SciPy

Benchmarking SciPy with Airspeed Velocity

This document introduces benchmarking, including reviewing SciPy benchmark test results online, writing a benchmark test, and running it locally. For a video run-through of writing a test and running it locally, see Benchmarking SciPy.

As written in the airspeed velocity (asv) documentation:

airspeed velocity (asv) is a tool for benchmarking Python packages over their lifetime. Runtime, memory consumption and even custom-computed values may be tracked. The results are displayed in an interactive web frontend that requires only a basic static webserver to host.

To see what this means, take a look at airspeed velocity of an unladen scipy. Each plot summarizes the execution time of a particular test over the commit history of the project; that is, as each commit is merged, the benchmark test is run, its execution time is measured, and the elapsed time is plotted. In addition to tracking the performance of the code a commit is intended to affect, running all benchmarks for each commit is helpful for identifying unintentional regressions: significant increases in the execution time of one or more benchmark tests. As SciPy is a web of interconnected code, the repercussions of a small change may not be immediately obvious to a contributor, so this benchmark suite makes it easier to detect regressions and identify the commit that caused them. When you contribute a substantial new feature - or notice a feature that doesn’t already have a benchmark test - please consider writing benchmarks.

Writing benchmarks

The Writing benchmarks section of the airspeed velocity documentation is the definitive guide to writing benchmarks. Please see also the SciPy benchmarks readme.

To see how benchmarks are written, take a look at scipy/benchmarks/benchmarks/optimize_linprog.py. Each subclass of Benchmark defines a benchmark test. For example, the KleeMinty class defines a benchmark test based on the Klee-Minty hypercube problem, a diabolical test of the simplex algorithm for linear programming. The class has four parts:

  • setup prepares the benchmark to run. The execution time of this function is not counted in the benchmark results, so this is a good place to set up all variables that define the problem. In the KleeMinty example, this involves generating arrays c, A_ub, and b_ub corresponding with a Klee-Minty hypercube in dims dimensions and storing them as instance variables.

  • time_klee_minty actually runs the benchmark test. This function executes after a KleeMinty object has been instantiated and setup has run, so it gets the arrays defining the problem from self. Note that the prefix time in the function name indicates to asv that the execution time of this function is to be counted in the benchmark results.

  • params is a list of lists defining parameters of the test. Benchmarks are run for all possible combinations of these parameters. For example, the first time the benchmark is run, the first element of methods (simplex) is passed into setup and time_klee_minty as the first argument, meth, and the first element of [3, 6, 9] (3) is passed into setup and time_klee_minty as the second argument, dims. The next time the benchmark is run, setup and time_klee_minty are passed revised simplex and 6 as arguments, and so this continues until all combinations of parameters have been used.

  • param_names is a list of human-readable names for each element of the params list. These are used for presenting results.

Results of this benchmark over the past few years are available by clicking on the KleeMinty.time_klee_minty link at airspeed velocity of an unladen scipy. Note that each trace of the plot corresponds with a combination of benchmark parameters and environment settings (e.g. Cython version), and that the visibility of the traces can be toggled using the control panel on the left.

Running benchmarks locally

Before beginning, ensure that airspeed velocity is installed.

After contributing new benchmarks, you should test them locally before submitting a pull request.

To run all benchmarks, navigate to the root SciPy directory at the command line and execute:

python runtests.py --bench

where --bench activates the benchmark suite instead of the test suite. This builds SciPy and runs the benchmarks. (Note: this could take a while. Benchmarks often take longer to run than unit tests, and each benchmark is run multiple times to measure the distribution in execution times.)

To run benchmarks from a particular benchmark module, such as optimize_linprog.py, simply append the filename without the extension:

python runtests.py --bench optimize_linprog

To run a benchmark defined in a class, such as KleeMinty from optimize_linprog.py:

python runtests.py --bench optimize_linprog.KleeMinty

To compare benchmark results between the active branch and another, such as master:

python runtests.py --bench-compare master optimize_linprog.KleeMinty

All of the commands above display the results in plain text in the console, and the results are not saved for comparison with future commits. For greater control, a graphical view, and to have results saved for future comparison, you can use scipy/benchmarks/run.py to run the benchmarks.

run.py is a “wrapper” for the asv terminal command, the use of which is described in Using airspeed velocity. run.py simply sets some environment variables for you, then sends all remaining command line arguments to asv.

To use it, navigate to scipy/benchmarks in the console and then execute:

python run.py run

Just like asv run from the asv documentation, this command runs the whole benchmark suite and saves the results for comparison against future commits.

To run only a single benchmark, such as KleeMinty from optimize_linprog.py:

python run.py run --bench optimize_linprog.KleeMinty

(Note that the --bench option here is sent to asv; its meaning is different than the --bench option for runtests.py.)

One great feature of asv is that it can automatically run a benchmark not just for the current commit, but for every commit in a range. linprog method='interior-point' was merged into SciPy with commit 7fa17f2369e0e5ad055b23cc1a5ee079f9e8ca32, so let’s run the KleeMinty benchmark for 10 commits between then and now to track its performance over time:

python run.py run --bench optimize_linprog.KleeMinty --steps 10 7fa17f..

Note

This will take a while, because SciPy has to be rebuilt for each commit! For more information about specifying ranges of commits, see the git revisions documentation.

To “publish” the results (prepare them to be viewed) and “preview” them in an interactive console:

python run.py publish
python run.py preview

ASV will report that it is running a server. Using any browser, you can review the results by navigating to http://127.0.0.1:8080 (local machine, port 8080).

For much more information about the asv commands accessible via run.py, see the airspeed velocity Commands documentation. (Tip: check out the asv find command and the --quick, --skip-existing-commits, and --profile options for asv run.)