From: John M. <jo...@zu...> - 2013-04-23 16:14:37
|
Hi list, I'm working on packaging pyode for Fedora. Everything has gone smoothly except the tests, which segfault after successful completion of all 110 tests. Has this been seen before? Below is the output of the test run and a gdb stack trace on the resulting core file. John $ python PyODE-snapshot-2010-03-22/tests/test_xode.py .............................................................................................................. ---------------------------------------------------------------------- Ran 110 tests in 1.014s OK Segmentation fault #0 0x00007f48659dc253 in dBodyDestroy () from /usr/lib64/libode.so.1 #1 0x00007f4865cb6434 in __pyx_f_3ode_4Body___dealloc__ ( o=<value optimized out>) at ode_trimesh.c:3355 #2 __pyx_tp_dealloc_3ode_Body (o=<value optimized out>) at ode_trimesh.c:14829 #3 0x00007f4865cb3eeb in __pyx_tp_dealloc_3ode_GeomObject (o=0x7f4866144650) at ode_trimesh.c:16892 #4 0x00007f486ccfe49b in PyDict_Clear () from /usr/lib64/libpython2.6.so.1.0 #5 0x00007f486ccfe529 in ?? () from /usr/lib64/libpython2.6.so.1.0 #6 0x00007f486cd87f6a in ?? () from /usr/lib64/libpython2.6.so.1.0 #7 0x00007f486cd88564 in PyGC_Collect () from /usr/lib64/libpython2.6.so.1.0 #8 0x00007f486cd798b6 in Py_Finalize () from /usr/lib64/libpython2.6.so.1.0 #9 0x00007f486cd79a08 in Py_Exit () from /usr/lib64/libpython2.6.so.1.0 #10 0x00007f486cd79b51 in ?? () from /usr/lib64/libpython2.6.so.1.0 #11 0x00007f486cd79dcd in PyErr_PrintEx () from /usr/lib64/libpython2.6.so.1.0 #12 0x00007f486cd7a297 in PyRun_SimpleFileExFlags () from /usr/lib64/libpython2.6.so.1.0 #13 0x00007f486cd86c32 in Py_Main () from /usr/lib64/libpython2.6.so.1.0 #14 0x00007f486c060cdd in __libc_start_main (main=0x400710, argc=2, ubp_av=0x7fff7c22c758, init=<value optimized out>, fini=<value optimized out>, rtld_fini=<value optimized out>, stack_end=0x7fff7c22c748) at libc-start.c:226 #15 0x0000000000400649 in ?? () #16 0x00007fff7c22c748 in ?? () #17 0x000000000000001c in ?? () #18 0x0000000000000002 in ?? () #19 0x00007fff7c22dc19 in ?? () #20 0x00007fff7c22dc20 in ?? () #21 0x0000000000000000 in ?? () |
From: John M. <jo...@zu...> - 2013-04-24 05:43:03
Attachments:
pyode-1.2.0-segfault.patch
|
Hi Ethan, Thanks for the quick reply! I must have been keyword challenged last time around, but this time I easily googled up a ready-made solution: http://comments.gmane.org/gmane.comp.python.pyode.user/174 If it matters, I'm building against ODE version 0.11.1. Attached is the patch to fix the segfault. This will be included in the Fedora package. If this patch makes it into git and you release a snapshot, I'll package up the new version & drop the patch. Thanks- John On 04/23/2013 11:12 PM, Ethan wrote: > Hi John, > > To be honest, I never used or understood the xode code. Sorry, I can't help. > > Ethan > > > On Tue, Apr 23, 2013 at 12:14 PM, John Morris <jo...@zu... > <mailto:jo...@zu...>> wrote: > > Hi list, > > I'm working on packaging pyode for Fedora. Everything has gone smoothly > except the tests, which segfault after successful completion of all 110 > tests. Has this been seen before? Below is the output of the test run > and a gdb stack trace on the resulting core file. > > John > > > $ python PyODE-snapshot-2010-03-22/tests/test_xode.py > .............................................................................................................. > ---------------------------------------------------------------------- > Ran 110 tests in 1.014s > > OK > Segmentation fault > > > > > > #0 0x00007f48659dc253 in dBodyDestroy () from /usr/lib64/libode.so.1 > #1 0x00007f4865cb6434 in __pyx_f_3ode_4Body___dealloc__ ( > o=<value optimized out>) at ode_trimesh.c:3355 > #2 __pyx_tp_dealloc_3ode_Body (o=<value optimized out>) > at ode_trimesh.c:14829 > #3 0x00007f4865cb3eeb in __pyx_tp_dealloc_3ode_GeomObject > (o=0x7f4866144650) > at ode_trimesh.c:16892 > #4 0x00007f486ccfe49b in PyDict_Clear () from > /usr/lib64/libpython2.6.so.1.0 > #5 0x00007f486ccfe529 in ?? () from /usr/lib64/libpython2.6.so.1.0 > #6 0x00007f486cd87f6a in ?? () from /usr/lib64/libpython2.6.so.1.0 > #7 0x00007f486cd88564 in PyGC_Collect () from > /usr/lib64/libpython2.6.so.1.0 > #8 0x00007f486cd798b6 in Py_Finalize () from > /usr/lib64/libpython2.6.so.1.0 > #9 0x00007f486cd79a08 in Py_Exit () from /usr/lib64/libpython2.6.so.1.0 > #10 0x00007f486cd79b51 in ?? () from /usr/lib64/libpython2.6.so.1.0 > #11 0x00007f486cd79dcd in PyErr_PrintEx () from > /usr/lib64/libpython2.6.so.1.0 > #12 0x00007f486cd7a297 in PyRun_SimpleFileExFlags () > from /usr/lib64/libpython2.6.so.1.0 > #13 0x00007f486cd86c32 in Py_Main () from /usr/lib64/libpython2.6.so.1.0 > #14 0x00007f486c060cdd in __libc_start_main (main=0x400710, argc=2, > ubp_av=0x7fff7c22c758, init=<value optimized out>, > fini=<value optimized out>, rtld_fini=<value optimized out>, > stack_end=0x7fff7c22c748) at libc-start.c:226 > #15 0x0000000000400649 in ?? () > #16 0x00007fff7c22c748 in ?? () > #17 0x000000000000001c in ?? () > #18 0x0000000000000002 in ?? () > #19 0x00007fff7c22dc19 in ?? () > #20 0x00007fff7c22dc20 in ?? () > #21 0x0000000000000000 in ?? () > > ------------------------------------------------------------------------------ > Try New Relic Now & We'll Send You this Cool Shirt > New Relic is the only SaaS-based application performance monitoring > service > that delivers powerful full stack analytics. Optimize and monitor your > browser, app, & servers with just a few lines of code. Try New Relic > and get this awesome Nerd Life shirt! > http://p.sf.net/sfu/newrelic_d2d_apr > _______________________________________________ > Pyode-user mailing list > Pyo...@li... > <mailto:Pyo...@li...> > https://lists.sourceforge.net/lists/listinfo/pyode-user > > |
From: John M. <jo...@zu...> - 2013-04-26 03:13:49
Attachments:
pyode-1.2.0-check_script_failures.patch
|
One more fix to those tests. They fail on Fedora but not el6 (el6 is quite a bit older), and on 64-bit but not 32-bit. The failure is because of a rounding error; the results differ by 6e-8. The attached patch adds a check to the unittests that compares the floats to within five decimals. It's tested to pass on el6 and f17-f20, and 64- and 32-bit. John On 04/24/2013 12:42 AM, John Morris wrote: > Hi Ethan, > > Thanks for the quick reply! > > I must have been keyword challenged last time around, but this time I > easily googled up a ready-made solution: > > http://comments.gmane.org/gmane.comp.python.pyode.user/174 > > If it matters, I'm building against ODE version 0.11.1. > > Attached is the patch to fix the segfault. This will be included in the > Fedora package. If this patch makes it into git and you release a > snapshot, I'll package up the new version & drop the patch. > > Thanks- > > John > > > On 04/23/2013 11:12 PM, Ethan wrote: >> Hi John, >> >> To be honest, I never used or understood the xode code. Sorry, I can't help. >> >> Ethan >> >> >> On Tue, Apr 23, 2013 at 12:14 PM, John Morris <jo...@zu... >> <mailto:jo...@zu...>> wrote: >> >> Hi list, >> >> I'm working on packaging pyode for Fedora. Everything has gone smoothly >> except the tests, which segfault after successful completion of all 110 >> tests. Has this been seen before? Below is the output of the test run >> and a gdb stack trace on the resulting core file. >> >> John >> >> >> $ python PyODE-snapshot-2010-03-22/tests/test_xode.py >> .............................................................................................................. >> ---------------------------------------------------------------------- >> Ran 110 tests in 1.014s >> >> OK >> Segmentation fault >> >> >> >> >> >> #0 0x00007f48659dc253 in dBodyDestroy () from /usr/lib64/libode.so.1 >> #1 0x00007f4865cb6434 in __pyx_f_3ode_4Body___dealloc__ ( >> o=<value optimized out>) at ode_trimesh.c:3355 >> #2 __pyx_tp_dealloc_3ode_Body (o=<value optimized out>) >> at ode_trimesh.c:14829 >> #3 0x00007f4865cb3eeb in __pyx_tp_dealloc_3ode_GeomObject >> (o=0x7f4866144650) >> at ode_trimesh.c:16892 >> #4 0x00007f486ccfe49b in PyDict_Clear () from >> /usr/lib64/libpython2.6.so.1.0 >> #5 0x00007f486ccfe529 in ?? () from /usr/lib64/libpython2.6.so.1.0 >> #6 0x00007f486cd87f6a in ?? () from /usr/lib64/libpython2.6.so.1.0 >> #7 0x00007f486cd88564 in PyGC_Collect () from >> /usr/lib64/libpython2.6.so.1.0 >> #8 0x00007f486cd798b6 in Py_Finalize () from >> /usr/lib64/libpython2.6.so.1.0 >> #9 0x00007f486cd79a08 in Py_Exit () from /usr/lib64/libpython2.6.so.1.0 >> #10 0x00007f486cd79b51 in ?? () from /usr/lib64/libpython2.6.so.1.0 >> #11 0x00007f486cd79dcd in PyErr_PrintEx () from >> /usr/lib64/libpython2.6.so.1.0 >> #12 0x00007f486cd7a297 in PyRun_SimpleFileExFlags () >> from /usr/lib64/libpython2.6.so.1.0 >> #13 0x00007f486cd86c32 in Py_Main () from /usr/lib64/libpython2.6.so.1.0 >> #14 0x00007f486c060cdd in __libc_start_main (main=0x400710, argc=2, >> ubp_av=0x7fff7c22c758, init=<value optimized out>, >> fini=<value optimized out>, rtld_fini=<value optimized out>, >> stack_end=0x7fff7c22c748) at libc-start.c:226 >> #15 0x0000000000400649 in ?? () >> #16 0x00007fff7c22c748 in ?? () >> #17 0x000000000000001c in ?? () >> #18 0x0000000000000002 in ?? () >> #19 0x00007fff7c22dc19 in ?? () >> #20 0x00007fff7c22dc20 in ?? () >> #21 0x0000000000000000 in ?? () >> >> ------------------------------------------------------------------------------ >> Try New Relic Now & We'll Send You this Cool Shirt >> New Relic is the only SaaS-based application performance monitoring >> service >> that delivers powerful full stack analytics. Optimize and monitor your >> browser, app, & servers with just a few lines of code. Try New Relic >> and get this awesome Nerd Life shirt! >> http://p.sf.net/sfu/newrelic_d2d_apr >> _______________________________________________ >> Pyode-user mailing list >> Pyo...@li... >> <mailto:Pyo...@li...> >> https://lists.sourceforge.net/lists/listinfo/pyode-user >> >> > |
From: John M. <jo...@zu...> - 2013-04-28 03:28:34
|
Hi Ethan, Thanks for committing our patches. Good news here, too: the Fedora review is all done, and now it's just a matter of getting the sources checked in and running it through the Fedora build servers and the unstable and finally stable package repositories. Probably about two weeks. Here's the bugzilla package review ticket: https://bugzilla.redhat.com/show_bug.cgi?id=927611 We're using the following tarball. The first patch wasn't applied there, but it's included in the package, and that fixes the segfaults. https://downloads.sourceforge.net/project/pyode/pyode/snapshot-2010-03-22/PyODE-snapshot-2010-03-22.tar.gz Anyway, I do see both patches in the git tree, thanks! If you want to make a release, we'll definitely pick it up in our packaging. No urgency though, since the two packages that depend on pyode seem to work well with 2010-03-22 and those patches added. When you get around to it, let me know and I'll make the update. Believe me, I understand about busy! John On 04/25/2013 10:37 PM, Ethan wrote: > Thanks for the patches, John! I meant to address this when you emailed > the first patch, but I've been pretty busy this week. > > The good news is the first patch was applied in 2010-10-13. From the > patch you sent, it looks like you're working off of version 2012-03-22. > It looks like I might have tried to cut a release for version 1.2.1 in > 2012, but I might have messed up somewhere. Let me know if you can't > find it anywhere. > > The other good news ;) is that I applied your other patch and pushed it. > If you need me to make a new release, let me know. > > Ethan > > > > On Thu, Apr 25, 2013 at 11:13 PM, John Morris <jo...@zu... > <mailto:jo...@zu...>> wrote: > > One more fix to those tests. They fail on Fedora but not el6 (el6 is > quite a bit older), and on 64-bit but not 32-bit. > > The failure is because of a rounding error; the results differ by 6e-8. > > The attached patch adds a check to the unittests that compares the > floats to within five decimals. It's tested to pass on el6 and f17-f20, > and 64- and 32-bit. > > John > > > > On 04/24/2013 12:42 AM, John Morris wrote: > > Hi Ethan, > > > > Thanks for the quick reply! > > > > I must have been keyword challenged last time around, but this time I > > easily googled up a ready-made solution: > > > > http://comments.gmane.org/gmane.comp.python.pyode.user/174 > > > > If it matters, I'm building against ODE version 0.11.1. > > > > Attached is the patch to fix the segfault. This will be included > in the > > Fedora package. If this patch makes it into git and you release a > > snapshot, I'll package up the new version & drop the patch. > > > > Thanks- > > > > John > > > > > > On 04/23/2013 11:12 PM, Ethan wrote: > >> Hi John, > >> > >> To be honest, I never used or understood the xode code. Sorry, I > can't help. > >> > >> Ethan > >> > >> > >> On Tue, Apr 23, 2013 at 12:14 PM, John Morris <jo...@zu... > <mailto:jo...@zu...> > >> <mailto:jo...@zu... <mailto:jo...@zu...>>> wrote: > >> > >> Hi list, > >> > >> I'm working on packaging pyode for Fedora. Everything has > gone smoothly > >> except the tests, which segfault after successful completion > of all 110 > >> tests. Has this been seen before? Below is the output of > the test run > >> and a gdb stack trace on the resulting core file. > >> > >> John > >> > >> > >> $ python PyODE-snapshot-2010-03-22/tests/test_xode.py > >> > .............................................................................................................. > >> > ---------------------------------------------------------------------- > >> Ran 110 tests in 1.014s > >> > >> OK > >> Segmentation fault > >> > >> > >> > >> > >> > >> #0 0x00007f48659dc253 in dBodyDestroy () from > /usr/lib64/libode.so.1 > >> #1 0x00007f4865cb6434 in __pyx_f_3ode_4Body___dealloc__ ( > >> o=<value optimized out>) at ode_trimesh.c:3355 > >> #2 __pyx_tp_dealloc_3ode_Body (o=<value optimized out>) > >> at ode_trimesh.c:14829 > >> #3 0x00007f4865cb3eeb in __pyx_tp_dealloc_3ode_GeomObject > >> (o=0x7f4866144650) > >> at ode_trimesh.c:16892 > >> #4 0x00007f486ccfe49b in PyDict_Clear () from > >> /usr/lib64/libpython2.6.so.1.0 > >> #5 0x00007f486ccfe529 in ?? () from > /usr/lib64/libpython2.6.so.1.0 > >> #6 0x00007f486cd87f6a in ?? () from > /usr/lib64/libpython2.6.so.1.0 > >> #7 0x00007f486cd88564 in PyGC_Collect () from > >> /usr/lib64/libpython2.6.so.1.0 > >> #8 0x00007f486cd798b6 in Py_Finalize () from > >> /usr/lib64/libpython2.6.so.1.0 > >> #9 0x00007f486cd79a08 in Py_Exit () from > /usr/lib64/libpython2.6.so.1.0 > >> #10 0x00007f486cd79b51 in ?? () from > /usr/lib64/libpython2.6.so.1.0 > >> #11 0x00007f486cd79dcd in PyErr_PrintEx () from > >> /usr/lib64/libpython2.6.so.1.0 > >> #12 0x00007f486cd7a297 in PyRun_SimpleFileExFlags () > >> from /usr/lib64/libpython2.6.so.1.0 > >> #13 0x00007f486cd86c32 in Py_Main () from > /usr/lib64/libpython2.6.so.1.0 > >> #14 0x00007f486c060cdd in __libc_start_main (main=0x400710, > argc=2, > >> ubp_av=0x7fff7c22c758, init=<value optimized out>, > >> fini=<value optimized out>, rtld_fini=<value optimized out>, > >> stack_end=0x7fff7c22c748) at libc-start.c:226 > >> #15 0x0000000000400649 in ?? () > >> #16 0x00007fff7c22c748 in ?? () > >> #17 0x000000000000001c in ?? () > >> #18 0x0000000000000002 in ?? () > >> #19 0x00007fff7c22dc19 in ?? () > >> #20 0x00007fff7c22dc20 in ?? () > >> #21 0x0000000000000000 in ?? () > >> > >> > ------------------------------------------------------------------------------ > >> Try New Relic Now & We'll Send You this Cool Shirt > >> New Relic is the only SaaS-based application performance > monitoring > >> service > >> that delivers powerful full stack analytics. Optimize and > monitor your > >> browser, app, & servers with just a few lines of code. Try > New Relic > >> and get this awesome Nerd Life shirt! > >> http://p.sf.net/sfu/newrelic_d2d_apr > >> _______________________________________________ > >> Pyode-user mailing list > >> Pyo...@li... > <mailto:Pyo...@li...> > >> <mailto:Pyo...@li... > <mailto:Pyo...@li...>> > >> https://lists.sourceforge.net/lists/listinfo/pyode-user > >> > >> > > > > |