[Pkg-exppsy-maintainers] Segfault example

Yaroslav Halchenko debian at onerussian.com
Thu Jan 17 00:55:03 UTC 2008 

cool... so I think now it is even more important to file a but against
numpy ;-) good catch!

As for confusion -- you hit a stone -- time to refactor... I think we
might better have Classifier and Regressor (both childs of Machine). It
gets convoluted at SVM interface a bit since SVMBase does everything but
things might change ;)
then Regressor's wouldn't have confusion matrix at all, but should have
some error associated to keep training error (RMSE most common right?)

On Wed, 16 Jan 2008, Per B. Sederberg wrote:

> Now here's a new turn!

> If I change over to using the scipy.linalg.lstsq instead of
> numpy.linalg.lstsq it works on my machine!

> So, that really points to a numpy bug.

> I'm switching the code in pymvpa and will test some more.

> It also doesn't make sense to run a confusion matrix on the ridge
> regression so I'm going to turn that off for that classifier.

> Latro,
> P

> On Jan 16, 2008 5:49 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:

> > > I'll file that bug and see if anyone responds.
> > yeah... buzz us again if nothing happens... we might do some bughunting
> > party ;-)

> > > Yes, my new laptop can run amd64 (Intel Core 2 Duo), but I didn't put
> > > / in a logical drive, so it'll be a bit more difficult to do the
> > > reinstallation.  I sure would like to start over, but I have a pretty
> > > happy system right now and I'm reluctant to start fiddlin'.
> > don't you have any free space left? I am not sure if you have LVM or
> > not... if there is a partition with lots of space you can easily shrink
> > it ;-)

> > or another approach would simply be -- install amd64 kernel (instead of
> > default i686 which comes with i686 arch) from amd64 architecture (just
> > --force-architecture... and with 2.6.24 I think there would be no
> > difference between the two so it would not be even needed to mangle that
> > way) and install amd64 chroot anywhere where you have space. This way
> > you will have fully functional amd64 environment

> > > And yes, it's Debian (Lenny for the most part) and I don't plan on
> > > going back to Ubuntu :).  I could use some more ammunition to convince
> > > others in my lab, but at least I'm in Debian-land.
> > that is great that you got Debian working and I hope it wasn't too much
> > of hassle (besides some peculiarities).
> > At least with Debian you will get the freshest releases of what we do
> > for Debian ;-)


> > > P


> > > > On Wed, 16 Jan 2008, Per B. Sederberg wrote:

> > > > > Here ya go:

> > > > > $ dpkg -l refblas3 lapack3
> > > > > ||/ Name                Version             Description
> > > > > +++-===================-===================-======================================================
> > > > > ii  lapack3             3.0.20000531a-6.1   library of linear algebra
> > > > > routines 3 - shared version
> > > > > ii  refblas3            1.2-8               Basic Linear Algebra
> > > > > Subroutines 3, shared library



> > > > > On Jan 16, 2008 5:17 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> > > > > > oppa - so what libraries of lapack/blas are used?

> > > > > > although now it seems that the main possible factor is an architecture
> > > > > > -- we have it failing on i386 but not on amd64... let me also give a
> > > > > > spin on ia64


> > > > > > On Wed, 16 Jan 2008, Per B. Sederberg wrote:

> > > > > > > Here's mine:

> > > > > > > $ uname -a
> > > > > > > Linux flow 2.6.23-1-686 #1 SMP Fri Dec 21 13:57:07 UTC 2007 i686 GNU/Linux

> > > > > > > $ dpkg -l python-numpy atlas3-base python2.4  libc6
> > > > > > > Desired=Unknown/Install/Remove/Purge/Hold
> > > > > > > | Status=Not/Installed/Config-files/Unpacked/Failed-config/Half-installed
> > > > > > > |/ Err?=(none)/Hold/Reinst-required/X=both-problems (Status,Err: uppercase=bad)
> > > > > > > ||/ Name                Version             Description
> > > > > > > +++-===================-===================-======================================================
> > > > > > > un  atlas3-base         <none>              (no description available)
> > > > > > > ii  libc6               2.7-5               GNU C Library: Shared libraries
> > > > > > > ii  python-numpy        1:1.0.4-5           Numerical Python adds a
> > > > > > > fast array facility to the Pyt
> > > > > > > ii  python2.4           2.4.4-7             An interactive high-level
> > > > > > > object-oriented language (ve


> > > > > > > P

> > > > > > > On Jan 16, 2008 5:06 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> > > > > > > > What I meant is smth like

> > > > > > > > $> uname -a
> > > > > > > > Linux belka 2.6.22-2-686 #1 SMP Fri Aug 31 00:24:01 UTC 2007 i686
> > > > > > > > GNU/Linux

> > > > > > > > *$> dpkg -l python-numpy atlas3-base python2.4  libc6
> > > > > > > > ii  atlas3-base    3.6.0-20.6     Automatically Tuned Linear Algebra Software,
> > > > > > > > ii  libc6          2.7-2          GNU C Library: Shared libraries
> > > > > > > > ii  python-numpy   1:1.0.3-1      Numerical Python adds a fast array facility
> > > > > > > > ii  python2.4      2.4.4-5        An interactive high-level object-oriented la

> > > > > > > > I will check it on amd64 box too...


> > > > > > > > On Wed, 16 Jan 2008, Per B. Sederberg wrote:

> > > > > > > > > Veeerrry interesting!

> > > > > > > > > I, too, ran on a i386 machine, but Michael's was running amd64.  My
> > > > > > > > > numpy version is:

> > > > > > > > > $ python2.4
> > > > > > > > > Python 2.4.4 (#2, Jan  3 2008, 13:36:28)
> > > > > > > > > [GCC 4.2.3 20071123 (prerelease) (Debian 4.2.2-4)] on linux2
> > > > > > > > > Type "help", "copyright", "credits" or "license" for more information.
> > > > > > > > > >>> import numpy
> > > > > > > > > >>> numpy.version.version
> > > > > > > > > '1.0.4'


> > > > > > > > > Thanks for trying it out.  I have yet to find anything on the web
> > > > > > > > > about this, but will let you know if I do.

> > > > > > > > > Thanks,
> > > > > > > > > Per


> > > > > > > > > On Jan 16, 2008 4:54 PM, Yaroslav Halchenko <debian at onerussian.com> wrote:
> > > > > > > > > > Sorry I didn't follow up -- I did run and reproduced -- it puked many times and
> > > > > > > > > > at the end with (which is I think what you got also). I was going to debug it a
> > > > > > > > > > bit more but yet had a chance... will do later...  From Michael we should get
> > > > > > > > > > versions of involved packages (numpy, blas, lapack) to see what makes the
> > > > > > > > > > difference... Also - I ran it on i386 box...  what did you run it on?

> > > > > > > > > > ==10429== Invalid read of size 4
> > > > > > > > > > ==10429==    at 0x503DD6D: ATL_dcopy_xp1yp1aXbX (in /usr/lib/atlas/libblas.so.3.0)
> > > > > > > > > > ==10429==  Address 0x5A8B5A0 is 8 bytes after a block of size 880,000 alloc'd
> > > > > > > > > > ==10429==    at 0x40244B0: malloc (vg_replace_malloc.c:149)
> > > > > > > > > > ==10429==    by 0x470FCA0: (within /usr/lib/python2.4/site-packages/numpy/core/multiarray.so)
> > > > > > > > > > ==10429==    by 0x4711EF3: (within /usr/lib/python2.4/site-packages/numpy/core/multiarray.so)
> > > > > > > > > > ==10429==    by 0x4712071: (within /usr/lib/python2.4/site-packages/numpy/core/multiarray.so)
> > > > > > > > > > ==10429==    by 0x80B9C49: PyEval_EvalFrame (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80BB0E4: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80B9319: PyEval_EvalFrame (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80B99C3: PyEval_EvalFrame (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80B99C3: PyEval_EvalFrame (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80BB0E4: PyEval_EvalCodeEx (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80BB156: PyEval_EvalCode (in /usr/bin/python2.4)
> > > > > > > > > > ==10429==    by 0x80DDF79: PyRun_FileExFlags (in /usr/bin/python2.4)
> > > > > > > > > > --10429-- VALGRIND INTERNAL ERROR: Valgrind received a signal 11 (SIGSEGV) - exiting
> > > > > > > > > > --10429-- si_code=1;  Faulting address: 0x4;  sp: 0x6250EDBC

> > > > > > > > > > valgrind: the 'impossible' happened:
> > > > > > > > > >    Killed by fatal signal
> > > > > > > > > > ==10429==    at 0x3801FFEA: unlinkBlock (m_mallocfree.c:314)
> > > > > > > > > > ==10429==    by 0x380208A0: vgPlain_arena_free (m_mallocfree.c:1162)
> > > > > > > > > > ==10429==    by 0x38036501: vgPlain_cli_free (replacemalloc_core.c:108)
> > > > > > > > > > ==10429==    by 0x38001A1B: die_and_free_mem (mc_malloc_wrappers.c:111)
> > > > > > > > > > ==10429==    by 0x38036C82: do_client_request (scheduler.c:1158)
> > > > > > > > > > ==10429==    by 0x380385A0: vgPlain_scheduler (scheduler.c:869)
> > > > > > > > > > ==10429==    by 0x38058946: run_a_thread_NORETURN (syswrap-linux.c:87)

> > > > > > > > > > sched status:
> > > > > > > > > >   running_tid=1

> > > > > > > > > > Thread 1: status = VgTs_Runnable
> > > > > > > > > > ==10429==    at 0x40240CA: free (vg_replace_malloc.c:233)
> > > > > > > > > > ==10429==    by 0x505495E: ATL_dmmJIK (in /usr/lib/atlas/libblas.so.3.0)




> > > > > > > > > > On Wed, 16 Jan 2008, Per B. Sederberg wrote:

> > > > > > > > > > > Hi Yarik:

> > > > > > > > > > > Did you have the chance to run the ridge regression example code that
> > > > > > > > > > > is breaking on my machine?  Michael ran it on his machine and could
> > > > > > > > > > > not reproduce the error.

> > > > > > > > > > > This is getting quite weird and I'm not sure where to go from here.
> > > > > > > > > > > It breaks at the same point (returning from the _train call) for all
> > > > > > > > > > > of my actual data.  The call to the numpy.linalg.lstsqr runs with no
> > > > > > > > > > > error and returns the correct values while inside the _train call, but
> > > > > > > > > > > all goes haywire upon the return from that method when the python
> > > > > > > > > > > garbage collection kicks in.

> > > > > > > > > > > Any thoughts on how to proceed are more than welcome from all.

> > > > > > > > > > > Thanks,
> > > > > > > > > > > Per


> > > > > > > > > > --
> > > > > > > > > > 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



> > > > > > --

> > > > > > 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



> > > > --

> > > > 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



> > --

> > 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

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