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

Yaroslav Halchenko debian at onerussian.com
Tue Jan 15 04:18:00 UTC 2008


actually for that I thought to implement a mapper at some moment... or
you can create a mapper... I think that would be the right approach...

On Mon, 14 Jan 2008, Per B. Sederberg wrote:

> 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,
> Per


> 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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> > Pkg-exppsy-maintainers at lists.alioth.debian.org
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-- 
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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