Lecture 3: Troubleshooting & Testing
Lecture by Charles Frye.
Notes by James Le and Vishnu Rachakonda.
Published August 22, 2022. Download slides.
1 - Testing Software
The general approach is that tests will help us ship faster with fewer bugs, but they won't catch all of our bugs.
That means we will use testing tools but won't try to achieve 100% coverage.
Similarly, we will use linting tools to improve the development experience but leave escape valves rather than pedantically following our style guides.
Finally, we'll discuss tools for automating these workflows.
1.1 - Tests Help Us Ship Faster. They Don't Catch All Bugs
Tests are code we write that are designed to fail intelligibly when our other code has bugs. These tests can help catch some bugs before they are merged into the main product, but they can't catch all bugs. The main reason is that test suites are not certificates of correctness. In some formal systems, tests can be proof of code correctness. But we are writing in Python (a loosely goosey language), so all bets are off in terms of code correctness.
Nelson Elhage framed test suites more like classifiers. The classification problem is: does this commit have a bug, or is it okay? The classifier output is whether the tests pass or fail. We can then treat test suites as a "prediction" of whether there is a bug, which suggests a different way of designing our test suites.
When designing classifiers, we need to trade off detection and false alarms. If we try to catch all possible bugs, we can inadvertently introduce false alarms. The classic signature of a false alarm is a failed test - followed by a commit that fixes the test rather than the code.
To avoid introducing too many false alarms, it's useful to ask yourself two questions before adding a test:
Which real bugs will this test catch?
Which false alarms will this test raise?
If you can think of more examples for the second question than the first one, maybe you should reconsider whether you need this test.
One caveat is that: in some settings, correctness is important. Examples include medical diagnostics/intervention, self-driving vehicles, and banking/finance. A pattern immediately arises here: If you are operating in a high-stakes situation where errors have consequences for people's lives and livelihoods, even if it's not regulated yet, it might be regulated soon. These are examples of low-feasibility, high-impact ML projects discussed in the first lecture.
1.2 - Use Testing Tools, But Don't Chase Coverage
Pytest is the standard tool for testing Python code. It has a Pythonic implementation and powerful features such as creating separate suites, sharing resources across tests, and running parametrized variations of tests.
Pure text docs can't be checked for correctness automatically, so they are hard to maintain or trust. Python has a nice module, [doctests], for checking code in the documentation and preventing rot.
Notebooks help connect rich media (charts, images, and web pages) with code execution. A cheap and dirty solution to test notebooks is adding some asserts and using nbformat to run the notebooks.
Once you start adding different types of tests and your codebase grows, you will want coverage tools for recording which code is checked or "covered" by tests. Typically, this is done in lines of code, but some tools can be more fine-grained. We recommend Codecov, which generates nice visualizations you can use to drill down and get a high-level overview of the current state of your testing. Codecov helps you understand your tests and can be incorporated into your testing. You can say you want to reject commits not only where tests fail, but also where test coverage goes down below a certain threshold.
However, we recommend against that. Personal experience, interviews, and published research suggest that only a small fraction of the tests you write will generate most of your value. The right tactic, engineering-wise, is to expand the limited engineering effort we have on the highest-impact tests and ensure that those are super high quality. If you set a coverage target, you will instead write tests in order to meet that coverage target (regardless of their quality). You end up spending more effort to write tests and deal with their low quality.
1.3 - Use Linting Tools, But Leave Escape Valves
Clean code is of uniform and standard style.
Uniform style helps avoid spending engineering time on arguments over style in pull requests and code review. It also helps improve the utility of our version control by cutting down on noisy components of diffs and reducing their size. Both benefits make it easier for humans to visually parse the diffs in our version control system and make it easier to build automation around them.
Standard style makes it easier to accept contributions for an open-source repository and onboard new team members for a closed-source system.
One aspect of consistent style is consistent code formatting (with things like whitespace). The standard tool for that in Python is [the] [black] Python formatter. It's a very opinionated tool with a fairly narrow scope in terms of style. It focuses on things that can be fully automated and can be nicely integrated into your editor and automated workflows.
For non-automatable aspects of style (like missing docstrings), we recommend [flake8]. It comes with many extensions and plugins such as docstring completeness, type hinting, security, and common bugs.
ML codebases often have both Python code and shell scripts in them. Shell scripts are powerful, but they also have a lot of sharp edges. shellcheck knows all the weird behaviors of bash that often cause errors and issues that aren't immediately obvious. It also provides explanations for why it's raising a warning or an error. It's very fast to run and can be easily incorporated into your editor.
One caveat to this is: pedantic enforcement of style is obnoxious. To avoid frustration with code style and linting, we recommend:
Filtering rules down to the minimal style that achieves the goals we set out (sticking with standards, avoiding arguments, keeping version control history clean, etc.)
Having an "opt-in" application of rules and gradually growing coverage over time - which is especially important for existing codebases (which may have thousands of lines of code that we need to be fixed).
1.4 - Always Be Automating
To make the best use of testing and linting practices, you want to automate these tasks and connect to your cloud version control system (VCS). Connecting to the VCS state reduces friction when trying to reproduce or understand errors. Furthermore, running things outside of developer environments means that you can run tests automatically in parallel to other development work.
Popular, open-source repositories are the best place to learn about automation best practices. For instance, the PyTorch Github library has tons of automated workflows built into the repo - such as workflows that automatically run on every push and pull.
The tool that PyTorch uses (and that we recommend) is GitHub Actions, which ties automation directly to VCS. It is powerful, flexible, performant, and easy to use. It gets great documentation, can be used with a YAML file, and is embraced by the open-source community. There are other options such as pre-commit.ci, CircleCI, and Jenkins; but GitHub Actions seems to have won the hearts and minds in the open-source community in the last few years.
To keep your version control history as clean as possible, you want to be able to run tests and linters locally before committing. We recommend pre-commit to enforce hygiene checks. You can use it to run formatting, linting, etc. on every commit and keep the total runtime to a few seconds. pre-commit is easy to run locally and easy to automate with GitHub Actions.
Automation to ensure the quality and integrity of our software is a productivity enhancer. That's broader than just CI/CD. Automation helps you avoid context switching, surfaces issues early, is a force multiplier for small teams, and is better documented by default.
One caveat is that: automation requires really knowing your tools. Knowing Docker well enough to use it is not the same as knowing Docker well enough to automate it. Bad automation, like bad tests, takes more time than it saves. Organizationally, that makes automation a good task for senior engineers who have knowledge of these tools, have ownership over code, and can make these decisions around automation.
Automate tasks with GitHub Actions to reduce friction.
Use the standard Python toolkit for testing and cleaning your projects.
Choose testing and linting practices with the 80/20 principle, shipping velocity, and usability/developer experience in mind.
2 - Testing ML Systems
Testing ML is hard, but not impossible.
We should stick with the low-hanging fruit to start.
Test your code in production, but don't release bad code.
2.1 - Testing ML Is Hard, But Not Impossible
Software engineering is where many testing practices have been developed. In software engineering, we compile source code into programs. In machine learning, training compiles data into a model. These components are harder to test:
Data is heavier and more inscrutable than source code.
Training is more complex and less well-defined.
Models have worse tools for debugging and inspection than compiled programs.
In this section, we will focus primarily on "smoke" tests. These tests are easy to implement and still effective. They are among the 20% of tests that get us 80% of the value.
2.2 - Use Expectation Testing on Data
We test our data by checking basic properties. We express our expectations about the data, which might be things like there are no nulls in this column or the completion date is after the start date. With expectation testing, you will start small with only a few properties and grow them slowly. You only want to test things that are worth raising alarms and sending notifications to others.
We recommend [great_expectations] for data testing. It automatically generates documentation and quality reports for your data, in addition to built-in logging and alerting designed for expectation testing. To get started, check out this MadeWithML tutorial on great_expectations.
To move forward, you want to stay as close to the data as possible:
A common pattern is that there's a benchmark dataset with annotations (in academia) or an external annotation team (in the industry). A lot of the detailed information about that data can be extracted by simply looking at it.
One way for data to get internalized into the organization is that at the start of the project, model developers annotate data ad-hoc (especially if you don't have the budget for an external annotation team).
However, if the model developers at the start of the project move on and more developers get onboarded, that knowledge is diluted. A better solution is an internal annotation team that has a regular information flow with the model developers is a better solution.
The best practice (recommended by Shreya Shankar) is to have a regular on-call rotation where model developers annotate data themselves. Ideally, these are fresh data so that all members of the team who are developing models know about the data and build intuition/expertise in the data.
2.3 - Use Memorization Testing on Training
Memorization is the simplest form of learning. Deep neural networks are very good at memorizing data, so checking whether your model can memorize a very small fraction of the full data set is a great smoke test for training. If a model can\'t memorize, then something is clearly very wrong!
Only really gross issues with training will show up with this test. For example, your gradients may not be calculated correctly, you have a numerical issue, or your labels have been shuffled; serious issues like these. Subtle bugs in your model or your data are not going to show up. A way to catch smaller bugs is to include the length of run time in your test coverage. It's a good way to detect if smaller issues are making it harder for your model to learn. If the number of epochs it takes to reach an expected performance suddenly goes up, it may be due to a training bug. PyTorch Lightning has an "overfit_batches" feature that can help with this.
Make sure to tune memorization tests to run quickly, so you can regularly run them. If they are under 10 minutes or some short threshold, they can be run every PR or code change to better catch breaking changes. A couple of ideas for speeding up these tests are below:
Overall, these ideas lead to memorization tests that implement model training on different time scale and allow you to mock out scenarios.
A solid, if expensive idea for testing training is to rerun old training jobs with new code. It's not something that can be run frequently, but doing so can yield lessons about what unexpected changes might have happened in your training pipeline. The main drawback is the potential expense of running these tests. CI platforms like CircleCI charge a great deal for GPUs, while others like Github Actions don't offer access to the relevant machines easily.
The best option for testing training is to regularly run training with new data that's coming in from production. This is still expensive, but it is directly related to improvements in model development, not just testing for breakages. Setting this up requires a data flywheel similar to what we talked about in Lecture 1. Further tooling needed to achieve will be discussed down the line.
2.4 - Adapt Regression Testing for Models
Models are effectively functions. They have inputs and produce outputs like any other function in code. So, why not test them like functions with regression testing? For specific inputs, we can check to see whether the model consistently returns the same outputs. This is best done with simpler models like classification models. It's harder to maintain such tests with more complex models. However, even in a more complex model scenario, regression testing can be useful for comparing changes from training to production.
A more sophisticated approach to testing for ML models is to use loss values and model metrics to build documented test suites out of your data. Consider this similar to the test-driven development (TDD) code writing paradigm. The test that is written before your code in TDD is akin to your model's loss performance; both represent the gap between where your code needs to be and where it is. Over time, as we improve the loss metric, our model is getting closer to passing "the test" we've imposed on it. The gradient descent we use to improve the model can be considered a TDD approach to machine learning models!
While gradient descent is somewhat like TDD, it's not exactly the same because simply reviewing metrics doesn't tell us how to resolve model failures (the way traditional software tests do).
To fill in this gap, start by looking at the data points that have the highest loss. Flag them for a test suite composed of "hard" examples. Doing this provides two advantages: it helps find where the model can be improved, and it can also help find errors in the data itself (i.e. poor labels).
As you examine these failures, you can aggregate types of failures into named suites. For example in a self-driving car use case, you could have a "night time" suite and a "reflection" suite. Building these test suites can be considered the machine learning version of regression testing, where you take bugs that you\'ve observed in production and add them to your test suite to make sure that they don\'t come up again.
The method can be quite manual, but there are some options for speeding it up. Partnering with the annotation team at your company can help make developing these tests a lot faster. Another approach is to use a method called Domino that uses foundation models to find errors. Additionally, for testing NLP models, use the CheckList approach.
2.5 - Test in Production, But Don't YOLO
It's crucial to test in true production settings. This is especially true for machine learning models, because data is an important component of both the production and the development environments. It's difficult to ensure that both are very close to one another.
The best way to solve the training and production difference is to test in production.
Testing in production isn't sufficient on its own. Rather, testing in production allows us to develop tooling and infrastructure that allows us to resolve production errors quickly (which are often quite expensive). It reduces pressure on other kinds of testing, but does not replace them.
We will cover in detail the tooling needed for production monitoring and continual learning of ML systems in a future lecture.
2.6 - ML Test Score
So far, we have discussed writing "smoke" tests for ML: expectation tests for data, memorization tests for training, and regression tests for models.
As your code base and team mature, adopt a more full-fledged approach to testing ML systems like the approach identified in the ML Test Score paper. The ML Test Score is a rubric that evolved out of machine learning efforts at Google. It's a strict rubric for ML test quality that covers data, models, training, infrastructure, and production monitoring. It overlaps with, but goes beyond some of the recommendations we've offered.
It's rather expensive, but worth it for high stakes use cases that need to be really well-engineered! To be really clear, this rubric is really strict. Even our Text Recognizer system we've designed so far misses a few categories. Use the ML Test Score as inspiration to develop the right testing approach that works for your team's resources and needs.
3 - Troubleshooting Models
Tests help us figure out something is wrong, but troubleshooting is required to actually fix broken ML systems. Models often require the most troubleshooting, and in this section we'll cover a three step approach to troubleshooting them.
"Make it run" by avoiding common errors.
"Make it fast" by profiling and removing bottlenecks.
"Make it right" by scaling model/data and sticking with proven architectures.
3.1 - Make It Run
This is the easiest step for models; only a small portion of bugs cause the kind of loud failures that prevent a model from running at all. Watch out for these bugs in advance and save yourself the trouble of models that don't run.
The first type of bugs that prevent models from running at all are shape errors. When the shape of the tensors don't match for the operations run on them, models can't be trained or run. Prevent these errors by keeping notes on the expected size of tensors, annotate the sizes in the code, and even step through your model code with a debugger to check tensor size as you go.
The second type of bugs is out of memory errors. This occurs when you try to push a tensor to a GPU that is too large to fit. PyTorch Lightning has good tools to prevent this. Make sure you're using the lowest precision your training can tolerate; a good default is 16 bit precision. Another common reason for this is trying to run a model on too much data or too large a batch size. Use the autoscale batch size feature in PyTorch Lightning to pick the right size batch. You can use gradient accumulation if these batch sizes get too small. If neither of these options work, you can look into manual techniques like tensor parallelism and gradient checkpoints.
Numerical errors also cause machine learning failures. This is when NaNs or infinite values show up in tensors. These issues most commonly appear first in the gradient and then cascade through the model. PyTorch Lightning has a good tool for tracking and logging gradient norms. A good tip to check whether these issues are caused by precision issues is to switch to Python 64 bit floats and see if that causes these issues to go away. Normalization layers tend to cause these issues, generally speaking. So watch out for how you do normalization!
3.2 - Make It Fast
Once you can run a model, you'll want it to run fast. This can be tricky because the performance of DNN training code is very counterintuitive. For example, transformers can actually spend more time in the MLP layer than the attention layer. Similarly, trivial components like loading data can soak up performance.
To solve these issues, the primary solution is to roll up your sleeves and profile your code. You can often find pretty easy Python changes that yield big results. Read these two tutorials by Charles and Horace for more details.
3.3 - Make It Right
After you make it run fast, make the model right. Unlike traditional software, machine learning models never are truly perfect. Production performance is never perfect. As such, it might be more appropriate to say "make it as right as needed".
Knowing this, making the model run and run fast allows us to make the model right through applying scale. To achieve performance benefits, scaling a model or its data are generally fruitful and achievable routes. It's a lot easier to scale a fast model. Research from OpenAI and other institutions is showing that benefits from scale can be rigorously measured and predicted across compute budget, dataset size, and parameter count.
If you can't afford to scale yourself, consider finetuning a model trained at scale for your task.
So far, all of the advice given has been model and task-agnostic. Anything more detailed has to be specific to the model and the relevant task. Stick close to working architectures and hyperparameters from places like HuggingFace, and try not to reinvent the wheel!
4 - Resources
Here are some helpful resources that discuss this topic.
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