[Pkg-exppsy-maintainers] Was: ridge... now VALGRIND time

Per B. Sederberg persed at princeton.edu
Tue Jan 15 04:16:14 UTC 2008

Hi Yarik:

Thanks for the tip, I'll try it out.  As for the bug being in my code,
I like to assume that it's me until I can prove otherwise.  We
programmers are humans that are good at telling the computer to do
something incorrectly :)

I'm also going to augment the ridge regression code to optionally
center and scale the data before calculating the regression.

Have a good night,

On Jan 14, 2008 11:10 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> what numpy version is that?
> I wonder what would happen if you valgrind it? I added suppression file
> where I enabled all recommended suppressions for non-patched (to do so)
> python.
> unfortunately on our cluster (amd64 etch) I run into lots of msgs
> similar to reported on
> http://projects.scipy.org/pipermail/numpy-tickets/2006-November/000528.html
> but I will backport numpy and install it -- may be it will fix some of
> them
> on i386 sid box it is not that bad but also puked a bit. I adjusted
> suppressions (they are under tools), so now just use THE TOOL, in a way:
> tools/valgrind_python blah.py
> where blah.py is your code. Running it on almost (it is still running
> since it is slow but so far it is salient) all the tests is salient
> (verify that first since I adjusted suppressions only for somewhat
> uptodate Debian sid i686 with python2.4).
> so if it pukes out smth on your data (but not on tests) -- see
> where that happens -- it might provide you with a hint.
> Indeed I bet it is not your code, although everything could happen -- I
> can write a single line with quite a few subtle bugs ( ;-) )
> > I'm actually having a big error with it right now, however, which is
> > segfaulting python when trying to free some memory.  Both the unit
> > test and the pylab example (modified to use RidgeReg) run without a
> > problem, but when I try and use it to train on my real data it
> > segfaults upon returning from the self._train call:
> > > /usr/lib/python2.4/site-packages/mvpa/clfs/classifier.py(164)train()
> > -> result = self._train(dataset)
> > (Pdb) n
> > *** glibc detected *** python: free(): invalid pointer: 0x914e5008 ***
> > I don't see anything wrong in my code, so my current guess is that
> > it's an error in numpy.
> --
> Yaroslav Halchenko
> Research Assistant, Psychology Department, Rutgers-Newark
> Student  Ph.D. @ CS Dept. NJIT
> Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171
>         101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102
> WWW:     http://www.linkedin.com/in/yarik
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