[Pkg-exppsy-maintainers] Was: ridge... now VALGRIND time
Per B. Sederberg
persed at princeton.edu
Tue Jan 15 19:22:22 UTC 2008
I'd like to provide a small sample dataset for ya'll to try (it breaks
on a single split of my NFoldSplitter, so it's not a lot of data and
it's also been preprocessed and feature-selected by that point),
however, what is a good way to export it?
As an aside, this is one of my main complaints about python and numpy
is that there is no standard data format that I can write out that I
can be sure people can read in. If I pickle it, then if you have a
slightly different architeture or version then you may have problems
reading it in. It's a pain to save things to text files because then
you have to read them back in.
Given that I've already preprocessed and reduced the dimensions of
these data, it doesn't make sense to use the original niftidataset and
write it out to nifti. Sadly, the best format for writing out a bunch
of ndarrays may be a matlab mat file via scipy.io.savemat and
scipy.io.loadmat. This seems ridiculous to me.
Soooo, do you have any suggestions for better ways to export a couple
ndarrays so you can easily load them in and create a dataset?
Thanks,
Per
On Jan 15, 2008 6:07 AM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> might be might be but I can't say for sure... it might be that our code
> brought it there somehow? may be you should enable debugging output so
> valgrind output is interspersed with informative debugging information?
> may be you could share small sample of dataset on which it still is the
> case (have you tried it on smaller/toy dataset)?
>
>
> On Tue, 15 Jan 2008, Per B. Sederberg wrote:
>
> > 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
>
> > > > > _______________________________________________
> > > > > Pkg-exppsy-maintainers mailing list
> > > > > 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
>
> > > _______________________________________________
> > > Pkg-exppsy-maintainers mailing list
> > > Pkg-exppsy-maintainers at lists.alioth.debian.org
> > > http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-maintainers
>
>
> > per at flow:~/fmri/frSemTem/scripts$ ~/code/pymvpa/tools/valgrind-python mvpa_cv.py frST003
> > ==31548== Memcheck, a memory error detector.
> > ==31548== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
> > ==31548== Using LibVEX rev 1804, a library for dynamic binary translation.
> > ==31548== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
> > ==31548== Using valgrind-3.3.0-Debian, a dynamic binary instrumentation framework.
> > ==31548== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
> > ==31548== For more details, rerun with: -v
> > ==31548==
> > Loading regressors
> > Loading the dataset
> > ==31548== Warning: set address range perms: large range 376569856 (defined)
> > ==31548== Warning: set address range perms: large range 376569856 (undefined)
> > ==31548== Warning: set address range perms: large range 140388976 (undefined)
> > ==31548== Warning: set address range perms: large range 376569888 (noaccess)
> > ==31548== Warning: set address range perms: large range 376569888 (noaccess)
> > Z-scoring by chunk
> > ==31548== Warning: set address range perms: large range 561555904 (undefined)
> > ==31548== Warning: set address range perms: large range 140389008 (noaccess)
> > Selecting TRs of interest
> > Processing Split 0
> > Selecting top features
> > Training and Testing Classifier
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E4869F: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4b8 is 8 bytes after a block of size 880,000 alloc'd
> > ==31548== at 0x4024AB8: malloc (vg_replace_malloc.c:207)
> > ==31548== by 0x47A9B19: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABDB3: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABF31: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BB4C6: PyEval_EvalCode (in /usr/bin/python2.4)
> > ==31548== by 0x80DE71C: PyRun_FileExFlags (in /usr/bin/python2.4)
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E487A0: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E487EB: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x4E488A8: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4b8 is 8 bytes after a block of size 880,000 alloc'd
> > ==31548== at 0x4024AB8: malloc (vg_replace_malloc.c:207)
> > ==31548== by 0x47A9B19: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABDB3: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABF31: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BB4C6: PyEval_EvalCode (in /usr/bin/python2.4)
> > ==31548== by 0x80DE71C: PyRun_FileExFlags (in /usr/bin/python2.4)
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x4E489BA: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x4E489FD: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E48FA5: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4b8 is 8 bytes after a block of size 880,000 alloc'd
> > ==31548== at 0x4024AB8: malloc (vg_replace_malloc.c:207)
> > ==31548== by 0x47A9B19: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABDB3: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABF31: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BB4C6: PyEval_EvalCode (in /usr/bin/python2.4)
> > ==31548== by 0x80DE71C: PyRun_FileExFlags (in /usr/bin/python2.4)
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E49086: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E490CA: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E4911A: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4d0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E49149: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4d8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E49179: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4e0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid write of size 8
> > ==31548== at 0x4E491B2: dlasd7_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4e8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F67F9: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4b8 is 8 bytes after a block of size 880,000 alloc'd
> > ==31548== at 0x4024AB8: malloc (vg_replace_malloc.c:207)
> > ==31548== by 0x47A9B19: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABDB3: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x47ABF31: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BB4C6: PyEval_EvalCode (in /usr/bin/python2.4)
> > ==31548== by 0x80DE71C: PyRun_FileExFlags (in /usr/bin/python2.4)
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F6804: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== by 0x4E47E77: dlasd6_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E4C6F2: dlasda_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4E174A4: dlalsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x4DB2890: dgelsd_ (in /usr/lib/liblapack.so.3.0)
> > ==31548== by 0x5B99B79: (within /usr/lib/python-support/python-numpy/python2.4/numpy/linalg/
> > lapack_lite.so)
> > ==31548== by 0x80B9ECB: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== Address 0x2063e4c8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F6844: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e4e0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F684A: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e4e8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F684E: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e4f0 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F6854: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e4f8 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F685A: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e500 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F6860: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e508 is not stack'd, malloc'd or (recently) free'd
> > ==31548==
> > ==31548== Invalid read of size 8
> > ==31548== at 0x52F6866: dcopy_ (in /usr/lib/libblas.so.3.0)
> > ==31548== Address 0x2063e510 is not stack'd, malloc'd or (recently) free'd
>
> > valgrind: m_mallocfree.c:194 (mk_plain_bszB): Assertion 'bszB != 0' failed.
> > ==31548== at 0x3801806D: report_and_quit (m_libcassert.c:140)
> > ==31548== by 0x38018361: vgPlain_assert_fail (m_libcassert.c:200)
> > ==31548== by 0x3802156A: mkFreeBlock (m_mallocfree.c:194)
> > ==31548== by 0x380217BD: vgPlain_arena_free (m_mallocfree.c:1284)
> > ==31548== by 0x38033548: vgPlain_cli_free (replacemalloc_core.c:108)
> > ==31548== by 0x38001C11: die_and_free_mem (mc_malloc_wrappers.c:122)
> > ==31548== by 0x38002687: vgMemCheck_free (mc_malloc_wrappers.c:319)
> > ==31548== by 0x38035B6F: vgPlain_scheduler (scheduler.c:1269)
> > ==31548== by 0x38048B18: run_a_thread_NORETURN (syswrap-linux.c:89)
>
> > sched status:
> > running_tid=1
>
> > Thread 1: status = VgTs_Runnable
> > ==31548== at 0x402465C: free (vg_replace_malloc.c:323)
> > ==31548== by 0x47B420D: (within /usr/lib/python-support/python-numpy/python2.4/numpy/core/mu
> > ltiarray.so)
> > ==31548== by 0x8100F33: (within /usr/bin/python2.4)
> > ==31548== by 0x80BAEE2: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BA7BA: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BA8ED: PyEval_EvalFrame (in /usr/bin/python2.4)
> > ==31548== by 0x80BB365: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > ==31548== by 0x80BB4C6: PyEval_EvalCode (in /usr/bin/python2.4)
> > ==31548== by 0x80DE71C: PyRun_FileExFlags (in /usr/bin/python2.4)
> > ==31548== by 0x80DE948: PyRun_SimpleFileExFlags (in /usr/bin/python2.4)
> > ==31548== by 0x8057679: Py_Main (in /usr/bin/python2.4)
> > ==31548== by 0x8056AD1: main (in /usr/bin/python2.4)
>
>
> > Note: see also the FAQ.txt in the source distribution.
> > It contains workarounds to several common problems.
>
> > If that doesn't help, please report this bug to: www.valgrind.org
>
> > In the bug report, send all the above text, the valgrind
> > version, and what Linux distro you are using. Thanks.
>
>
>
> --
>
> 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
>
> _______________________________________________
> Pkg-exppsy-maintainers mailing list
> Pkg-exppsy-maintainers at lists.alioth.debian.org
> http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-maintainers
>
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