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
<co...@lpta.in2p3.fr <mailto:co...@lpta.in2p3.fr>> wrote:
more fun :
[co...@jarrett tests]$ pwd
/home/cohen/sources/python/numpy/numpy/core/tests
[co...@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 :
[co...@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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