On Wednesday, November 14, 2012 8:58:45 PM UTC-6, Jean-Pierre Flori wrote:
>
>
>
> On Wednesday, November 14, 2012 5:42:27 PM UTC-6, Nils Bruin wrote:
>>
>> However, in an effort to make memory errors during testing a little
>> more reproducible I made this little edit to local/bin/sagedoctest.py
>> to ensure the garbage collector is run before every doctested line:
>>
>> --------------------------------------------------------------------
>> diff --git a/sagedoctest.py b/sagedoctest.py
>> --- a/sagedoctest.py
>> +++ b/sagedoctest.py
>> @@ -1,7 +1,9 @@
>> from __future__ import with_statement
>>
>> import ncadoctest
>> +import gc
>> import sage.misc.randstate as randstate
>> +import sys
>>
>> OrigDocTestRunner = ncadoctest.DocTestRunner
>> class SageDocTestRunner(OrigDocTestRunner):
>> @@ -35,6 +37,8 @@ class SageDocTestRunner(OrigDocTestRunne
>> except Exception, e:
>> self._timeit_stats[key] = e
>> # otherwise, just run the example
>> + sys.stderr.write('testing example %s\n'%example)
>> + gc.collect()
>> OrigDocTestRunner.run_one_example(self, test, example,
>> filename, compileflags)
>>
>> def save_timeit_stats_to_file_named(self, output_filename):
>> --------------------------------------------------------------------
>>
>> (i.e., just add a gc.collect() to run_one_example)
>>
>> and it causes a reliable failure in crypto/mq/mpolynomialsystem.py:
>>
>> Trying:
>> C[Integer(0)].groebner_basis()###line 84:_sage_ sage:
>> C[0].groebner_basis()
>> Expecting:
>> Polynomial Sequence with 26 Polynomials in 16 Variables
>> testing example <ncadoctest.Example instance at 0x69706c8>
>> ok
>> Trying:
>> A,v = mq.MPolynomialSystem(r2).coefficient_matrix()###line
>> 87:_sage_ sage: A,v = mq.MPolynomialSystem(r2).coefficient_matrix()
>> Expecting nothing
>> testing example <ncadoctest.Example instance at 0x6970710>
>> *** glibc detected *** python: double free or corruption (out):
>> 0x00000000075c58c0 ***
>> ======= Backtrace: =========
>> /lib64/libc.so.6[0x31cfe7da76]
>> /lib64/libc.so.6[0x31cfe7ed5e]
>> /usr/local/sage/5.5b2/local/lib/python/site-packages/sage/rings/
>> polynomial/pbori.so(+0x880aa)[0x7fa5eba7e0aa]
>> /usr/local/sage/5.5b2/local/lib/python/site-packages/sage/rings/
>> polynomial/pbori.so(+0x1d993)[0x7fa5eba13993]
>> ...
>>
>> Running it under sage -t --gdb gives:
>>
>> (gdb) bt
>> #0 0x00000031cfe36285 in raise () from /lib64/libc.so.6
>> #1 0x00000031cfe37b9b in abort () from /lib64/libc.so.6
>> #2 0x00000031cfe7774e in __libc_message () from /lib64/libc.so.6
>> #3 0x00000031cfe7da76 in malloc_printerr () from /lib64/libc.so.6
>> #4 0x00000031cfe7ed5e in _int_free () from /lib64/libc.so.6
>> #5 0x00007fffce5cb0aa in
>> Delete<polybori::groebner::ReductionStrategy> (mem=0x547db30)
>> at /usr/local/sage/5.5b2/local/include/csage/ccobject.h:77
>> #6
>> __pyx_pf_4sage_5rings_10polynomial_5pbori_17ReductionStrategy_2__dealloc__
>>
>> (__pyx_v_self=<optimized out>)
>> at sage/rings/polynomial/pbori.cpp:37868
>> #7
>> __pyx_pw_4sage_5rings_10polynomial_5pbori_17ReductionStrategy_3__dealloc__
>>
>> (__pyx_v_self=0x54bf390)
>> at sage/rings/polynomial/pbori.cpp:37834
>> #8
>> __pyx_tp_dealloc_4sage_5rings_10polynomial_5pbori_ReductionStrategy
>> (o=0x54bf390) at sage/rings/polynomial/pbori.cpp:52283
>> #9 0x00007fffce560993 in
>> __pyx_tp_clear_4sage_5rings_10polynomial_5pbori_GroebnerStrategy
>> (o=0x54baeb0)
>> at sage/rings/polynomial/pbori.cpp:52545
>> #10 0x00007ffff7d4b637 in delete_garbage (old=0x7ffff7fe19e0,
>> collectable=0x7fffffffbb60) at Modules/gcmodule.c:769
>> #11 collect (generation=2) at Modules/gcmodule.c:930
>> #12 0x00007ffff7d4bdc9 in gc_collect (self=<optimized out>,
>> args=<optimized out>, kws=<optimized out>) at Modules/gcmodule.c:1067
>>
>> which should give a pretty good pointer for pbori people to figure out
>> which memory deallocation is actually botched.
>>
> We dealt with something very similar in one of the "memleaks" tickets.
> Not sure it was 715 or 11521, but maybe 12313 (the figures here might be
> wrong...).
> So the fix is potentially not included in 5.5.beta2 if it was in the later.
>
>
Ok, I took the time to check and you actually posted in 13710 that the fix
is included in 12313, so not in 5.5.beta2 if I'm not wrong (nor 5.0 of
course).
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