#19334: Update to Cython-0.23.3
-------------------------------------+-------------------------------------
Reporter: vbraun | Owner:
Type: defect | Status: needs_work
Priority: major | Milestone: sage-6.9
Component: packages: | Resolution:
standard | Merged in:
Keywords: | Reviewers: François Bissey
Authors: Volker Braun | Work issues:
Report Upstream: N/A | Commit:
Branch: | a15ae13c5a9ff74d345525c8b028f4ebdfac0d56
u/vbraun/update_to_cython_0_23_3 | Stopgaps:
Dependencies: |
-------------------------------------+-------------------------------------
Comment (by vbraun):
I can confirm that; Bug in asteroidal triples?
{{{
$ sage -valgrind
┌────────────────────────────────────────────────────────────────────┐
│ SageMath Version 6.9.rc1, Release Date: 2015-10-01 │
│ Type "notebook()" for the browser-based notebook interface. │
│ Type "help()" for help. │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable. ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
Using default flags: --leak-resolution=high --leak-check=full --num-
callers=25
--suppressions=/home/vbraun/Code/sage.git/local/share/sage/ext/valgrind/python.supp
--suppressions=/home/vbraun/Code/sage.git/local/share/sage/ext/valgrind/pyalloc.supp
--suppressions=/home/vbraun/Code/sage.git/local/share/sage/ext/valgrind/sage.supp
--suppressions=/home/vbraun/Code/sage.git/local/share/sage/ext/valgrind
/sage-additional.supp
==16537== Memcheck, a memory error detector
==16537== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
==16537== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright
info
==16537== Command: python /home/vbraun/Code/sage.git/local/bin/sage-
ipython -i
==16537==
sage: sage: from sage.graphs.asteroidal_triples import *
sage: sage: G = graphs.CompleteGraph(5)
sage: sage: is_asteroidal_triple_free(G)
==16537== Invalid read of size 8
==16537== at 0x3FCA844D:
__pyx_f_4sage_6graphs_18asteroidal_triples_bitset_add
(asteroidal_triples.c:3100)
==16537== by 0x3FCA844D:
__pyx_f_4sage_6graphs_18asteroidal_triples_is_asteroidal_triple_free_C
(asteroidal_triples.c:6922)
==16537== by 0x3FCA844D:
__pyx_pf_4sage_6graphs_18asteroidal_triples_is_asteroidal_triple_free.isra.11
(asteroidal_triples.c:6451)
==16537== by 0x3FCA906F:
__pyx_pw_4sage_6graphs_18asteroidal_triples_1is_asteroidal_triple_free
(asteroidal_triples.c:6146)
==16537== by 0x4F3C070: call_function (ceval.c:4033)
==16537== by 0x4F3C070: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3D798: PyEval_EvalCode (ceval.c:667)
==16537== by 0x4F3BDDD: exec_statement (ceval.c:4730)
==16537== by 0x4F3BDDD: PyEval_EvalFrameEx (ceval.c:1881)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3C393: fast_function (ceval.c:4129)
==16537== by 0x4F3C393: call_function (ceval.c:4054)
==16537== by 0x4F3C393: PyEval_EvalFrameEx (ceval.c:2679)
==16537== by 0x4F3D67B: PyEval_EvalCodeEx (ceval.c:3265)
==16537== by 0x4F3D798: PyEval_EvalCode (ceval.c:667)
==16537== by 0x4F60D79: run_mod (pythonrun.c:1365)
==16537== by 0x4F60D79: PyRun_FileExFlags (pythonrun.c:1351)
==16537== by 0x4F62126: PyRun_SimpleFileExFlags (pythonrun.c:943)
==16537== by 0x4F785FD: Py_Main (main.c:640)
==16537== by 0x5B806FF: (below main) (in /usr/lib64/libc-2.21.so)
==16537== Address 0x511adfa8 is not stack'd, malloc'd or (recently)
free'd
==16537==
---------------------------------------------------------------------------
SignalError Traceback (most recent call
last)
<ipython-input-3-b56905c730da> in <module>()
----> 1 is_asteroidal_triple_free(G)
/home/vbraun/Code/sage.git/src/sage/graphs/asteroidal_triples.pyx in
sage.graphs.asteroidal_triples.is_asteroidal_triple_free
(build/cythonized/sage/graphs/asteroidal_triples.c:6442)()
169
170 try:
--> 171 sig_on()
172 ret = is_asteroidal_triple_free_C(n, sd,
connected_structure, waiting_list, seen)
173 sig_off()
/home/vbraun/Code/sage.git/src/sage/ext/interrupt/interrupt.pyx in
sage.ext.interrupt.interrupt.sig_raise_exception
(build/cythonized/sage/ext/interrupt/interrupt.c:1356)()
108 if msg == NULL:
109 msg = "Segmentation fault"
--> 110 raise SignalError(msg)
111
112 raise SystemError("unknown signal number %s"%sig)
SignalError: Segmentation fault
}}}
Its here
{{{
(gdb) frame 0
#0 __pyx_f_4sage_6graphs_18asteroidal_triples_is_asteroidal_triple_free_C
(__pyx_v_sd=0x7fffffffbd30,
__pyx_v_seen=<synthetic pointer>, __pyx_v_waiting_list=0x2c2c5e0,
__pyx_v_connected_structure=0x2ced6a0,
__pyx_v_n=<optimized out>) at
build/cythonized/sage/graphs/asteroidal_triples.c:6922
6922
__pyx_f_4sage_6graphs_18asteroidal_triples_bitset_add(__pyx_v_seen,
__pyx_v_v);
(gdb) l
6917 * idx_cc += 1
6918 * bitset_add(seen, v) # <<<<<<<<<<<<<<
6919 * connected_structure[source][v] = idx_cc
6920 *
6921 */
6922
__pyx_f_4sage_6graphs_18asteroidal_triples_bitset_add(__pyx_v_seen,
__pyx_v_v);
6923
6924 /* "sage/graphs/asteroidal_triples.pyx":252
6925 * idx_cc += 1
6926 * bitset_add(seen, v)
}}}
--
Ticket URL: <http://trac.sagemath.org/ticket/19334#comment:6>
Sage <http://www.sagemath.org>
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