Microbench

Microbench is a small Python package for benchmarking Python functions, and optionally capturing extra runtime/environment information. It is most useful in clustered/distributed environments, where the same function runs under different environments, and is designed to be extensible with new functionality. In addition to benchmarking, this can help reproducibility by e.g. logging the versions of key Python packages, or even all packages loaded into the global environment.

Requirements

Microbench has no dependencies outside of the Python standard library, although pandas is recommended to examine results. The line_profiler package needs to be installed for line-by-line code benchmarking (described in a later section).

Installation

To install using pip:

pip install microbench

Usage

Microbench is designed for benchmarking Python functions. These examples will assume you have already defined a Python function myfunction that you wish to benchmark:

def myfunction(arg1, arg2, ...):
    ...

Minimal example

First, create a benchmark suite, which specifies the configuration and information to capture. By default, benchmarks are appended to a file in JSON format (one record per line) to a filename specified by outfile.

Here's a minimal, complete example:

from microbench import MicroBench

class BasicBench(MicroBench):
    outfile = '/home/user/my-benchmarks'
    
basic_bench = BasicBench()

To attach the benchmark to your function, simply use basic_bench as a decorator, like this:

@basic_bench
def myfunction(arg1, arg2, ...):
    ...

That's it! Benchmark information will be appended to the file specified in outfile. This example captures the fields start_time, finish_time and function_name. See the Examine results section for further information.

Extended example

Here's a more complete example using mixins (the MB prefixed class names) to extend functionality. Note that keyword arguments can be supplied to the constructor (in this case some_info=123) to specify additional information to capture.

from microbench import *
import numpy, pandas

class MyBench(MicroBench, MBFunctionCall, MBPythonVersion, MBHostInfo):
    outfile = '/home/user/my-benchmarks'
    capture_versions = (numpy, pandas)  # Or use MBGlobalPackages
    env_vars = ('SLURM_ARRAY_TASK_ID', )
    
benchmark = MyBench(some_info=123)

To capture package versions, you can either specify them individually (as above), or you can capture the versions of every package in the global environment. In the following example, we would capture the versions of microbench, numpy, and pandas automatically.

from microbench import *
import numpy, pandas

class Bench2(MicroBench, MBGlobalPackages):
    outfile = '/home/user/bench2'

bench2 = Bench2()

The capture_versions option from the example creates fields like <package name>_version, e.g. numpy_version. This is captured from the package's __name__ attribute, or left as null where not available.

The env_vars option from the example above specifies a list of environment variables to capture as env_<variable name>. In this example, the slurm array task ID will be stored as env_SLURM_ARRAY_TASK_ID. Where the environment variable is not set, the value will be null.

Examine results

Each result is a JSON object. When using the outfile option, a JSON object for each @benchmark call is stored on a separate line in the file. The output from the minimal example above for a single run will look similar to the following:

{"start_time": "2018-08-06T10:28:24.806493", "finish_time": "2018-08-06T10:28:24.867456", "function_name": "my_function"}

The simplest way to examine results in detail is to load them into a pandas dataframe:

import pandas
results = pandas.read_json('/home/user/my-benchmarks', lines=True)

Pandas has powerful data manipulation capabilities. For example, to calculate the average runtime by Python version:

# Calculate runtime for each run
results['runtime'] = results['finish_time'] - results['start_time']

# Average runtime by Python version
results.groupby('python_version')['runtime'].mean()

Many more advanced operations are available. The pandas tutorial is recommended.

Interactive usage

Microbench can be used in scripts, packages, or interactively from the Python prompt, IPython prompt, or a Jupyter Notebook. When using the package interactively, you may not want to write the results to a file. In that case, you can use io.StringIO to capture the output as a string:

from microbench import *
import io

class MyBench(MicroBench):
    outfile = io.stringIO()

my_bench = MyBench()

# Dummy function for testing
@my_bench
def test():
    pass

# Call the dummy function twice
# (triggering benchmark capture both times)
test()
test()

# Read the benchmark results
import pandas
results = pandas.read_json(my_bench.outfile.getvalue(), lines=True)

# results is a Pandas DataFrame containing captured metadata

Line profiler support

Microbench also has support for line_profiler, which shows the execution time of each line of Python code. Note that this will slow down your code, so only use it if needed, but it's useful for discovering bottlenecks within a function. Requires the line_profiler package to be installed (e.g. pip install line_profiler).

from microbench import MicroBench, MBLineProfiler
import io
import pandas

# Create our benchmark suite using the MBLineProfiler mixin
class LineProfilerBench(MicroBench, MBLineProfiler):
    outfile = io.StringIO()

lpbench = LineProfilerBench()

# Decorate our function with the benchmark suite
@lpbench
def my_function():
    """ Inefficient function for line profiler """
    acc = 0
    for i in range(1000000):
        acc += i

    return acc

# Call the function as normal
my_function()

# Read the results into a Pandas DataFrame
results = pandas.read_json(lpbench.outfile.getvalue(), lines=True)

# Get the line profiler report as an object
lp = MBLineProfiler.decode_line_profile(results['line_profiler'][0])

# Print the line profiler report
MBLineProfiler.print_line_profile(results['line_profiler'][0])

The last line of the previous example will print the line profiler report, showing the execution time of each line of code. Example:

Timer unit: 1e-06 s

Total time: 0.476723 s
File: /home/user/my_test.py
Function: my_function at line 12

Line #      Hits         Time  Per Hit   % Time  Line Contents
==============================================================
    12                                               @lpbench
    13                                               def my_function():
    14                                                   """ Inefficient function for line profiler """
    15         1          2.0      2.0      0.0          acc = 0
    16   1000001     217874.0      0.2     45.7          for i in range(1000000):
    17   1000000     258846.0      0.3     54.3              acc += i
    18
    19         1          1.0      1.0      0.0          return acc

Extending microbench

Microbench includes a few mixins for basic functionality as described in the extended example, above.

You can add functions to your benchmark suite to capture extra information at runtime. These functions must be prefixed with capture_ for them to run automatically after the function has completed. They take a single argument, bm_data, a dictionary to be extended with extra data. Care should be taken to avoid overwriting existing key names.

Here's an example to capture the machine type (i386, x86_64 etc.):

from microbench import MicroBench
import platform

class Bench(MicroBench):
    outfile = '/home/user/my-benchmarks'

    def capture_machine_platform(self, bm_data):
        bm_data['platform'] = platform.machine()
        
benchmark = Bench()

Redis support

By default, microbench appends output to a file, but output can be directed elsewhere, e.g. redis - an in-memory, networked data source. This option is useful when a shared filesystem is not available.

Redis support requires redis-py.

To use this feature, inherit from MicroBenchRedis instead of MicroBench, and specify the redis connection and key name as in the following example:

from microbench import MicroBenchRedis

class RedisBench(MicroBenchRedis):
    # redis_connection contains arguments for redis.StrictClient()
    redis_connection = {'host': 'localhost', 'port': 6379}
    redis_key = 'microbench:mykey'

benchmark = RedisBench()

To retrieve results, the redis package can be used directly:

import redis
import pandas

# Establish the connection to redis
rconn = redis.StrictRedis(host=..., port=...)

# Read the redis data from 'myrediskey' into a list of byte arrays
redis_data = redis.lrange('myrediskey', 0, -1)

# Convert the list into a single string
json_data = '\n'.join(r.decode('utf8') for r in redis_data)

# Read the string into a pandas dataframe
results = pandas.read_json(json_data, lines=True)

Feedback

Please note this is a recently created, experimental package. Please let me know your feedback or feature requests in Github issues.