Python is slow?

Robert Singer rsinger at
Tue Sep 23 15:44:56 CEST 2008

On Tue, 23 Sep 2008 06:23:12 -0700 (PDT), sturlamolden
<sturlamolden at> wrote:

>I have recently been playing with a kd-tree for solving the "post
>office problem" in a 12-dimensional space. This is pure cpu bound
>number crunching, a task for which I suspected Python to be

Well, python is not a number crunching language. However much we would
like it to be (we would ? :-). No scripting language is.
Developing time is shorter, I agree, but when you have, for example a
problem which takes 8,31 minutes to go through in optimized fortran
code (like the one I had the other day), then that hardly matters.

>My prototype in Python 2.5 using NumPy required 0.41 seconds to
>construct the tree from 50,000 samples. Unfortunately, searching it
>felt a bit slow, finding the 11 nearest-neighbours of 1,000 points
>took 29.6 seconds (and there were still 49,000 to go). Naturally, I
>blamed this on Python. It would be 100 times faster if I used C++,

Not necessarily.
Before resorting to rewriting the problem try psyco. It speeds up
things sometimes.
Also, (I'm not that familiar with python yet, so I don't know how to
do it in python), try finding the bottlenecks of your calculation. Are
the loops where most of the processing time is wasted, or disk
accessing, or ... ?

>After having a working Python prototype, I resorted to rewrite the
>program in C++. The Python prototype took an hour to make, debug and
>verify. The same thing in C++ took me almost a day to complete, even
>with a working prototype as model. To my surprise, the resulting beast
>of C++ required 64.3 seconds to construct the same kd-tree. Searching
>the tree was not faster either, 1,000 points required 38.8 seconds. I
>wasted a day, only to find my Python prototype being the faster.

>We may conclude that I'm bad at programming C++, but I suspect that is
>not the case here. Albeit micro-benchmarks may indicate that Python is
>100-200 times slower than C++, they may not be applicable to the real
>world. Python can be very efficient. And when combined with libraries
>like NumPy, beating it's performance with hand-crafted C++ is
>difficult. At least, my 10 years experience programming scientific
>software in various languages was not sufficient to beat my own Python
>prototype with C++.
>That is not to say I have never seen C++ run a lot faster than Python.
>But it tends to be very short pieces of CPU bound code, no more than a
>function or two. But as the problem grows in complexity, C++
>accumulates too much of its own bloat.

Well, personally, I try to combine fortran (being a fortran programmer
by trade) with python (in the last few years), as I find fortran to
be, by two grades, more comfortable for solving scientific problems
then c (or python for that matter, although it has its merits).
Starting from ith his capabilities for "normal" array handling, to
optimisation and easy readability, to whatnot.

Best regards

More information about the Python-list mailing list