Python advocacy in scientific computation

[Robert Kern]

Re: Python advocacy in scientific computation

Brian Blais wrote:[color=blue]
> here, I've found python to be good, but not great. matplotlib (pylab) is a really
> great thing, but is not as straightforward as plotting in Matlab. Either, you have a
> window which locks the process until you close it, or you do interactive mode, but
> the window results disappear if any other window is put on top (like your shell), and
> has to be manually redrawn. This makes it far less convenient to deal with in
> interactive mode.[/color]

All I can say is that I've never seen anything like that behavior. Are you tried
using ipython in pylab mode?

--
Robert Kern
robert.kern@gma il.com

"In the fields of hell where the grass grows high
Are the graves of dreams allowed to die."
-- Richard Harter

[Brian Blais]

Re: Python advocacy in scientific computation

Robert Kern wrote:[color=blue]
>
> That said, we have an excellent array object far superior to Matlab's.
>
> http://numeric.scipy.org/
>[/color]

I'd like to ask, being new to python, in which ways is this array object far superior
to Matlab's? (I'm not being sarcastic, I really would like to know!)

I've heard similar things about matplotlib, about how it surpasses Matlab's graphics.
I haven't personally experienced this, but I'd like to know in which ways it is.



bb



--
-----------------

bblais@bryant.e du

http://web.bryant.edu/~bblais

[sturlamolden]

Re: Python advocacy in scientific computation


Robert Kern wrote:
[color=blue]
> 1. Write grant proposals.
>
> 2. Advise and teach students.[/color]

Sorry I forgot the part about writing grant applications. As for
teaching students, I have thankfully not been bothered with that too
much.


[color=blue]
> Yes, and this is why you will keep saying, "My simulation is running too
> slowly," and "My simulation is running out of memory." All the vectorization you
> do won't make a quadratic algorithm run in O(n log(n)) time. Knowing the right
> algorithm and the right data structures to use will save you programming time
> and execution time. Time is money, remember, and every hour you spend tweaking
> Matlab code to get an extra 5% of speed is just so much grant money down the drain.[/color]

Yes, and that is why I use C (that is ISO C99, not ANSI C98) instead of
Matlab for everything except trivial tasks. The design of Matlab's
language is fundamentally flawed. I once wrote a tutorial on how to
implement things like lists and trees in Matlab (using functional
programming, e.g. using functions to represent list nodes), but it's
just a toy. And as Matlab's run-time does reference counting insted of
proper garbage collection, any datastructure more complex than arrays
are sure to leak memory (I believe Python also suffered from this as
some point). Matlab is not useful for anything except plotting data
quickly. And as for the expensive license, I am not sure its worth it.
I have been considering a move to Scilab for some time, but it too
carries the burden of working with a flawed language.

[Michael Tobis]

Re: Python advocacy in scientific computation

> $ rm `find . -name "*.pyc"`

Ouch. Is that a true story?

While we're remeniscing about bad typos and DEC, I should tell the
story about the guy who clobberred his work because his English wasn't
very strong.

Under RT-11, all file management was handled by a program called PIP.
For example to get a list of files in the current working directory you
would enter PIP *.* /LI . Well this fellow, from one of those countries
where our long "e" sound is their "i" sound, mournfully announced

"I vanted a deerectory so I typed 'PIP *.* /DE' "

That one is true.

mt

[Robert Kern]

Re: Python advocacy in scientific computation

Michael Tobis wrote:[color=blue][color=green]
>> $ rm `find . -name "*.pyc"`[/color]
>
> Ouch. Is that a true story?[/color]

Yup. Fortunately, it was a small, purely personal project, so it was no huge
loss. It was enough for me to start using CVS on my small, purely personal
projects, though!

--
Robert Kern
robert.kern@gma il.com

"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

[Alex Martelli]

Re: Python advocacy in scientific computation

sturlamolden <sturlamolden@y ahoo.no> wrote:
[color=blue]
> just a toy. And as Matlab's run-time does reference counting insted of
> proper garbage collection, any datastructure more complex than arrays
> are sure to leak memory (I believe Python also suffered from this as
> some point).[/color]

Yes, that was fixed in the move from 1.5.2 to 2.0 (I don't recall if the
intermediate short-lived 1.6 also fixed it, but nobody used that
anyway;-).
[color=blue]
> Matlab is not useful for anything except plotting data
> quickly. And as for the expensive license, I am not sure its worth it.
> I have been considering a move to Scilab for some time, but it too
> carries the burden of working with a flawed language.[/color]

There was a pyscilab once, still around at
<http://pdilib.sourcefo rge.net/>, but I don't think it ever matured
beyond a "proof of concept" release 0.1 or something.


Alex

[Robert Kern]

Re: Python advocacy in scientific computation

sturlamolden wrote:[color=blue]
> Robert Kern wrote:[/color]
[color=blue][color=green]
>>Yes, and this is why you will keep saying, "My simulation is running too
>>slowly," and "My simulation is running out of memory." All the vectorization you
>>do won't make a quadratic algorithm run in O(n log(n)) time. Knowing the right
>>algorithm and the right data structures to use will save you programming time
>>and execution time. Time is money, remember, and every hour you spend tweaking
>>Matlab code to get an extra 5% of speed is just so much grant money down the drain.[/color]
>
> Yes, and that is why I use C (that is ISO C99, not ANSI C98) instead of
> Matlab for everything except trivial tasks. The design of Matlab's
> language is fundamentally flawed. I once wrote a tutorial on how to
> implement things like lists and trees in Matlab (using functional
> programming, e.g. using functions to represent list nodes), but it's
> just a toy. And as Matlab's run-time does reference counting insted of
> proper garbage collection, any datastructure more complex than arrays
> are sure to leak memory (I believe Python also suffered from this as
> some point).[/color]

Python still uses reference counting and has several very good data structures
more complex than arrays. And yet, most programs don't leak memory.
[color=blue]
> Matlab is not useful for anything except plotting data
> quickly. And as for the expensive license, I am not sure its worth it.
> I have been considering a move to Scilab for some time, but it too
> carries the burden of working with a flawed language.[/color]

And you need to ask why Python is a better Matlab than Matlab?

--
Robert Kern
robert.kern@gma il.com

"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 Kern]

Re: Python advocacy in scientific computation

Brian Blais wrote:[color=blue]
> Robert Kern wrote:
>[color=green]
>>That said, we have an excellent array object far superior to Matlab's.
>>
>> http://numeric.scipy.org/[/color]
>
> I'd like to ask, being new to python, in which ways is this array object far superior
> to Matlab's? (I'm not being sarcastic, I really would like to know!)[/color]

Matlab takes the view that "everything is a rank-2 matrix of floating point values."

Our arrays have been N-dimensional since day one. They really are arrays, not
matrices. You have complete control over the types.

--
Robert Kern
robert.kern@gma il.com

"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 advocacy in scientific computation

Robert Kern wrote:
[color=blue]
> And you need to ask why Python is a better Matlab than Matlab?[/color]


First there are a few things I don't like:

1. Intendation as a part of the syntax, really annoying.

2. The "self.something " syntax is really tedious (look to ruby)!

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.

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.


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).

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.

3. Speed. I haven't seen any performance benchmarks that actually deals
with things that are important for scientific programs.

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.


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.

[Duncan Booth]

Re: Python advocacy in scientific computation

sturlamolden wrote:
[color=blue]
> First there are a few things I don't like:
>
> 1. Intendation as a part of the syntax, really annoying.[/color]

Each to his own. I find having the compiler enforce indentation rules is a
real benefit. There's nothing quite so annoying as having 'coding
standards' you are supposed to be following which aren't enforced (so
nobody else working on the code followed them either). C code which never
executes a for loop because of a spurious ';' can be pretty annoying too.
[color=blue]
>
> 2. The "self.something " syntax is really tedious (look to ruby)![/color]

I find it really useful to use a similar style when programming in other
languages such as Java or C#. In particular it means that you can
instantly see when you are referring to a member variable (without
having to prefix them all with m_ or some other abomination) and when you
have method arguments which get assigned to member variables you don't have
to think of different names for each.
[color=blue]
>
> 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.[/color]

Multithreading and parallel execution work fine. The only problem is that
you don't get the full benefit when you have multiple processors. This one
will become more of an annoyance in the future though as more systems have
hyperthreading and multi-core processors.
[color=blue]
>
> 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).
>[/color]
Python only does "pass by reference", although it is more normally referred
to as "pass by object reference" to distinguish it from language where the
references refer to variables rather than objects.

What it doesn't do is let you rebind a variable in the caller's scope which
is what many people expect as a consequence of pass by reference. If you
pass an object to a function (and in Python *every* value is an object)
then when you mutate the object the changes are visible to everything else
using the same object. Of course, some objects aren't mutable so it isn't
that easy to tell that they are always passed by reference.

[sturlamolden]

Re: Python advocacy in scientific computation

Dennis Lee Bieber wrote:
[color=blue][color=green]
> > 1. Can python do "pass by reference"? Are datastructures represented by
> > references as in Java (I don't know yet).
> >[/color]
> Everything in Python is a reference to an object. I think the
> question you want is more on the lines of: Can I change an object that
> has been passed? Short answer: depends on what type of object is at the
> end of the reference. A mutable container object (list, dictionary,
> maybe a class instance) can have its contents changed.[/color]

Thank you.

[Evan Monroig]

Re: Python advocacy in scientific computation

> First there are a few things I don't like:

Hi, I will respond to things that others haven't responded yet
[color=blue]
> 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.[/color]

I don't know because I haven't managed to get it working either. But
other people have and I guess it should not be so difficult.

I personally use gnuplot-py (gnuplot-py.sourceforge. net) which I adapted
to the new NumPy/SciPy (see below) by searching-and-replacing "Numeric"
by "numpy". It allows to use raw gnuplot commands.
[color=blue]
> 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[/color]

Yes !

There is the excellent SciPy package, which you can get at www.scipy.org

Personnally I use it a lot for linear algebra (linked to
LAPACK/ATLAS/BLAS), but there are also libraries for statistics,
optimization, signal processing, etc.

There has been many changes recently, including package names, so don't
get confused and be sure to get recent versions of NumPy and SciPy ;).

Evan

[Alex Martelli]

Re: Python advocacy in scientific computation

Robert Kern <robert.kern@gm ail.com> wrote:
...[color=blue][color=green]
> > just a toy. And as Matlab's run-time does reference counting insted of
> > proper garbage collection, any datastructure more complex than arrays
> > are sure to leak memory (I believe Python also suffered from this as
> > some point).[/color]
>
> Python still uses reference counting and has several very good data structures
> more complex than arrays. And yet, most programs don't leak memory.[/color]

Python uses reference counting *AND* cyclic-garbage collection for the
kind of garbage that wouldn't go away by RC due to reference-cycles
(plus, also, weak references for yet another helper). To leak memory
despite all of that, you really need to do it on purpose (e.g. via a
C-coded container extension-type that does NOT play nice with gc;-).


Alex

[Steve Holden]

Re: Python advocacy in scientific computation

sturlamolden wrote:[color=blue]
> Robert Kern wrote:
>
>[color=green]
>>And you need to ask why Python is a better Matlab than Matlab?[/color]
>
>
>
> First there are a few things I don't like:
>
> 1. Intendation as a part of the syntax, really annoying.
>[/color]
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?
[color=blue]
> 2. The "self.something " syntax is really tedious (look to ruby)!
>[/color]
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"?
[color=blue]
> 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.
>[/color]
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.
[color=blue]
> 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.
>[/color]
Slicing *is* a part of the language, inserted into the grammar (as far
as I know) precisely to support the numeric/scientific community.[color=blue]
>
> 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).
>[/color]
All assignments store references.
[color=blue]
> 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.
>[/color]
Good enough to keep you away, apparently ;-) (Sorry, I don't use these
features).
[color=blue]
> 3. Speed. I haven't seen any performance benchmarks that actually deals
> with things that are important for scientific programs.
>[/color]
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.
[color=blue]
> 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.
>[/color]
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?
[color=blue]
>
> 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.
>[/color]

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.blogs pot.com

[Michael Tobis]

Re: Python advocacy in scientific computation

1) indentation:

I claim that this is a trivial matter. Indentation is enforced, but if
you want to end all your blocks with #end, feel free.

Or write a preprocessor to go from your preferred block style to
python's

2) self.something tedious to look at.

Again, you can somewhat work around this if you like. Just use "s" or
"_" instead of "self".

3) missing

4) multithreading and parallel execution impossible

This is simply false, though admittedly the MPI libraries need a little
work. Mike Steder of our group is likely to release an alternative. A
good way to think of Python is as a powerful extension to C. So using
MPI from Python just amounts to setting up a communicator in C and
wrapping the MPI calls.

As for less tightly coupled threads on a single processor, Python is
adept at it. I think the issues with multiple processors are much more
those of a server farm than those of a computational cluster.

We have been encountering no fundamental difficulty in cluster programs
using Python.

5) "I don't like numpy's array slicing" ?

this is unclear. It is somewhat different form Matlab's, but much more
powerful.

1) pass by reference

Python names are all references. The model is a little peculiar to
Fortran and C people, but rather similar to the Java model.

2) matplotlib

A correct install can be difficult, but once it works it rocks. ipython
(a.k.a. pylab) is also a very nice work environment.

3D plots remain unavailable at present.

3) speed

Speed matters less in Python than in other languages because Python
plays so well with others. For many applications, NumPy is fine.
Otherwise write your own C or C++ or F77; building the Python bindings
is trivial. (F9* is problematic, though in fact we do some calling of
F90 from Python using the Babel toolkit)

4) useful libraries

yes. for your svd example see Hinsen's Scientific package. In general,
Python's claim of "batteries included" applies to scientific code.

mt