[Pkg-exppsy-maintainers] Segfault example

Yaroslav Halchenko debian at onerussian.com
Wed Jan 16 22:16:22 UTC 2008 

ha... indeed it doesn't crash on amd64 -- just produces
Total Correct {0 out of 53}
but no crash!

there I have
ii  atlas3-base    3.6.0-20.6     Automatically Tuned Linear Algebra Software,
ii  libc6          2.3.6.ds1-13et GNU C Library: Shared libraries
ii  python-numpy   1.0.1-1        Numerical Python adds a fast array facility 
ii  python2.4      2.4.4-3        An interactive high-level object-oriented la

Linux node13 2.6.18-4-amd64 #1 SMP Fri May 4 00:37:33 UTC 2007 x86_64 GNU/Linux

So -- atlas3-base is the ssame... numpy is different and python is pretty much
the same... So I wonder if that is purely architecture issue...
let me run in i686 env on the same kind of box... but that will need to wait unfortunately

On Wed, 16 Jan 2008, Yaroslav Halchenko 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

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