[Numpy-discussion] Seg. fault when running tests

Julian Taylor jtaylor.debian@googlemail....
Sat Jun 15 14:15:53 CDT 2013


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?



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