On Tue, Mar 9, 2010 at 5:52 PM, Johann Cohen-Tanugi <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 > > > > > > _______________________________________________ > NumPy-Discussion mailing > listnumpy-discuss...@scipy.orghttp://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 > listnumpy-discuss...@scipy.orghttp://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
_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
