[Numpy-discussion] crash at prompt exit after running test
Johann Cohen-Tanugi
cohen at lpta.in2p3.fr
Wed Mar 10 04:24:30 EST 2010
Ubuntu has a much shorter cycle of updates than Fedora, indeed.
On 03/10/2010 06:27 AM, Charles R Harris wrote:
>
>
> On Tue, Mar 9, 2010 at 5:52 PM, Johann Cohen-Tanugi
> <cohen at lpta.in2p3.fr <mailto:cohen at lpta.in2p3.fr>> wrote:
>
> more fun :
> [cohen at jarrett tests]$ pwd
> /home/cohen/sources/python/numpy/numpy/core/tests
> [cohen at jarrett tests]$ python -c 'import test_ufunc'
>
> python: Modules/gcmodule.c:277: visit_decref: Assertion
> `gc->gc.gc_refs != 0' failed.
> Aborted (core dumped)
>
> and in the debugger:
> (gdb) run
> Starting program: /usr/bin/python
> warning: .dynamic section for "/lib/libpthread.so.0" is not at the
> expected address
>
> warning: difference appears to be caused by prelink, adjusting
> expectations
> warning: .dynamic section for "/lib/libdl.so.2" is not at the
> expected address
>
> warning: difference appears to be caused by prelink, adjusting
> expectations
> warning: .dynamic section for "/lib/libc.so.6" is not at the
> expected address
>
> warning: difference appears to be caused by prelink, adjusting
> expectations
> [Thread debugging using libthread_db enabled]
>
> Python 2.6.2 (r262:71600, Jan 25 2010, 18:46:45)
> [GCC 4.4.2 20091222 (Red Hat 4.4.2-20)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import test_ufunc
>
> >>>
> >>>
> python: Modules/gcmodule.c:277: visit_decref: Assertion
> `gc->gc.gc_refs != 0' failed.
>
> Program received signal SIGABRT, Aborted.
> 0x00aab416 in __kernel_vsyscall ()
> Missing separate debuginfos, use: debuginfo-install
> atlas-3.8.3-12.fc12.i686 libgcc-4.4.3-4.fc12.i686
> libgfortran-4.4.3-4.fc12.i686
> (gdb) bt
> #0 0x00aab416 in __kernel_vsyscall ()
> #1 0x00159a91 in raise (sig=6) at
> ../nptl/sysdeps/unix/sysv/linux/raise.c:64
> #2 0x0015b35a in abort () at abort.c:92
> #3 0x00152be8 in __assert_fail (assertion=<value optimized out>,
> file=<value optimized out>, line=<value optimized out>,
> function=<value optimized out>) at assert.c:81
> #4 0x0050931e in visit_decref (op=<value optimized out>,
> data=<value optimized out>) at Modules/gcmodule.c:277
> #5 0x0047c8c2 in dict_traverse (op=<value optimized out>,
> visit=<value optimized out>, arg=<value optimized out>) at
> Objects/dictobject.c:2003
> #6 0x00509af3 in subtract_refs (generation=<value optimized out>)
> at Modules/gcmodule.c:296
>
> #7 collect (generation=<value optimized out>) at
> Modules/gcmodule.c:817
> #8 0x0050a640 in PyGC_Collect () at Modules/gcmodule.c:1292
> #9 0x004fb0f0 in Py_Finalize () at Python/pythonrun.c:424
> #10 0x0050868f in Py_Main (argc=<value optimized out>, argv=<value
> optimized out>) at Modules/main.c:625
> #11 0x080485c8 in main (argc=<value optimized out>, argv=<value
> optimized out>) at Modules/python.c:23
>
> which looks identical to the bt I sent to Robert earlier on.
>
> HTH,
> Johann
>
>
> On 03/10/2010 12:43 AM, Johann Cohen-Tanugi wrote:
>>
>>
>> On 03/10/2010 12:33 AM, Johann Cohen-Tanugi wrote:
>>>
>>>
>>> On 03/10/2010 12:07 AM, Pauli Virtanen wrote:
>>>> ti, 2010-03-09 kello 21:14 +0100, Johann Cohen-Tanugi kirjoitti:
>>>>
>>>>> thinking about it, this morning there was a fedora update to python, so
>>>>> I am using 2.6.2-4.fc12.
>>>>> Looks like the problem is in python itself, hence this piece of info.
>>>>>
>>>> That the problem would be in Python is not so clear to me. Can you try
>>>> running it with the previous Python shipped by Fedora? Do you see the
>>>> problem then? What's the previous version, btw?
>>>>
>>> 2.6.2-1 IIRC. I would have to check, and I am not sure how to
>>> either query this information or step back one update up with yum :(
>>>> Memory errors are somewhat difficult to debug. Can you try running only
>>>> a certain subset of the tests, first
>>>>
>>>> nosetests numpy.core
>>>>
>>> crash
>>>> Be sure to set Pythonpath so that you get the correct Numpy version. If
>>>> it segfaults, proceed to (under numpy/core/tests)
>>>>
>>>> nosetests test_multiarray.py
>>>> nosetests test_multiarray.py:TestNewBufferProtocol
>>>>
>>> neither crash, so the problem is not there....
>> I followed your lead and tried each script and ended up with :
>> [cohen at jarrett tests]$ nosetests test_ufunc.py
>> .............
>> ----------------------------------------------------------------------
>> Ran 13 tests in 1.146s
>>
>> OK
>> python: Modules/gcmodule.c:277: visit_decref: Assertion
>> `gc->gc.gc_refs != 0' failed.
>> Aborted (core dumped)
>>
>> so test_ufunc.py seems to be at stake
>>
>>>> Since the crash occurs in cyclic garbage collection, I'm doubting a bit
>>>> the numpy/core/src/multiarray/numpymemoryview.c implementation, since
>>>> that's the only part in Numpy that supports that.
>>>>
>>>> Alternatively, just replace numpymemoryview.c with the attached one
>>>> which has cyclic GC stripped, and see if you still get the crash.
>>>>
>>>> Cheers,
>>>> Pauli
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> NumPy-Discussion mailing list
>>>> NumPy-Discussion at scipy.org <mailto:NumPy-Discussion at scipy.org>
>>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>>
>>>
>>> --
>>> This message has been scanned for viruses and
>>> dangerous content by *MailScanner*
>>> <http://www.mailscanner.info/>, and is
>>> believed to be clean.
>>>
>>>
>>> _______________________________________________
>>> NumPy-Discussion mailing list
>>> NumPy-Discussion at scipy.org <mailto:NumPy-Discussion at scipy.org>
>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>
>>
>
> Python 2.6.2 is rather old by now, the bugfix releases are up to
> 2.6.4. I don't know that that is related, but I haven't seen any
> crashes on ubuntu with 2.6.4.
>
> Chuck
>
> --
> This message has been scanned for viruses and
> dangerous content by *MailScanner* <http://www.mailscanner.info/>, and is
> believed to be clean.
>
>
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion at scipy.org
> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/numpy-discussion/attachments/20100310/6747594d/attachment.html>
More information about the NumPy-Discussion
mailing list