Python is slow?

[Kay Schluehr]

Re: Python is slow?

On 23 Sep., 21:23, J Peyret <jpey...@gmail. comwrote:

On Sep 23, 8:31 am, bearophileH...@ lycos.com wrote:
>
Guys, this looks like a great data structure/algo for something I am
working on.
>
But... where do I find some definitions of the original BK-tree idea?

*geometric data structures*. Just google for it.

[Robert Kern]

Re: Python is slow?

sturlamolden wrote:

On Sep 23, 9:17 pm, Robert Kern <robert.k...@gm ail.comwrote:
>

>You could also drop it on the scipy.org wiki in the Cookbook category.

>
Yes, if I could figure out how to use it...

What's confusing? You do have to create a profile:

http://www.scipy.org/UserPreferences

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

[sturlamolden]

Re: Python is slow?

On Sep 23, 10:05 pm, Robert Singer <rsinger@____.c omwrote:

May I ask what are your main objections to it ?

1. gfortran is not Absoft.

2. If I program the same in C99 and Fortran 95, and compile with gcc
and gfortran, the C99 code runs a lot faster (I've only tested with
wavelet transforms).

3. gfortran is not Absoft.

[sturlamolden]

Re: Python is slow?

On Sep 23, 10:16 pm, Robert Kern <robert.k...@gm ail.comwrote:

What's confusing? You do have to create a profile:

How do I add a new page to the wiki? I'm only able to edit the front
page of the cookbook. But it doesn't help to add link there if I have
no page to link. (I may be incredibly stupid though.)

[Robert Kern]

Re: Python is slow?

sturlamolden wrote:

On Sep 23, 10:16 pm, Robert Kern <robert.k...@gm ail.comwrote:
>

>What's confusing? You do have to create a profile:

>
How do I add a new page to the wiki? I'm only able to edit the front
page of the cookbook. But it doesn't help to add link there if I have
no page to link. (I may be incredibly stupid though.)

You just navigate to the URL you want:

http://www.scipy.org/Cookbook/KDTree

This will show you a page saying:

"""
This page does not exist yet. You can create a new empty page, or use one of the
page templates. Before creating the page, please check if a similar page already
exists.

Create new empty page
"""

The latter is a link that you can click.

Looking at the other Cookbook page sources, I notice that you should add the
following to the bottom of your page to categorize it appropriately.

"""
----
. CategoryCookboo k
"""

Then put the link on the main Cookbook page (or do that first, then navigate
through the link to create the page).

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

[Robert Singer]

Re: Python is slow?

On Tue, 23 Sep 2008 13:34:10 -0700 (PDT), sturlamolden
<sturlamolden@y ahoo.nowrote:

>1. gfortran is not Absoft.

I find this comment absurd. What did you mean by it ?
Yes, gfortran is not Absoft, just as red is not blue (?!).

I also don't understand whether you're looking for a free or a
commercial compiler. I got the impression from your previous post that
money was an object.

>2. If I program the same in C99 and Fortran 95, and compile with gcc
>and gfortran, the C99 code runs a lot faster (I've only tested with
>wavelet transforms).

Hmm. Unfortunatelly, i have none whatsoever experience in that field.
Completely different area of study here, so without seeing at least
some code, I cannot comment anything on that part.

And 'a lot faster' is a very relative term.

>
>3. gfortran is not Absoft.
>

True.

Best regards
Bob

[sturlamolden]

Re: Python is slow?

On Sep 23, 8:52 pm, bearophileH...@ lycos.com wrote:

Is this a good or bad thing? ;-)

It seems we have been implementing different algorithms. kd-trees are
not BK-trees.

http://www.scipy.org/Cookbook/KDTree

[Robert Kern]

Re: Python is slow?

Robert Kern wrote:

J Peyret wrote:

>On Sep 23, 8:31 am, bearophileH...@ lycos.com wrote:
>>
>Guys, this looks like a great data structure/algo for something I am
>working on.
>>
>But... where do I find some definitions of the original BK-tree idea?

>
Uh, actually we're talking about kd-trees, not BK-trees. kd-trees are
for searching through point sets in a k-dimensional space.

My apologies. I did not actually follow bearophile's link, and thought he was
talking about kd-trees like Sturla was.

--
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
that is made terrible by our own mad attempt to interpret it as though it had
an underlying truth."
-- Umberto Eco

[bearophileHUGS@lycos.com]

Re: Python is slow?

sturlamolden:

It seems we have been implementing different algorithms. kd-trees are
not BK-trees.
http://www.scipy.org/Cookbook/KDTree

Sorry for my silly mistake :-)

Note: in your code I don't know if the collections.deq ue data
structure may help (it's faster than list for appending), but I
presume that's not a bottleneck.

Bye,
bearophile

[Eric Brunel]

Re: Python is slow?

On Tue, 23 Sep 2008 15:23:12 +0200, sturlamolden <sturlamolden@y ahoo.no>
wrote:
[...]

Would it be possible to post this text to some "persistent " web page with
(links to) the code you wrote in both languages? This would be a very
interesting resource for people experiencing some resistence when they
suggest Python as a possible language because of the 'Python is slow'
myth...
--
python -c "print ''.join([chr(154 - ord(c)) for c in
'U(17zX(%,5.zmz 5(17l8(%,5.Z*(9 3-965$l7+-'])"

[sturlamolden]

Re: Python is slow?


For those who are interested:

I've updated the cookbook tutorial on the kd-tree:

http://scipy.org/Cookbook/KDTree

It now also includes parallel search for multicore CPUs
(multiprocessin g standard module). Even if you are not genuinely
interested in kd-trees, it shows how to do parallel processing in
Python despite of the GIL.

[sturlamolden]

Re: Python is slow?


I have updated the cookbook entry for yesterday to also include
parallel processing for large data sets. Even if you're not interested
in kd-trees, it is a good example of what the new multiprocessing
standard module can do. There are still people being scared by the
GIL, thinking it prevents Python from utilizing multicore processors.

http://www.scipy.org/Cookbook/KDTree

[David Cournapeau]

Re: Python is slow?

On Wed, Sep 24, 2008 at 3:07 AM, sturlamolden <sturlamolden@y ahoo.nowrote:

On Sep 23, 3:44 pm, Robert Singer <rsinger@____.c omwrote:
>

>Well, python is not a number crunching language. However much we would
>like it to be (we would ? :-).

>

>No scripting language is.

>
Not even Matlab, R, IDL, Octave, SciLab, S-PLUS or Mathematica?

I am fairly experienced in matlab (have been using it extensively for
5 years in academical context), and now with numpy, and generally,
they are comparable speed-wise. Matlab has some niceties which makes
it faster in some simple cases (JIT for loops, function calls faster,
sometimes COW semantics means it faster), but numpy (at its core at
least) is much more powerful IMHO. Also, matlab is horrible when you
want to interface some C to it (the C api is basically broken; in
particular, there is no way to gurantee you won't leak memory when you
Ctrl+C custom C extensions because the C api does not have facility to
deal with signals). I totally gave up matlab for numpy 2 years ago,
and never regretted it.

I think speed is not the issue when comparing matlab, R and co.
Availability of functionalities matter much more. R is quite hard to
beat if you need to do advanced statistics, specially since it is the
tool of choice for most academic statisticians. I hope numpy/scipy
will be there sometime, but it is honestly still quite far in that
domain.

cheers,

David

[Aahz]

Re: Python is slow?

In article <Y7CdnYRzU-8naEXVnZ2dnUVZ_ sDinZ2d@posted. visi>,
Grant Edwards <grante@visi.co mwrote:

>
>AFAICT, _everybody_ is bad at programming C++.
>
>One begins to suspect it's not the fault of the programmers.

http://www.netfunny.com/rhf/jokes/98/May/stroustrup.html

--
Aahz (aahz@pythoncra ft.com) <* http://www.pythoncraft.com/

"Argue for your limitations, and sure enough they're yours." --Richard Bach

[Fly Away]

Re: Python is slow?

Matlab's strongest side is data visualization though. Although we have
matplotlib, mayavi and possibility of interfacing with gnuplot, it's
not anywhere near the capabilities of Matlab.

What particular Matlab visualization features are you referring to? I
can't think of anything that would justify using the "not anywhere
near" term.

Cheers,
Victor.