[SciPy-user] More on speed comparisons

Ivo Maljevic ivo.maljevic@gmail....
Mon Jun 16 09:55:06 CDT 2008


I know, the wrong sum call was the problem. The built in mean and var don't
make any difference, as long as I include sum (which I didn't the first
time).

Thanks,
Ivo

2008/6/16 Matthieu Brucher <matthieu.brucher@gmail.com>:

> Hi,
>
> Try with complete Numpy support :
>
> # rand_test_2.py
> from numpy import random, sin, sqrt, mean, var
>
> N = 1000000
> x = random.rand(N)
> x = 3.14*sqrt(x)
> x = sin(x)
>
> mean_ = mean(x)
> var_  = var(x)
>
> print 'Mean=%g, var=%g' % (mean_, var_)
>
> You can use numpy.sum as well.
>
> Matthieu
>
> 2008/6/16 Ivo Maljevic <ivo.maljevic@gmail.com>:
> > I was planing to refrain from this, but I believe this might be an
> > interesting comparison for people who seriously think about switching to
> > SciPy/NumPy.
> >
> > Few days ago I wrote about speed comparison between the scalar and
> > vectorized versions of function calls. Based on several comments, I
> > concluded that the same story that applies to Matlab and Octave applies
> > here: vectorize thy code, and speed gain will come.
> >
> > Before I show the results of vectorized vs. non-vectorized results, just
> > want to go on the record and say that I am by no means sayhing that
> > SciPy/NumPy is not good. I still like what has been done here. There is a
> > particular scenario that I use at my work where SciPy, combined with
> > matplotlib, is extremely useful. That scenario is the following.
> >
> > In my wireless lab, I have basestations, mobile stations, whole bunch of
> > instruments and PCs either connected via network or GPIB cables (for
> > instruments).I use Python here to automate test cases and data collection
> > and the ability to do SSH and GPIB communication is very useful. Once I
> > collect data, I use SciPy for some simple postprocessing and I generate
> PNG
> > plots, and finally, I generate HTML pages with results shown as tables
> and
> > plots. So, it is all done in a single language/script instead of having
> to
> > break the processing into several languages/scripts.
> >
> > However, I wanted to see if SciPy would be good enough speedwise to
> > completely replace Matlab. An, at least for the type of processing I do,
> it
> > comes nowhere near it. I wrote a small toy program that does some simple
> > random variable manipulation in several languages. The python code
> consists
> > of two versions, one uses for loop and basic pathon libraries and the
> other
> > uses nympy's vectorized form (there was no difference between numpy and
> > scipy).
> >
> > Here are the relative results after running the code on two machines:
> >
> > 64-bit Ubunty 8.04:
> > =================
> >
> > Fortran    C       Octave    SciPy   Pure Python
> > =================================================
> > 1          1.2      2.2      16      20
> >
> >
> > 32-Bit openSUSE 10.3:
> > ==================
> >
> > Fortran    C       Octave    SciPy   Pure Python
> > =================================================
> > 1          1.2      2.4      15      19.4
> >
> >
> > The numbers are rounded a little bit, but they are in that range. I see
> two
> > problems here:
> >
> > 1. SciPy is very slow, even when compared to Octave 3.0
> > 2. It is only sligtly faster than Python with a for loop.
> >
> > Below is the source code for the two python versions. While this
> processing
> > is not from any real application,
> > it is not very different from the processing I normally do.
> >
> > Now, it is very likely that for different type of processing people will
> > find SciPy fast enough (matrix inversions, eigenvalues, etc), but for the
> > type of
> > processing I need it is not fast enough.
> >
> > Ivo
> >
> >
> ##########################################################################
> > # rand_test_1.py
> > from random import random
> > from math import sqrt, sin
> >
> > N = 1000000
> >
> > mean = 0
> > var  = 0
> >
> > for i in range(N):
> >   x = random()
> >   x = 3.14*sqrt(x)
> >   x = sin(x)
> >   mean += x
> >   var += x**2
> >
> > mean = mean/N
> > var  = var/N - mean**2
> > print 'Mean=%g, var=%g' % (mean, var)
> >
> > # rand_test_2.py
> > from numpy import random, sin, sqrt
> >
> > N = 1000000
> >
> > x = random.rand(N)
> > x = 3.14*sqrt(x)
> > x = sin(x)
> >
> > mean = sum(x)/N
> > var  = sum(x**2)/N - mean**2
> >
> > print 'Mean=%g, var=%g' % (mean, var)
> >
> >
> > _______________________________________________
> > SciPy-user mailing list
> > SciPy-user@scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-user
> >
> >
>
>
>
> --
> French PhD student
> Website : http://matthieu-brucher.developpez.com/
> Blogs : http://matt.eifelle.com and http://blog.developpez.com/?blog=92
> LinkedIn : http://www.linkedin.com/in/matthieubrucher
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