Python advocacy in scientific computation

[Steve Holden]

sturlamolden wrote:
> Robert Kern wrote:
> 
> 
>>And you need to ask why Python is a better Matlab than Matlab?
> 
> 
> 
> First there are a few things I don't like:
> 
> 1. Intendation as a part of the syntax, really annoying.
> 
Troll. You think this is going away because *you* don't like it? Am I to 
presume that you don't bother to indent your C code according to its 
nested block structure? If you *do* indent your C code, perhaps you can 
explain the additional benefits of the braces?

> 2. The "self.something" syntax is really tedious (look to ruby)!
> 
This is done because of a preference from explicit references over 
implied ones. It does avoid a lot of namespace confusion.

By the way, anyone who can't count shouldn't be criticising programming 
languages. What happened to "3"?

> 4. Multithreading and parallel execution is impossible AFAIK because of
> the so-called GIL (global interpreter lock). Matlab is perhaps even
> worse in this respect.
> 
Right. So kindly tell us how to write thread-safe code without using a 
GIL. This is not an easy problem, and you shouldn't assume that all you 
have to do to get rid of the GIL is to wave your magic wand. There are 
deep reasons why the GIL is there.

> 5. I don't like numpy's array slicing. Array operations should be a
> part of the language, as in Matlab, Fortran 90, Ada 95, D, Octave.
> 
Slicing *is* a part of the language, inserted into the grammar (as far 
as I know) precisely to support the numeric/scientific community.
> 
> And there is a couple of questions I need answered:
> 
> 1. Can python do "pass by reference"? Are datastructures represented by
> references as in Java (I don't know yet).
> 
All assignments store references.

> 2. How good is matplotlib/pylab? I tried to install it but only get
> error messages so I haven't tested it. But plotting capabilities is
> really major issue.
> 
Good enough to keep you away, apparently ;-) (Sorry, I don't use these 
features).

> 3. Speed. I haven't seen any performance benchmarks that actually deals
> with things that are important for scientific programs.
> 
The major fact here is that no matter how fast a language is there is 
always a need for more speed in certain areas.

Suffice it to say that Python is being used for a wide range of 
scientific and engineering problems to the evident satisfaction of its 
users.

> 4. Are there "easy to use" libraries containing other stuff important
> for scientific programs, e.q. linear algebra (LU, SVD, Cholesky),
> Fourier transforms, etc. E.g. in Matlab I can just type,
> 
>    [u,s,v] = svd(x) % which calls LAPACK linked to ATLAS or
> vendor-optimized BLAS
> 
> Even though the language itself is very limited this type of library
> functionality more than makes up for it.
> 
The more people who join in and write libraries to add to the growing 
corpus of scientific and engineering libraries the sooner the answer to 
this question will be "we have everything you want".

For the moment, however, since apparently Google isn't available where 
you are, a quick search for "Python LAPACK" gave

   http://mdp-toolkit.sourceforge.net/faq.html

as its first hit. This appears to include information about how to have 
LAPACK make use of ATLAS' faster LAPACK routines. Satisfied?

> 
> I have looked for alternatives to Matlab for quite a while, mainly due
> to the cost, the åpoor speed and poor memory management. I am not sure
> it is Python but so far I have not found anything mor promising either.
> 

You know, recently the Python community has acquired a reputation in 
certain quarters for defensive support of the status quo. With 
ill-informed criticism like this from self-confessed beginners it's not 
hard to see how this myth has arisen.

I'd be very surprised if Python doesn't already give you 95% of what you 
appear to want. If you prejudices about indented code and self-relative 
references blind you to the clear advantages of the Python environment 
then frankly you are a lost cause, and good riddance.

If, on the other hand, you are prepared to engage the community and do a 
little bit of learning rather than just trolling, you may find that one 
of the most valuable features of Python is its supportive user base, 
whom at the moment you seem to be doing your best to offend.

regards
  Steve
-- 
Steve Holden       +44 150 684 7255  +1 800 494 3119
Holden Web LLC/Ltd                 www.holdenweb.com
Love me, love my blog         holdenweb.blogspot.com