[Numpy-discussion] Seg. fault when running tests

Charles R Harris charlesr.harris@gmail....
Sat Jun 15 14:26:27 CDT 2013


On Sat, Jun 15, 2013 at 1:15 PM, Julian Taylor <
jtaylor.debian@googlemail.com> wrote:

> On 15.06.2013 21:12, Charles R Harris wrote:
> >
> >
> > On Sat, Jun 15, 2013 at 9:50 AM, Warren Weckesser
> > <warren.weckesser@gmail.com <mailto:warren.weckesser@gmail.com>> wrote:
> >
> >
> >     On Sat, Jun 15, 2013 at 11:43 AM, Warren Weckesser
> >     <warren.weckesser@gmail.com <mailto:warren.weckesser@gmail.com>>
> wrote:
> >
> >         I'm getting a seg. fault in master when I run the tests.  I'm on
> >         Ubuntu 12.04 64 bit, with Python 3.3.2 (64 bits):
> >
> >         $ python3 -c "import numpy as np; np.test('full')"
> >         Running unit tests for numpy
> >         NumPy version 1.8.0.dev-fa5bc1c
> >         NumPy is installed in
> >         /home/warren/local_py332/lib/python3.3/site-packages/numpy
> >         Python version 3.3.2 (default, Jun 14 2013, 12:12:22) [GCC 4.6.3]
> >         nose version 1.3.0
> >
> .............................S.........................................................................................................................................................S.......................................................................................................................................................S....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
>  .........
>
> .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K............................................................................................................................................................................................SSS.
>  .........
>
> .......................................................................................K.....................................................................................................................................................................................Segmentation
> >         fault
> >
> >         The seg. fault is occurring in ma/tests/test_mrecords.py:
> >
> >         $ nosetests test_mrecords.py
> >         .Segmentation fault
> >
> >         More info:
> >
> >         $ python3
> >         Python 3.3.2 (default, Jun 14 2013, 12:12:22)
> >         [GCC 4.6.3] on linux
> >         Type "help", "copyright", "credits" or "license" for more
> >         information.
> >         >>> import numpy as np
> >         >>> np.show_config()
> >         atlas_threads_info:
> >             library_dirs = ['/usr/lib/atlas-base/atlas',
> >         '/usr/lib/atlas-base']
> >             include_dirs = ['/usr/include/atlas']
> >             language = f77
> >             libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
> >             define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
> >         atlas_blas_threads_info:
> >             library_dirs = ['/usr/lib/atlas-base']
> >             include_dirs = ['/usr/include/atlas']
> >             language = c
> >             libraries = ['ptf77blas', 'ptcblas', 'atlas']
> >             define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
> >         mkl_info:
> >           NOT AVAILABLE
> >         lapack_opt_info:
> >             library_dirs = ['/usr/lib/atlas-base/atlas',
> >         '/usr/lib/atlas-base']
> >             include_dirs = ['/usr/include/atlas']
> >             language = f77
> >             libraries = ['lapack', 'ptf77blas', 'ptcblas', 'atlas']
> >             define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
> >         blas_opt_info:
> >             library_dirs = ['/usr/lib/atlas-base']
> >             include_dirs = ['/usr/include/atlas']
> >             language = c
> >             libraries = ['ptf77blas', 'ptcblas', 'atlas']
> >             define_macros = [('ATLAS_INFO', '"\\"3.8.4\\""')]
> >         lapack_mkl_info:
> >           NOT AVAILABLE
> >         blas_mkl_info:
> >           NOT AVAILABLE
> >         >>>
> >
> >         gdb:
> >
> >         $ gdb python3
> >         GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
> >         Copyright (C) 2012 Free Software Foundation, Inc.
> >         License GPLv3+: GNU GPL version 3 or later
> >         <http://gnu.org/licenses/gpl.html>
> >         This is free software: you are free to change and redistribute
> it.
> >         There is NO WARRANTY, to the extent permitted by law.  Type
> >         "show copying"
> >         and "show warranty" for details.
> >         This GDB was configured as "x86_64-linux-gnu".
> >         For bug reporting instructions, please see:
> >         <http://bugs.launchpad.net/gdb-linaro/>...
> >         Reading symbols from /home/warren/local_py332/bin/python3...done.
> >         (gdb) run test_mrecords.py
> >         Starting program: /home/warren/local_py332/bin/python3
> >         test_mrecords.py
> >         [Thread debugging using libthread_db enabled]
> >         Using host libthread_db library
> >         "/lib/x86_64-linux-gnu/libthread_db.so.1".
> >         .
> >         Program received signal SIGSEGV, Segmentation fault.
> >         0x00007ffff5f080a4 in
> >         _aligned_strided_to_contig_size8_srcstride0 (dst=<optimized out>,
> >             dst_stride=<optimized out>, src=<optimized out>,
> >         __NPY_UNUSED_TAGGEDsrc_stride=<optimized out>,
> >             N=<optimized out>,
> >         __NPY_UNUSED_TAGGEDsrc_itemsize=<optimized out>,
> >         __NPY_UNUSED_TAGGEDdata=0x0)
> >             at numpy/core/src/multiarray/lowlevel_strided_loops.c.src:190
> >         190            *((@type@ *)dst) = temp;
> >         (gdb)
> >
> >
> >
> >
> > Is this repeatable? Just asking as I don't see that here with gcc 4.7.2.
> > Looks like Julian's changes to lowlevel_strided_loops may be responsible.
> >
> > Chuck
> >
>
> I can't reproduce it on ubuntu 12.04 with python 3.2 (don't have 3.3.2)
> the changes made are very minimal, from looking at them again I don't
> see how they could cause this (especially on a x86 platform).
>
> @warren, can you please bisect the commit causing this?
>

Also, 32 or 64 bit? Intel hardware? Clean install? Works here with python
3.3.0.

Chuck
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