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

Johann Cohen-Tanugi cohen@lpta.in2p3...
Wed Mar 10 03:24:30 CST 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@lpta.in2p3.fr <mailto:cohen@lpta.in2p3.fr>> wrote:
>
>     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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>>
>
> 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
>
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