## Friday, March 22, 2013

Hi all,

I've been working on in the last weeks at a little project that I developed called benchy.  The goal of benchy is answer some trivial questions about which code is faster ?  Or which algorithm consumes more memory ?  I know that there are several tools suitable for this task, but I would like to create some performance reports  by myself using Python.

Why did I create it ?  Since the beginning of the year I decided to rewrite all the code at Crab, a python framework for building recommender systems.  And one of the main components that required some refactoring was the pairwise metrics such as cosine, pearson, euclidean, etc.  I needed to unit test the performance of several versions of code for those functions. But doing this manually ? It's boring. That's why benchy came for!

What benchy can do ?

Benchy is a lightweight Python library for running performance benchmarks over alternative versions of code.  How can we use it ?

Let's see the cosine function, a popular pairwise function for comparing the similarity between two vectors and matrices in recommender systems.

Let's define the benchmarks to test:

With all benchmarks created, we could test a simple benchmark by calling the method run:

The dict associated to the key memory represents the memory performance results. It gives you the number of calls repeat to the statement, the average consumption usage in units . In addition, the key 'runtime' indicates the runtime performance in timing results. It presents the number of calls repeat following the average time to execute it timing in units.

Do you want see a more presentable output ? It is possible calling the method to_rst with the results as parameter:

Benchmark setup
import numpy
X = numpy.random.uniform(1,5,(1000,))

import scipy.spatial.distance as ssd
X = X.reshape(-1,1)
def cosine_distances(X, Y):
return 1. - ssd.cdist(X, Y, 'cosine')
Benchmark statement
cosine_distances(X, X)
namerepeattimingloopsunits
scipy.spatial 0.8.0318.3610ms

Now let's check which one is faster and which one consumes less memory. Let's create a BenchmarkSuite. It is referred as a container for benchmarks.:

Finally, let's run all the benchmarks together with the BenchmarkRunner. This class can load all the benchmarks from the suite and run each individual analysis and print out interesting reports:

Next, we will plot the relative timings. It is important to measure how faster the other benchmarks are compared to reference one. By calling the method plot_relative:

As you can see the graph aboe the scipy.spatial.distance function is 2129x slower and the sklearn approach is 19x. The best one is the numpy approach. Let's see the absolute timings. Just call the method plot_absolute:

You may notice besides the bar representing the timings, the line plot representing the memory consumption for each statement. The one who consumes the less memory is the nltk.cluster approach!

Finally, benchy also provides a full repport for all benchmarks by calling the method to_rst:

## Performance Benchmarks

These historical benchmark graphs were produced with benchy.
Produced on a machine with
• Intel Core i5 950 processor
• Mac Os 10.6
• Python 2.6.5 64-bit
• NumPy 1.6.1

### scipy.spatial 0.8.0

Benchmark setup
import numpy
X = numpy.random.uniform(1,5,(1000,))

import scipy.spatial.distance as ssd
X = X.reshape(-1,1)
def cosine_distances(X, Y):
return 1. - ssd.cdist(X, Y, 'cosine')
Benchmark statement
cosine_distances(X, X)
namerepeattimingloopsunits
scipy.spatial 0.8.0319.1910ms

### sklearn 0.13.1

Benchmark setup
import numpy
X = numpy.random.uniform(1,5,(1000,))

from sklearn.metrics.pairwise import cosine_similarity as cosine_distances
Benchmark statement
cosine_distances(X, X)
namerepeattimingloopsunits
sklearn 0.13.130.18121000ms

### nltk.cluster

Benchmark setup
import numpy
X = numpy.random.uniform(1,5,(1000,))

from nltk import cluster
def cosine_distances(X, Y):
return 1. - cluster.util.cosine_distance(X, Y)
Benchmark statement
cosine_distances(X, X)
namerepeattimingloopsunits
nltk.cluster30.010241e+04ms

### numpy

Benchmark setup
import numpy
X = numpy.random.uniform(1,5,(1000,))

import numpy, math
def cosine_distances(X, Y):
return 1. -  numpy.dot(X, Y) / (math.sqrt(numpy.dot(X, X)) *
math.sqrt(numpy.dot(Y, Y)))
Benchmark statement
cosine_distances(X, X)
namerepeattimingloopsunits
numpy30.0093391e+05ms

### Final Results

namerepeattimingloopsunitstimeBaselines
scipy.spatial 0.8.0319.1910ms2055
sklearn 0.13.130.18121000ms19.41
nltk.cluster30.010241e+04ms1.097
numpy30.0093391e+05ms1

Final code!

I might say this micro-project is still a prototype, however  I tried to build it to be easily extensible. I have several ideas to extend it, but feel free to fork it and send suggestions and bug fixes.  This project was inspired by the open-source project vbench, a framework for performance benchmarks over your source repository's history. I recommend!

For me, benchy will assist me to test several pairwise alternative functions in Crab. :)  Soon I will publish the performance results that we got with the pairwise functions that we built for Crab :)

I hope you enjoyed,

Regards,

Marcel Caraciolo

#### 2 comments:

1. Thank you for your comparison of several ways to calculate cosine similarity, it saved me time!

2. Thanks for your sharing