[Numpy-discussion] crash at prompt exit after running test

Johann Cohen-Tanugi cohen@lpta.in2p3...
Tue Mar 9 17:52:40 CST 2010


more fun :
[cohen@jarrett tests]$ pwd
/home/cohen/sources/python/numpy/numpy/core/tests
[cohen@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@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
>>>
>>>
>>>    
>>>
>>>
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>>> NumPy-Discussion@scipy.org
>>> http://mail.scipy.org/mailman/listinfo/numpy-discussion
>>>    
>>
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