#12497: GeneralDiscreteDistribution can segv sage
--------------------------------------------------------+-------------------
Reporter: ppurka | Owner: amhou
Type: defect | Status:
needs_work
Priority: major | Milestone:
sage-5.0
Component: statistics | Resolution:
Keywords: segfault GeneralDiscreteDistribution | Work issues: needs
rebase
Report Upstream: N/A | Reviewers:
Authors: | Merged in:
Dependencies: #9770 | Stopgaps:
--------------------------------------------------------+-------------------
Old description:
> Running the following segfaults sage.
> {{{
> GeneralDiscreteDistribution([0.1, -0.1]).get_random_element()
> }}}
> If you run it on a notebook then it segfaults sage silently in the
> background with no feedback to the nb.
> {{{
> ~/tmp> snd a.sagenb
> ----------------------------------------------------------------------
> | Sage Version 4.7.2, Release Date: 2011-10-29 |
> | Type notebook() for the GUI, and license() for information. |
> ----------------------------------------------------------------------
>
> Please wait while the Sage Notebook server starts...
> ...
> notebook(directory=r'''a.sagenb''')
> The notebook files are stored in: a.sagenb
> **************************************************
> * *
> * Open your web browser to http://localhost:8080 *
> * *
> **************************************************
> 2012-02-11 22:11:00+0800 [-] Log opened.
> 2012-02-11 22:11:00+0800 [-] twistd 11.1.0
> (/home/punarbasu/Installations/sage-4.8/local/bin/python 2.6.4) starting
> up.
> 2012-02-11 22:11:00+0800 [-] reactor class:
> twisted.internet.pollreactor.PollReactor.
> 2012-02-11 22:11:00+0800 [-] QuietSite starting on 8080
> 2012-02-11 22:11:00+0800 [-] Starting factory <__builtin__.QuietSite
> instance at 0x4c86e18>
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] got EOF subprocess
> must have crashed...
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(print_backtrace+0x31)[0x7f6d900db9f1]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(sigdie+0x14)[0x7f6d900dba23]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(sage_signal_handler+0x20e)[0x7f6d900db670]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /lib64/libpthread.so.0[0x38630102e0]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libgsl.so.0(gsl_ran_discrete+0xe)[0x7f6d8a0bb82e]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/python2.6/site-
> packages/sage/gsl/probability_distribution.so(+0x6201)[0x7f6d6a8ad201]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4d68)[0x7f6d92ba5488]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x5392)[0x7f6d92ba5ab2]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0xb0)[0x7f6d92bc8d80]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(+0xe3dde)[0x7f6d92b9ddde]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4ecc)[0x7f6d92ba55ec]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x5392)[0x7f6d92ba5ab2]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0xb0)[0x7f6d92bc8d80]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(+0xe3dde)[0x7f6d92b9ddde]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4ecc)[0x7f6d92ba55ec]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_InteractiveOneFlags+0x182)[0x7f6d92bc9bf2]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_InteractiveLoopFlags+0x4e)[0x7f6d92bc9dee]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_AnyFileExFlags+0x4c)[0x7f6d92bca42c]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(Py_Main+0xb65)[0x7f6d92bd8665]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /lib64/libc.so.6(__libc_start_main+0xfd)[0x386242209d]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> /home/punarbasu/Installations/sage-4.8/local/bin/python[0x4006e9]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> ------------------------------------------------------------------------
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] Unhandled SIGSEGV: A
> segmentation fault occurred in Sage.
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] This probably
> occurred because a *compiled* component of Sage has a bug
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] in it and is not
> properly wrapped with sig_on(), sig_off(). You might
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] want to run Sage
> under gdb with 'sage -gdb' to debug this.
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] Sage will now
> terminate.
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> ------------------------------------------------------------------------
> 2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
> }}}
> This type of invalid input should be caught and an appropriate error
> given to the user.
>
> ----
> Apply either
>
> 1. [attachment:trac_12497-fix-sage-segv.patch] to devel/sage for sage-4.8
>
> 2. [attachment:trac_12497-fix-sage-segv.2.patch] to devel/sage for
> sage-5.0beta*
New description:
Running the following segfaults sage.
{{{
GeneralDiscreteDistribution([0.1, -0.1]).get_random_element()
}}}
If you run it on a notebook then it segfaults sage silently in the
background with no feedback to the nb.
{{{
~/tmp> snd a.sagenb
----------------------------------------------------------------------
| Sage Version 4.7.2, Release Date: 2011-10-29 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
Please wait while the Sage Notebook server starts...
...
notebook(directory=r'''a.sagenb''')
The notebook files are stored in: a.sagenb
**************************************************
* *
* Open your web browser to http://localhost:8080 *
* *
**************************************************
2012-02-11 22:11:00+0800 [-] Log opened.
2012-02-11 22:11:00+0800 [-] twistd 11.1.0
(/home/punarbasu/Installations/sage-4.8/local/bin/python 2.6.4) starting
up.
2012-02-11 22:11:00+0800 [-] reactor class:
twisted.internet.pollreactor.PollReactor.
2012-02-11 22:11:00+0800 [-] QuietSite starting on 8080
2012-02-11 22:11:00+0800 [-] Starting factory <__builtin__.QuietSite
instance at 0x4c86e18>
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] got EOF subprocess
must have crashed...
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(print_backtrace+0x31)[0x7f6d900db9f1]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(sigdie+0x14)[0x7f6d900dba23]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libcsage.so(sage_signal_handler+0x20e)[0x7f6d900db670]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/lib64/libpthread.so.0[0x38630102e0]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libgsl.so.0(gsl_ran_discrete+0xe)[0x7f6d8a0bb82e]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/python2.6/site-
packages/sage/gsl/probability_distribution.so(+0x6201)[0x7f6d6a8ad201]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4d68)[0x7f6d92ba5488]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x5392)[0x7f6d92ba5ab2]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0xb0)[0x7f6d92bc8d80]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(+0xe3dde)[0x7f6d92b9ddde]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4ecc)[0x7f6d92ba55ec]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x5392)[0x7f6d92ba5ab2]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_FileExFlags+0xb0)[0x7f6d92bc8d80]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(+0xe3dde)[0x7f6d92b9ddde]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x4ecc)[0x7f6d92ba55ec]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x8ac)[0x7f6d92ba707c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyEval_EvalCode+0x32)[0x7f6d92ba7152]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_InteractiveOneFlags+0x182)[0x7f6d92bc9bf2]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_InteractiveLoopFlags+0x4e)[0x7f6d92bc9dee]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(PyRun_AnyFileExFlags+0x4c)[0x7f6d92bca42c]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/lib/libpython2.6.so.1.0(Py_Main+0xb65)[0x7f6d92bd8665]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x386242209d]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
/home/punarbasu/Installations/sage-4.8/local/bin/python[0x4006e9]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
------------------------------------------------------------------------
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] Unhandled SIGSEGV: A
segmentation fault occurred in Sage.
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] This probably occurred
because a *compiled* component of Sage has a bug
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] in it and is not
properly wrapped with sig_on(), sig_off(). You might
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] want to run Sage under
gdb with 'sage -gdb' to debug this.
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1] Sage will now
terminate.
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
------------------------------------------------------------------------
2012-02-11 22:15:56+0800 [HTTPChannel,17,127.0.0.1]
}}}
This type of invalid input should be caught and an appropriate error given
to the user.
----
Apply [attachment:trac_12497-fix-sage-segv.3.patch] to devel/sage for
sage-5.0beta10
--
Comment (by ppurka):
Replying to [comment:7 davidloeffler]:
> This is conflicting with something (see patchbot logs) -- I suspect
#9770.
Sigh. I thought I had rebased to recent enough beta. Updated another
rebased patch.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12497#comment:8>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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