[Numpy-discussion] Seg. fault when running tests

Warren Weckesser warren.weckesser@gmail....
Sat Jun 15 14:28:54 CDT 2013


On Sat, Jun 15, 2013 at 3:26 PM, Charles R Harris <charlesr.harris@gmail.com
> wrote:

>
>
> 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.
>
>
64 bit, intel, clean install.  Bisecting now...

Warren



> Chuck
>
>
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