Making Python math 196* faster with shedskin

Dr. Michael Thomas approached me with an interesting A.I. job to see if we could speed up his neural network code from a 10 year old research platform called PlaNet. Using new Sun boxes they weren’t getting the speed-ups they expected, old libs or other monkey business were suspected.

As a first investigation I took Neil Schemenauer’s (a 200 line back-prop artificial neural network library with doc and comparison). The intention was to see how much faster the code might run using psyco and shedskin.

The results were really quite surprising, notes and src follow.

Addition – Leonardo Maffi has written a companion piece showing that his ShedSkin output is 1.5 to 7* slower than hand-coded C.  He also shows solutions using the D language and runtimes for Python 2.6 (I use Python 2.5 below).  He notes:

“I have translated the Python code to D (using my D libraries) in just few minutes, something like 15-20 minutes, and the translation was mostly painless and sometimes almost mechanical. I have translated the D code to C in many hours. Translating Python => C may require something like 20-30 times the time you need to translate Python => D + my libs. And this despite I have used a rigorous enough method to perform the translation, and despite at the end I am not sure the C code is bug-free. This is an enormous difference.”

End addition.

Addition – Robert Bradshaw has created a Cython version with src, see comments. End addition.

The run-time in minutes for the my harder test case are below.  Note that these are averages of 4 runs each:

  1. Vanilla Python 153 minutes
  2. Python + Psyco 57 minutes (2.6* faster)
  3. Shedskin 0.0.29 0.78 minutes [47 seconds] (196* faster)

The test machines uses Python 2.5.2 on Ubuntu 8.04. The box is an Intel Core Duo 2.4GHz running a single process.

The ‘hard’ problem trains the ANN using 508 patterns with 57 input neurons, 50 hidden and 62 output neurons over 1000 iterations. If you know ANNs then the configuration (0.1 learning rate, 0 momentum) might seem unusual, be assured that this is correct for my researcher’s problem.

There is a shorter version of this problem using just 2 patterns, this is useful if you want to replicate these results but don’t want to wait 3 hours on your first run.

My run times for the shorter problem are (again averaged using 4 runs):

  1. Vanilla Python 42 seconds
  2. Python + Psyco 14 seconds
  3. Shedskin 0.2 seconds (210* faster)

Shedskin has an issue with numerical stability – it seems that internally some truncation occurs with floating point math. Whilst the results for vanilla Python and Python+Psyco were identical, the results with Shedskin were similar but with fractional divergences in each result.

Whilst these divergences caused some very different results in the final weights for the ANN, my researcher confirms that all the results look equivalent.

Mark Dufour (Shedskin’s author) confirms that Python’s C double is used the same in Shedskin but notes that rounding (or a bug) may be the culprit. Shedskin is a young project, Mark will welcome extra eyes if you want to look into this.

Running the code with Shedskin was fairly easy. On Ubuntu I had to install libgc-dev and libpcre3-dev (detailed in the Shedskin docs) and g++, afterwards shedskin was ready. From download to first run was 15 minutes.

On my first attempt to compile with Shedskin I received an error as the ‘raise’ keyword isn’t yet supported. I replaced the ‘raise’ calls with ‘assert False’ for sanity, afterwards compilation was fine.

Edit – Mark notes that the basic form of ‘raise’ is supported but the version used in isn’t yet supported.  Something like ‘raise ValueError(‘some msg’)’ works fine.

Mark notes that Shedskin currently works well up to 500 lines (maybe up to 1000), since is only 200 lines compilation is quick.

Note that if you can’t use Psyco because you aren’t on x86, Shedskin might be useful to you since it’ll work anywhere that Python and g++ compile.

Running this yourself

If you want to recreate my results, download You’ll see, this is the main code. includes either ‘’ or ‘’, short is the easier 2 pattern problem and full has 508 patterns.

Note that these patterns are stored as lists of tuples (Shedskin doesn’t support the csv module so I hardcoded the input patterns to speed development), the full version is over 500 lines of Python and this slows Shedskin’s compilation somewhat.

By default the imports for Psyco are commented out and the short problem is configured. At the command line you’ll get an output like this:

Using 2 examples
ANN uses 57 input, 50 hidden, 62 output, 1000 iterations, 0.100000 learning rate, 0.000000 momentum
error 65.454309      2008-11-17 15:22:58.318593
error 45.176110      2008-11-17 15:22:59.060787
error 44.616933      2008-11-17 15:23:00.246280
error 44.026883      2008-11-17 15:23:01.743821
error 44.049276      2008-11-17 15:23:02.815876
error 44.905183      2008-11-17 15:23:03.860352
error 44.674506      2008-11-17 15:23:05.270307
error 43.365627      2008-11-17 15:23:06.757126
error 43.299160      2008-11-17 15:23:08.244466
error 42.540076      2008-11-17 15:23:09.732035
Elapsed: 0:00:41.472192

If you uncomment the two Psyco lines your code will run about 2.6* faster.

Using Shedskin

To use shedskin, first run the Python through shedskin and then ‘make’ the result. The compiled binary will run much faster than the vanilla Python code, the result below shows the short problem taking 0.19 seconds compared to 41 seconds above.

*** SHED SKIN Python-to-C++ Compiler 0.0.29 ***
Copyright 2005-2008 Mark Dufour; License GNU GPL version 3 (See LICENSE)
[iterative type analysis..]
iterations: 3 templates: 519
[generating c++ code..]
*WARNING* function (class NN, 'weights') not called!
*WARNING* function (class NN, 'test') not called!

g++  -O2 -pipe -Wno-deprecated  -I. -I/usr/lib/shedskin/lib /usr/lib/shedskin/lib/string.cpp /usr/lib/shedskin/lib/random.cpp /usr/lib/shedskin/lib/datetime.cpp examples_short.cpp bpnn_shedskin.cpp /usr/lib/shedskin/lib/builtin.cpp /usr/lib/shedskin/lib/time.cpp /usr/lib/shedskin/lib/math.cpp -lgc  -o bpnn_shedskin

Using 2 examples
ANN uses 57 input, 50 hidden, 62 output, 1000 iterations, 0.100000 learning rate, 0.000000 momentum
error 65.454309      2008-11-17 16:11:08.452087
error 44.970416      2008-11-17 16:11:08.476869
error 46.444249      2008-11-17 16:11:08.506324
error 44.209054      2008-11-17 16:11:08.519375
error 44.058518      2008-11-17 16:11:08.532430
error 45.655892      2008-11-17 16:11:08.545741
error 44.518816      2008-11-17 16:11:08.558520
error 43.643572      2008-11-17 16:11:08.571705
error 44.800429      2008-11-17 16:11:08.584241
error 43.710905      2008-11-17 16:11:08.597465
Elapsed: 0:00:00.198747

Why is the math different?

An open question remains as to why the evolution of the floating point arithmetic is different between Python and Shedskin. If anyone is interested in delving in to this, I’d be very interested in hearing from you.

Extension modules

Mark notes that the extension module support is perhaps a more useful way to use Shedskin for this sort of problem.

A single module can be compiled (e.g. ‘shedskin -e’) and with Python you just import it (e.g. ‘import module’) and use it…with a big speed-up.

This ties the code to your installed libs – not so great for easy distribution but great for lone researchers needing a speed boost.

Shedskin 0.1 in the works

Mark’s plan is to get 0.1 released over the coming months. One aim is to get the extension module to a similar level of functionality as SWIG and improve the core library support so that Shedskin comes with (some more) Batteries Included.

Mark is open to receiving code (up to 1000 lines) that doesn’t compile.  The project would always happily accept new contributors.

See the Shedskin homepage, blog and group.

Ian is a Chief Interim Data Scientist via his Mor Consulting. Sign-up for Data Science tutorials in London and to hear about his data science thoughts and jobs. He lives in London, is walked by his high energy Springer Spaniel and is a consumer of fine coffees.


  • Christian Heimes
    I'm interested to see how Cython/Pyrex fits into your benchmark. I'm using Cython a lot for company and personal work. There was also a discussion about using Cython for Python 3.1 and 2.7.
  • Hi Christian, I'd be interested in seeing that too. You can download my src above (it is just 3 files, you need 1+1 of the others for the simple or hard problem) and Leonardo's src is linked in his blog post. Just run a baseline using vanilla python on your machine so we can compare relative timings, then try your other techniques. I'd be happy to link to the results.
  • I went ahead and ran your code under Cython. The result is about the same speed as Shedskin (0.20 seconds for the small example, 44 second for the large on a Intel Core Duo 2.3Ghz running as a single process). However, I did end up doing a fair amount of static typing and malloc memory manually. In retrospect, I would highly suggest using Cython's builtin buffer support with NumPy arrays for essentially the same speed and completely automatic memory management. If some of your updates/backtracking can be rephrased as matrix multiplications then you could take advantage of a good BLAS which I would imagine would be a significant speedup. Edit - Robert's code is here:
  • Mike Hansen
    Using Numpy is only about twice as slow as Shedskin and has the advantage of making the code more clear. You can find my code and timings at They were run on a 2.0GHz Core 2 Duo with Numpy 1.2.0, Python 2.5.2 on Ubuntu 8.10.