf Gommers.



PyTorch is a very popular open source deep learning framework, primarily developed by Meta AI. If you are making deep learning models, chances are you are using PyTorch. Not only is Quansight a major contributor to the development of PyTorch, but we also use it in applied data science consulting projects as our go-to framework for building deep learning models.

PyTorch draws on many of the battle-tested concepts introduced by NumPy, and adds new features used in modern deep learning such as GPU and TPU acceleration; forward, backward, and higher-order automatic differentiation; automatic mixed-precision; distributed training; CNNs; building blocks for neural networks, and more.

We have been involved in the development of PyTorch for the last three years, bringing in our 10+ years of experience in open source software (OSS) work in the PyData world.

PyTorch is a particularly large library, with more than 2 million lines of code (LOC), mostly C++ with Python bindings on top. To put the size of the project in perspective, this is 10 times the LOC in NumPy. It is also a very fast-paced project, with 800+ active contributors totaling over 20k commits just in the last year.

Quansight Contributions


We have a team of 15+ engineers involved in the various aspects of PyTorch development. We distinguish the following as our main topic areas: scientific computing, compatibility with the Python Array API standard and NumPy, maintainability, Torchvision, and research.


Python Array API and NumPy Compatibility

In 2010, if a user needed to perform some numerical computations using multidimensional data, they would import NumPy or its extension SciPy, store their data in an array, and start taking advantage of the speed of the operations implemented in C from the comfort of the Python language. Nowadays, the landscape is rather different. We have libraries with autograd, GPU, and TPU support oriented towards deep learning. This includes PyTorch, Tensorflow, JAX, or MXNet, libraries that provide a CUDA extension for NumPy-like code, such as CuPy or cluster-level parallelism, like Dask.

At the same time, not only are these libraries used by millions, but they also serve as the basic building blocks for the lion's share of tools in the PyData world. Most libraries for data science in Python, such as pandas, scikit-learn, or Matplotlib use and consume arrays, and build on top of them to implement higher-level functionality.

The Python Array API standard aims to serve as a bridge between these two realities. It is a standard that aims to provide a common API. Then, if libraries write their code in terms of this API, their code becomes library-agnostic. This means that the user could choose the backend library that is used to manage the arrays internally depending on their use case. For this to be possible, the Python Array API is largely based on (a curated subset of) NumPy’s API, which is the gold standard that most other libraries follow.

From a user perspective, if they have a large codebase written in NumPy they want to migrate to another library, and the other library implements the Python Array API, doing so should be as easy as changing the imports.

PyTorch decided to implement the Python Array API in May 2021. As of version 1.12, PyTorch implements >90% of its functionality. Quansight has been instrumental in the process in both directions: by extending the functionality that PyTorch provides to cover that specified in the API, and by improving and fine-tuning the API standard itself based on the knowledge acquired during years of developing PyTorch core alongside NumPy and SciPy.


Scientific PyTorch

Scientific computing was the branch of knowledge that first inspired data analysis. PyTorch, although a deep learning library at heart, is also widely used in the scientific community, where there is a growing trend of boosting classical numerical methods and algorithms with the parallelism of GPUs and the information given by autograd.

Quansight has a number of global experts in this area coming from the SciPy community, or more generally, the PyData community. As such, many of the contributions of Quansight within PyTorch have been in this realm. Mostly driven by Quansight efforts, PyTorch 1.12 includes a number of popular modules from SciPy, together with CUDA and autograd support.


Linear Algebra: torch.linalg

PyTorch 1.9 included a linalg module that implemented all the functionality from numpy.linalg in a NumPy-compatible way, together with CUDA acceleration and autograd support. Since its release, this module has been expanded to also include a number of popular functions from scipy.linalg and more. This module was created and is actively maintained by a group of Quansight engineers.


Forward and Backward AD

Automatic differentiation (AD) is arguably the main feature that deep learning frameworks bring to the table over traditional array libraries. Quansight is actively involved in the support and implementation of correct and efficient derivatives. In particular, it has helped in implementing many of the forward AD formulas to make possible the release of the support for forward AD mode in PyTorch 1.11.


Complex Numbers

PyTorch 1.10 came out with complex numbers support, and optimization over complex tensors. This feature was requested since the beginning of PyTorch, and has deep applications in fields ranging from signal processing to quantum mechanics. Quansight helped generalize the formulas for many functions and their derivatives to the complex case. The foundations of how to do so are not well-understood by the community, so a number of people from Quansight are currently working on publishing a paper formalizing the ideas and semantics that drive PyTorch’s design from a theoretical point of view.


Mathematical Functions: torch.special

PyTorch 1.9 introduced the torch.special module, modeled after scipy.special module. This module contains special functions used in mathematics such as the Riemann zeta function or the gamma function. These functions are paramount in fields like physics, mathematics, and statistics, but they also appear when modeling complex systems in biology and mechanics. This module expands on SciPy’s by adding GPU and autograd support to its functions. This module was implemented and is currently maintained by engineers at Quansight.


Fast Fourier Transforms: torch.fft

PyTorch 1.8 introduced the torch.fft module implementing fast Fourier transforms fully compatible with numpy.fft. All functions support CPU or GPU acceleration and complex autograd. There are plans to expand this module with discrete sine and cosine transform algorithms, compatible with scipy.fft. This module is written and maintained by Quansight engineers.


Interpolation

Up/down sampling algorithms are at the core of many algorithms in the field of computer vision. They are used both for preprocessing the data, but also as components to assess the quality of a given model. A paper published in 2021 showed that most major deep learning libraries suffered from poor scaling issues in their interpolation algorithms, giving vastly incorrect results. All these issues have been addressed and corrected by Quansight engineers, implementing new stable and efficient algorithms and their derivatives on CPU and GPU in PyTorch 1.11.


Maintainability

Given the speed of development of PyTorch, with 100+ people working full-time on the project, usual software engineering practices like testing, integration, benchmarking, and documentation are fundamental to providing a seamless user experience. The main challenge here is that textbook solutions often do not scale to projects of the size and complexity of PyTorch. By leveraging years of experience developing and maintaining many other large OSS projects, Quansight has been able to help in the sustainable growth of PyTorch.


Automated Testing

In 2021, PyTorch started to find a way to reduce and standardize its 100K+ lines of tests into what’s referred to as OpInfos and ModuleInfos. Given the number of subsystems within PyTorch (forward AD, backward AD, strided tensors, different JIT backends…) and its extensive API (2,000+ functions), it was not sustainable to manually write tests for each function against all subsystems. The solution was to create objects that encapsulate each PyTorch function together with its characteristics and a way to generate valid inputs for that function. Then, a test for a subsystem would process these objects and know whether it makes sense to test that function against the subsystem, and if so, how. Quansight engineers have been involved in the implementation of generic tests and in adding support for more and more operations to increase the test coverage. While doing this, the engineers at Quansight have also been involved in fixing bugs that were found in the process.


Testing utilities: torch.testing

Internally, PyTorch developed elaborate utilities needed for testing, e.g. creating random tensors for a given specification and comparing the results of tensor operations. With the ever-growing ecosystem, the demand for having these utilities publicly accessible also grew. Starting in 2021, Quansight engineers started to flesh out and implement a system that is able to handle the complex internal needs of the PyTorch project while providing downstream libraries the tools they need. Soon after its inception, torch.testing has seen adoption by other projects. In early 2022, not even a year after the beginning of the project, the module reached a stable state.


Structured Kernels

Even though the API surface of PyTorch is remarkably large, there are a few properties that most, if not all, functions within PyTorch share. A PyTorch function is fed one or more tensors and perhaps more arguments, and returns some new tensors. This simple remark allows us to factorize any PyTorch operation by first creating the output tensors given the input tensors, and then computing the values of the operation and filling the output tensors. This factorization allows us to, for example, skip the actual computation, figuring out the size and other properties of all the inner tensors of a neural network without really running the model. Quansight engineers have been involved in the design and implementation of parts of this mechanism, and are actively involved in the migration of PyTorch functions to this more flexible model.


Build Time Improvements

Editing any PyTorch operator often required rebuilding thousands of C++ and CUDA files and was highly disruptive to the development cycle. Quansight engineers have profiled and eliminated bottlenecks in PyTorch’s parallel builds, as well as fixed structural issues in PyTorch’s core C++ codebase, that led to thousands of files being rebuilt unnecessarily. Typical build times when switching branches went from 20 minutes to 5 or fewer minutes.


Docs and Docs Infrastructure

From a usability perspective, a library is as good as its documentation. Quansight engineers have been and currently are, involved in rewriting major sections of the documentation of PyTorch. We have also been involved in updating and maintaining the infrastructure that runs and hosts the documentation pages within PyTorch, improving the formatting of the docs and the overall user experience.


Type Annotations

Type annotations for PyTorch were an oft-requested feature by users. They help with catching errors and with code completion in IDEs. Two Quansight engineers improved type annotation support significantly by adding a testing framework, running Mypy in CI, moving existing type annotations in stubs inline, and fixing a large number of issues. By April 2021, type annotation support in PyTorch was declared complete.


Port Legacy Code From C to C++

PyTorch originally started as a Python port of the Lua library, Torch, which itself was a C library with Lua bindings. From its start, PyTorch decided to rewrite its backend completely in terms of two in-house C++ libraries. The process of migrating the macro-based C backend to the higher level C++ one started in 2016, and it was just completed at the end of 2021, with a final push from an engineer from Quansight, who helped migrate a large number of highly non-trivial functionality.


High Priority Issues

From our initial involvement in the project in 2019, Quansight has been actively involved in helping Meta deal with high-priority issues. These are bugs reported by users that are considered critical, or feature requests that got enough attention from the community to be deemed of particular interest. During the last year, Quansight engineers closed 116 high-priority issues.


Torchvision


Datasets & Transforms

torchvision.datasets and torchvision.transforms have been part of torchvision since the initial release in 2016. Their original purpose was to assist image classification scenarios and for this use case, they work well. Quickly after the beginning, demand grew for other vision tasks like object detection, video classification, and optical flow.

The original API was able to partially support these use cases as well, but there was never a general way. Starting in mid-2021, Quansight and Meta engineers started completely redesigning the API to achieve convergence between the different tasks. This work is still ongoing and can be found in the torchvision.prototype namespace.

Although the revamp brings a plethora of improvements, the most important change to highlight here is that datasets now return everything they have to offer, and transforms now handle that without any need for manual interference. For example, if a dataset provides a bounding box together with the image, all transformations that alter the shape of the image are also applied to the bounding box to keep them in sync.


Video Reading

We have seen widespread adoption of Torchvision video backends and datasets in 2021. Quansight engineers, in collaboration with community developers and Meta engineers, have continued to push the performance, reliability, and accuracy of video infrastructure in Torchvision to match the new demand. We refactored and updated the existing API to support the latest versions of FFmpeg system libraries and resolved numerous issues related to video modules. We have also worked closely with engineers from Meta and NVIDIA to bring the support for GPU decoding, one of the most-requested features, to Torchvision and have integrated it into the existing infrastructure.


Research Topics

Engineers at Quansight are also actively involved in the research aspect of PyTorch. This involves features that are expected to either be used by researchers or are implemented as a proof of concept for promising ideas, and do not necessarily have equivalents in other deep learning frameworks. These topics require strong design capabilities, together with a good knowledge of the current research literature on these topics, which fit well with the academic background of many of the engineers at Quansight.


Sparse Tensors

Sparse data appears naturally in fields with high-dimensional data points, like vision, chemistry and drug synthesis, or analysis of time sequences in geology or biology. While sparse tensors have been around for as long as data analysis, the semantics for sparse operations in the context of autograd are still far from well-understood. A team of Quansight engineers is involved in both the design and the implementation of sparse operations and their derivatives within PyTorch. The current goal is to have PyTorch match the capabilities of scipy.sparse, together with GPU support and sparse gradients when possible.


Functorch

With its release in 2019, JAX introduced a new way of thinking about machine learning. JAX showed what many programming languages researchers had theorized for years: It was not only possible but sound to implement an efficient ML framework based on functional programming principles. Functorch (for Functional PyTorch) is an approach to marry the benefits and simplicity of the higher-order functional transformations from JAX with the simplicity of use of the eager mode and class-based approach from PyTorch. Quansight has a number of engineers participating in this project, which will be released as an external library for PyTorch 1.12. This library is intended to stay as an out-of-tree project until its design is stable. Then, it is planned to be merged into core PyTorch.


Parametrizations

In the same way, that data is often preprocessed and cleaned up before being analyzed, preprocessing weights of layers by transforming them before being used within a layer can be used as a regularizer to stabilize the training of a network. PyTorch 1.9 added a way to parametrize parameters of neural networks in a composable and extensible way. The design of this feature stemmed from the research carried out by one of the engineers at Quansight during their doctoral studies, who then went on to implement this feature in PyTorch core.


Closing Remarks


This turned into a very long post, which reflects the huge amount of effort put in by our team of 15+ engineers. This was a true team effort, with contributions from: Ivan Yashchuk, Peter Bell, Mario Lezcano, Ralf Gommers, Nikita Vedeneev, Kurt Mohler, Kshiteej Kalambarkar, Thomas Fan, Philip Meier, Yukio Siraichi, Victor Fomin, Pearu Peterson, Kushashwa Shrimali, Sameer Deshmukh, Hameer Abbasi, Bruno Korbar, Nikita Karetnikov, Matti Picus, Antonio Cuni, Guilherme Leobas, Alexander Ocsa, Edgar Margffoy, and Anirudh Dagar.

All of this work wouldn't have been possible without the excellent collaboration with, and support from, PyTorch and Torchvision maintainers at Meta. We'd like to thank Mike Ruberry, Natalia Gimelschein, Edward Yang, Alban Desmaison, Anjali Chourdia, Christian Pursch, Joel Schlosser, Nikita Shulga, Richard Zou, Joe Spisak, and Joe Isaacson (PyTorch) and Vasilis Vryniotis, Francisco Massa, Prabhat Roy and Nicolas Hug (Torchvision) in particular.

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