[Pkg-exppsy-maintainers] Segfault example

Yaroslav Halchenko debian at onerussian.com
Thu Jan 17 17:23:52 UTC 2008


cool... the beast breaks on ia64 as well!
(I tested it with pymvpa checkout cdd944056900c8216b452).

just mention that in bug report 

On Wed, 16 Jan 2008, Yaroslav Halchenko wrote:

> in any case... bingo -- it fails on i386 with the same libraries as I
> have on amd64 system... so -- once again - architecture issue... I am
> not sure what is the root though. I think it would be ok if you file it
> against numpy since that is where it sprouts from. Sure thing you should
> mention all our findings that it works fine on amd64.

> Meanwhile analyze your data on amd64 box... don't you have a new laptop
> which can run in 64 bit? ;-) btw -- so do you have debian on it or
> ubuntu? ;-)

> 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        



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