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

[Per B. Sederberg]

Sadly, it looks like the error is in lapack.  I'm attaching the output
of the valgrind call.  If you have a sec, can you take a glance at it
to verify that it is indeed an error in lapack or blas?

Thanks,
Per


On Jan 14, 2008 11:18 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> 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
> > > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-maintainers
>
>
>
> --
>
> 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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